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Tuning of genome structure and function is accomplished by chromatin-binding proteins, which determine the transcriptome and phenotype of the cell. Here we investigate how communication between extracellular stress and chromatin structure may regulate cellular mechanical behaviors. We demonstrate that histone H1.0, which compacts nucleosomes into higher-order chromatin fibers, controls genome organization and cellular stress response. We show that histone H1.0 has privileged expression in fibroblasts across tissue types and that its expression is necessary and sufficient to induce myofibroblast activation. Depletion of histone H1.0 prevents cytokine-induced fibroblast contraction, proliferation and migration via inhibition of a transcriptome comprising extracellular matrix, cytoskeletal and contractile genes, through a process that involves locus-specific H3K27 acetylation. Transient depletion of histone H1.0 in vivo prevents fibrosis in cardiac muscle. These findings identify an unexpected role of linker histones to orchestrate cellular mechanical behaviors, directly coupling force generation, nuclear organization and gene transcription., Competing Interests: Competing interestsThe authors declare no competing interests., (© The Author(s) 2024.)

Cardiometabolic disorders encompass a broad range of cardiovascular complications associated with metabolic dysfunction. These conditions have an increasing share in the health burden worldwide due to worsening endemic of hypertension, obesity, and diabetes. Previous studies have identified Tumor Protein p53-inducible Nuclear Protein 2 (Trp53inp2) as a molecular link between hyperglycemia and cardiac hypertrophy. However, its role in cardiac pathology has never been determined in vivo . In this study, we generated a cardiac specific knockout model of Trp53inp2 (Trp53inp2-cKO) and investigated the impact of Trp53inp2 inactivation on the pathogenesis of heart failure under mechanic or/and metabolic stresses. Based on echocardiography assessment, inactivation of Trp53inp2 in heart led to accelerated onset of HFrEF in response to pressure-overload, with significantly reduced ejection fraction and elevated heart failure marker genes comparing to the control mice. In contrast, inactivation of Trp53inp2 ameliorated cardiac dysfunction induced by combined stresses of high fat diet and moderate pressure overload (Cardiometabolic Disorder Model). Moreover, Trp53inp2 inactivation led to reduced expression of glucose metabolism genes in lean, pressure-overloaded hearts. However, the same set of genes were significantly induced in the Trp53inp2-cKO hearts under both mechanical and metabolic stresses. In summary, we have demonstrated for the first time that cardiomyocyte Trp53inp2 has diametrically differential roles in the pathogenesis of heart failure and glucose regulation under mechanical vs. mechanical plus metabolic stresses. This insight suggests that Trp53inp2 may exacerbate the cardiac dysfunction during pressure overload injury but have a protective effect in cardiac diastolic function in cardiometabolic disease., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (© 2023 Liu, Liu, Ren, Zhu, Bouso, Mamlouk, Rau, Wang and Gao.)

Purpose: This paper presents a hierarchical modeling approach for estimating cardiomyocyte major and minor diameters and intracellular volume fraction (ICV) using diffusion-weighted MRI (DWI) data in ex vivo mouse hearts., Methods: DWI data were acquired on two healthy controls and two hearts 3 weeks post transverse aortic constriction (TAC) using a bespoke diffusion scheme with multiple diffusion times ( Δ $$ \Delta $$ ), q-shells and diffusion encoding directions. Firstly, a bi-exponential tensor model was fitted separately at each diffusion time to disentangle the dependence on diffusion times from diffusion weightings, that is, b-values. The slow-diffusing component was attributed to the restricted diffusion inside cardiomyocytes. ICV was then extrapolated at Δ = 0 $$ \Delta =0 $$ using linear regression. Secondly, given the secondary and the tertiary diffusion eigenvalue measurements for the slow-diffusing component obtained at different diffusion times, major and minor diameters were estimated assuming a cylinder model with an elliptical cross-section (ECS). High-resolution three-dimensional synchrotron X-ray imaging (SRI) data from the same specimen was utilized to evaluate the biophysical parameters., Results: Estimated parameters using DWI data were (control 1/control 2 vs. TAC 1/TAC 2): major diameter-17.4 μ $$ \mu $$ m/18.0 μ $$ \mu $$ m versus 19.2 μ $$ \mu $$ m/19.0 μ $$ \mu $$ m; minor diameter-10.2 μ $$ \mu $$ m/9.4 μ $$ \mu $$ m versus 12.8 μ $$ \mu $$ m/13.4 μ $$ \mu $$ m; and ICV-62%/62% versus 68%/47%. These findings were consistent with SRI measurements., Conclusion: The proposed method allowed for accurate estimation of biophysical parameters suggesting cardiomyocyte diameters as sensitive biomarkers of hypertrophy in the heart., (© 2023 The Authors. Magnetic Resonance in Medicine published by Wiley Periodicals LLC on behalf of International Society for Magnetic Resonance in Medicine.)

Competing Interests: Disclosures None.

Parallel to major changes in fatty acid and glucose metabolism, defect in branched-chain amino acid (BCAA) catabolism has also been recognized as a metabolic hallmark and potential therapeutic target for heart failure. However, BCAA catabolic enzymes are ubiquitously expressed in all cell types and a systemic BCAA catabolic defect is also manifested in metabolic disorder associated with obesity and diabetes. Therefore, it remains to be determined the cell-autonomous impact of BCAA catabolic defect in cardiomyocytes in intact hearts independent from its potential global effects. In this study, we developed two mouse models. One is cardiomyocyte and temporal-specific inactivation of the E1α subunit (BCKDHA-cKO) of the branched-chain α-ketoacid dehydrogenase (BCKDH) complex, which blocks BCAA catabolism. Another model is cardiomyocyte specific inactivation of the BCKDH kinase (BCKDK-cKO), which promotes BCAA catabolism by constitutively activating BCKDH activity in adult cardiomyocytes. Functional and molecular characterizations showed E1α inactivation in cardiomyocytes was sufficient to induce loss of cardiac function, systolic chamber dilation and pathological transcriptome reprogramming. On the other hand, inactivation of BCKDK in intact heart does not have an impact on baseline cardiac function or cardiac dysfunction under pressure overload. Our results for the first time established the cardiomyocyte cell autonomous role of BCAA catabolism in cardiac physiology. These mouse lines will serve as valuable model systems to investigate the underlying mechanisms of BCAA catabolic defect induced heart failure and to provide potential insights for BCAA targeted therapy., (© 2023. The Author(s).)

Heart failure with preserved ejection fraction (HFpEF) exhibits a sex bias, being more common in women than men, and we hypothesize that mitochondrial sex differences might underlie this bias. As part of genetic studies of heart failure in mice, we observe that heart mitochondrial DNA levels and function tend to be reduced in females as compared to males. We also observe that expression of genes encoding mitochondrial proteins are higher in males than females in human cohorts. We test our hypothesis in a panel of genetically diverse inbred strains of mice, termed the Hybrid Mouse Diversity Panel (HMDP). Indeed, we find that mitochondrial gene expression is highly correlated with diastolic function, a key trait in HFpEF. Consistent with this, studies of a "two-hit" mouse model of HFpEF confirm that mitochondrial function differs between sexes and is strongly associated with a number of HFpEF traits. By integrating data from human heart failure and the mouse HMDP cohort, we identify the mitochondrial gene Acsl6 as a genetic determinant of diastolic function. We validate its role in HFpEF using adenoviral over-expression in the heart. We conclude that sex differences in mitochondrial function underlie, in part, the sex bias in diastolic function., (© 2022. The Author(s).)

Understanding the function of biological tissues requires a coordinated study of physiology and structure, exploring volumes that contain complete functional units at a detail that resolves the relevant features. Here, we introduce an approach to address this challenge: Mouse brain tissue sections containing a region where function was recorded using in vivo 2-photon calcium imaging were stained, dehydrated, resin-embedded and imaged with synchrotron X-ray computed tomography with propagation-based phase contrast (SXRT). SXRT provided context at subcellular detail, and could be followed by targeted acquisition of multiple volumes using serial block-face electron microscopy (SBEM). In the olfactory bulb, combining SXRT and SBEM enabled disambiguation of in vivo-assigned regions of interest. In the hippocampus, we found that superficial pyramidal neurons in CA1a displayed a larger density of spine apparati than deeper ones. Altogether, this approach can enable a functional and structural investigation of subcellular features in the context of cells and tissues., (© 2022. The Author(s).)

X-ray ptychography is a coherent scanning imaging technique widely used at synchrotron facilities for producing quantitative phase images beyond the resolution limit of conventional x-ray optics. The scanning nature of the technique introduces an inherent overhead to the collection at every scan position and limits the acquisition time of each 2D projection. The overhead associated with motion can be minimised with a continuous-scanning approach. Here we present an acquisition architecture based on continuous-scanning and up-triggering which allows to record ptychographic datasets at up to 9 kHz. We demonstrate the method by applying it to record 2D scans at up to 273 µm 2 /s and 3D scans of a (20 µm) 3 volume in less than three hours. We discuss the current limitations and the outlook toward the development of sub-second 2D acquisition and minutes-long 3D ptychographic tomograms., (© 2022. The Author(s).)

Full-field transmission X-ray microscopy (TXM) is a very potent high-resolution X-ray imaging technique. However, it is challenging to achieve fast acquisitions because of the limited efficiency of the optics. Using a broader energy bandwidth, for example using a multilayer monochromator, directly increases the flux in the experiment. The advantage of more counts needs to be weighed against a deterioration in achievable resolution because focusing optics show chromatic aberrations. This study presents theoretical considerations of how much the resolution is affected by an increase in bandwidth as well as measurements at different energy bandwidths (ΔE/E = 0.013%, 0.27%, 0.63%) and the impact on achievable resolution. It is shown that using a multilayer monochromator instead of a classical silicon double-crystal monochromator can increase the flux by an order of magnitude with only a limited effect on the resolution., (open access.)

Biophysical models are a promising means for interpreting diffusion weighted magnetic resonance imaging (DW-MRI) data, as they can provide estimates of physiologically relevant parameters of microstructure including cell size, volume fraction, or dispersion. However, their application in cardiac microstructure mapping (CMM) has been limited. This study proposes seven new two-compartment models with combination of restricted cylinder models and a diffusion tensor to represent intra- and extracellular spaces, respectively. Three extended versions of the cylinder model are studied here: cylinder with elliptical cross section (ECS), cylinder with Gamma distributed radii (GDR), and cylinder with Bingham distributed axes (BDA). The proposed models were applied to data in two fixed mouse hearts, acquired with multiple diffusion times, q-shells and diffusion encoding directions. The cylinderGDR-pancake model provided the best performance in terms of root mean squared error (RMSE) reducing it by 25% compared to diffusion tensor imaging (DTI). The cylinderBDA-pancake model represented anatomical findings closest as it also allows for modelling dispersion. High-resolution 3D synchrotron X-ray imaging (SRI) data from the same specimen was utilized to evaluate the biophysical models. A novel tensor-based registration method is proposed to align SRI structure tensors to the MR diffusion tensors. The consistency between SRI and DW-MRI parameters demonstrates the potential of compartment models in assessing physiologically relevant parameters.

Background: Human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) have emerged as a promising tool for disease modeling and drug development. However, hiPSC-CMs remain functionally immature, which hinders their utility as a model of human cardiomyocytes., Objective: To improve the electrophysiological maturation of hiPSC-CMs., Methods and Results: On day 16 of cardiac differentiation, hiPSC-CMs were treated with 100 nmol/L triiodothyronine (T3) and 1 μmol/L Dexamethasone (Dex) or vehicle for 14 days. On day 30, vehicle- and T3 + Dex-treated hiPSC-CMs were dissociated and replated either as cell sheets or single cells. Optical mapping and patch-clamp technique were used to examine the electrophysiological properties of vehicle- and T3 + Dex-treated hiPSC-CMs. Compared to vehicle, T3 + Dex-treated hiPSC-CMs had a slower spontaneous beating rate, more hyperpolarized resting membrane potential, faster maximal upstroke velocity, and shorter action potential duration. Changes in spontaneous activity and action potential were mediated by decreased hyperpolarization-activated current (I f ) and increased inward rectifier potassium currents (I K1 ), sodium currents (I Na ), and the rapidly and slowly activating delayed rectifier potassium currents (I Kr and I Ks , respectively). Furthermore, T3 + Dex-treated hiPSC-CM cell sheets (hiPSC-CCSs) exhibited a faster conduction velocity and shorter action potential duration than the vehicle. Inhibition of I K1 by 100 μM BaCl 2 significantly slowed conduction velocity and prolonged action potential duration in T3 + Dex-treated hiPSC-CCSs but had no effect in the vehicle group, demonstrating the importance of I K1 for conduction velocity and action potential duration., Conclusion: T3 + Dex treatment is an effective approach to rapidly enhance electrophysiological maturation of hiPSC-CMs., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

We present a dynamic implementation of the beam-tracking x-ray imaging method providing absorption, phase, and ultrasmall angle scattering signals with microscopic resolution and high frame rate. We demonstrate the method's ability to capture dynamic processes with 22-ms time resolution by investigating the melting of metals in laser additive manufacturing, which has so far been limited to single-modality synchrotron radiography. The simultaneous availability of three contrast channels enables earlier segmentation of droplets, tracking of powder dynamic, and estimation of unfused powder amounts, demonstrating that the method can provide additional information on melting processes.

X-ray ptychography and X-ray fluorescence are complementary nanoscale imaging techniques, providing structural and elemental information, respectively. Both methods acquire data by scanning a localized beam across the sample. X-ray ptychography processes the transmission signal of a coherent illumination interacting with the sample, to produce images with a resolution finer than the illumination spot and step size. By enlarging both the spot and the step size, the technique can cover extended regions efficiently. X-ray fluorescence records the emitted spectra as the sample is scanned through the localized beam and its spatial resolution is limited by the spot and step size. The requisites for fast ptychography and high-resolution fluorescence appear incompatible. Here, a novel scheme that mitigates the difference in requirements is proposed. The method makes use of two probes of different sizes at the sample, generated by using two different energies for the probes and chromatic focusing optics. The different probe sizes allow to reduce the number of acquisition steps for the joint fluorescence-ptychography scan compared with a standard single beam scan, while imaging the same field of view. The new method is demonstrated experimentally using two undulator harmonics, a Fresnel zone plate and an energy discriminating photon counting detector., (open access.)

The human cell nucleus serves as an important organelle holding the genetic blueprint for life. In this work, X-ray ptychography was applied to assess the masses of human cell nuclei using its unique phase shift information. Measurements were carried out at the I13-1 beamline at the Diamond Light Source that has extremely large transverse coherence properties. The ptychographic diffractive imaging approach allowed imaging of large structures that gave quantitative measurements of the phase shift in 2D projections. In this paper a modified ptychography algorithm that improves the quality of the reconstruction for weak scattering samples is presented. The application of this approach to calculate the mass of several human nuclei is also demonstrated.

Osteogenesis imperfecta (OI or brittle bone disease) is a group of genetic disorders of the connective tissues caused mainly by mutations in the genes encoding collagen type I. Clinical manifestations of OI include skeletal fragility, bone deformities, and severe functional disabilities, such as hearing loss. Progressive hearing loss, usually beginning in childhood, affects approximately 70% of people with OI with more than half of the cases involving the inner ear. There is no cure for OI nor a treatment to ameliorate its corresponding hearing loss, and very little is known about the properties of OI ears. In this study, we investigate the morphology of the otic capsule and the cochlea in the inner ear of the oim mouse model of OI. High-resolution 3D images of 8-week old oim and WT inner ears were acquired using synchrotron microtomography. Volumetric morphometric measurements were conducted for the otic capsule, its intracortical canal network and osteocyte lacunae, and for the cochlear spiral ducts. Our results show that the morphology of the cochlea is preserved in the oim ears at 8 weeks of age but the otic capsule has a greater cortical thickness and altered intracortical bone porosity, with a larger number and volume density of highly branched canals in the oim otic capsule. These results portray a state of compromised bone quality in the otic capsule of the oim mice that may contribute to their hearing loss., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Individuals with heart failure (HF) frequently present with comorbidities, including obesity, insulin resistance, hypertension, and dyslipidemia. Many patients with HF experience cardiogenic dementia, yet the pathophysiology of this disease remains poorly understood. Using a swine model of cardiometabolic HF (Western diet+aortic banding; WD-AB), we tested the hypothesis that WD-AB would promote a multidementia phenotype involving cerebrovascular dysfunction alongside evidence of Alzheimer's disease (AD) pathology. The results provide evidence of cerebrovascular insufficiency coupled with neuroinflammation and amyloidosis in swine with experimental cardiometabolic HF. Although cardiac ejection fraction was normal, indices of arterial compliance and cerebral blood flow were reduced, and cerebrovascular regulation was impaired in the WD-AB group. Cerebrovascular dysfunction occurred concomitantly with increased MAPK signaling and amyloidogenic processing (i.e., increased APP, BACE1, CTF, and Aβ40 in the prefrontal cortex and hippocampus) in the WD-AB group. Transcriptomic profiles of the stellate ganglia revealed the WD-AB group displayed an enrichment of gene networks associated with MAPK/ERK signaling, AD, frontotemporal dementia, and a number of behavioral phenotypes implicated in cognitive impairment. These provide potentially novel evidence from a swine model that cerebrovascular and neuronal pathologies likely both contribute to the dementia profile in a setting of cardiometabolic HF.

Studies of the structural and functional role of chromosomes in cytogenetics have spanned more than 10 decades. In this work, we take advantage of the coherent X-rays available at the latest synchrotron sources to extract the individual masses of all 46 chromosomes of metaphase human B and T cells using hard X-ray ptychography. We have produced 'X-ray karyotypes' of both heavy metal-stained and unstained spreads to determine the gain or loss of genetic material upon low-level X-ray irradiation doses due to radiation damage. The experiments were performed at the I-13 beamline, Diamond Light Source, Didcot, UK, using the phase-sensitive X-ray ptychography method.

Heart failure (HF) patients with deteriorating right ventricular (RV) structure and function have a nearly twofold increased risk of death compared with those without. Despite the well-established clinical risk, few studies have examined the molecular signature associated with this HF condition. The purpose of this study was to integrate morphological, molecular, and functional data with the transcriptome data set in the RV of a preclinical model of cardiometabolic HF. Ossabaw swine were fed either normal diet without surgery (lean control, n = 5) or Western diet and aortic-banding (WD-AB; n = 4). Postmortem RV weight was increased and positively correlated with lung weight in the WD-AB group compared with CON. Total RNA-seq was performed and gene expression profiles were compared and analyzed using principal component analysis, weighted gene co-expression network analysis, module enrichment analysis, and ingenuity pathway analysis. Gene networks specifically associated with RV hypertrophic remodeling identified a hub gene in MAPK8 (or JNK1) that was associated with the selective induction of the extracellular matrix (ECM) component fibronectin. JNK1 and fibronectin protein were increased in the right coronary artery (RCA) of WD-AB animals and associated with a decrease in matrix metalloproteinase 14 protein, which specifically degrades fibronectin. RCA fibronectin content was correlated with increased vascular stiffness evident as a decreased elastin elastic modulus in WD-AB animals. In conclusion, this study establishes a molecular and transcriptome signature in the RV using Ossabaw swine with cardiometabolic HF. This signature was associated with altered ECM regulation and increased vascular stiffness in the RCA, with selective dysregulation of fibronectin.

Due to complex degradation mechanisms, disparities between the theoretical and practical capacities of lithium-ion battery cathode materials persist. Specifically, Ni-rich chemistries such as LiNi 0.8 Mn 0.1 Co 0.1 O 2 (or NMC811) are one of the most promising choices for automotive applications; however, they continue to suffer severe degradation during operation that is poorly understood, thus challenging to mitigate. Here we use operando Bragg coherent diffraction imaging for 4D analysis of these mechanisms by inspecting the individual crystals within primary particles at various states of charge (SoC). Although some crystals were relatively homogeneous, we consistently observed non-uniform distributions of inter- and intracrystal strain at all measured SoC. Pristine structures may already possess heterogeneities capable of triggering crystal splitting and subsequently particle cracking. During low-voltage charging (2.7-3.5 V), crystal splitting may still occur even during minimal bulk deintercalation activity; and during discharging, rotational effects within parallel domains appear to be the precursor for the nucleation of screw dislocations at the crystal core. Ultimately, this discovery of the central role of crystal grain splitting in the charge/discharge dynamics may have ramifications across length scales that affect macroscopic performance loss during real-world battery operation.

Background: The majority of quantitative genetic models used to map complex traits assume that alleles have similar effects across all individuals. Significant evidence suggests, however, that epistatic interactions modulate the impact of many alleles. Nevertheless, identifying epistatic interactions remains computationally and statistically challenging. In this work, we address some of these challenges by developing a statistical test for polygenic epistasis that determines whether the effect of an allele is altered by the global genetic ancestry proportion from distinct progenitors., Results: We applied our method to data from mice and yeast. For the mice, we observed 49 significant genotype-by-ancestry interaction associations across 14 phenotypes as well as over 1,400 Bonferroni-corrected genotype-by-ancestry interaction associations for mouse gene expression data. For the yeast, we observed 92 significant genotype-by-ancestry interactions across 38 phenotypes. Given this evidence of epistasis, we test for and observe evidence of rapid selection pressure on ancestry specific polymorphisms within one of the cohorts, consistent with epistatic selection., Conclusions: Unlike our prior work in human populations, we observe widespread evidence of ancestry-modified SNP effects, perhaps reflecting the greater divergence present in crosses using mice and yeast., Competing Interests: The authors have declared that no competing interests exist.

Cardiovascular diseases are the leading cause of death worldwide. Complex diseases with highly heterogenous disease progression among patient populations, cardiovascular diseases feature multifactorial contributions from both genetic and environmental stressors. Despite significant effort utilizing multiple approaches from molecular biology to genome-wide association studies, the genetic landscape of cardiovascular diseases, particularly for the nonfamilial forms of heart failure, is still poorly understood. In the past decade, systems-level approaches based on omics technologies have become an important approach for the study of complex traits in large populations. These advances create opportunities to integrate genetic variation with other biological layers to identify and prioritize candidate genes, understand pathogenic pathways, and elucidate gene-gene and gene-environment interactions. In this review, we will highlight some of the recent progress made using systems genetics approaches to uncover novel mechanisms and molecular bases of cardiovascular pathophysiological manifestations. The key technology and data analysis platforms necessary to implement systems genetics will be described, and the current major challenges and future directions will also be discussed. For complex cardiovascular diseases, such as heart failure, systems genetics represents a powerful strategy to obtain mechanistic insights and to develop individualized diagnostic and therapeutic regiments, paving the way for precision cardiovascular medicine.

We present here a new method of performing X-ray edge-subtraction ptychographic imaging by combining multiple harmonics from an undulator synchtrotron source and an energy discriminating photon counting detector. Conventionally, monochromatic far-field X-ray ptychography is used to perform edge subtraction through the use of multiple monochromatic energy scans to obtain spectral information for a variety of applications. Here, we use directly the undulator spectrum from a synchrotron source, selecting two separate harmonics post sample using the Pixirad-1/Pixie-III detector. The result is two monochromatic images, above and below an absorption edge of interest. The proposed method is applied to obtain Au L-edge subtraction imaging of a Au-Ni grid test sample. The Au L-edge subtraction is particularly relevant for the identification of gold nanoparticles for biomedical applications. Switching the energy scan mechanism from a mechanical monochromator to an electronic detector threshold allows for faster spectral data collection with improved stability.

In this Letter, we report on the creation of hard x-ray beams carrying orbital angular momentum of topological charge -ℏ and -3ℏ at a photon energy of 8.2 keV via spiral phase plates made out of fused silica by ultrashort-pulsed laser ablation. The phase plates feature a smooth phase ramp with a 0.5 μm nominal step height and a surface roughness of 0.5 μm. The measured vortex beams show submicrometer-sized donut rings and agree well with numerical modeling. Fused silica phase plates are potentially suited to manipulate the electromagnetic field in highly intense x-ray beams at x-ray free-electron laser sources.

We present a new method of single acquisition spectroscopic imaging with high spatial resolution. The technique is based on the combination of polychromatic synchrotron radiation and ptychographic imaging with a recently developed energy discriminating detector. We demonstrate the feasibility with a Ni-Cu test sample recorded at I13-1 of the Diamond Light Source, UK. The two elements can be clearly distinguished and the Ni absorption edge is identified. The results prove the feasibility of obtaining high-resolution structural and chemical images within a single acquisition using a polychromatic X-ray beam. The capability of resolving the absorption edge applies to a wide range of research areas, such as magnetic domains imaging and element specific investigations in biological, materials, and earth sciences. The method utilises the full available radiation spectrum and is therefore well suited for broadband radiation sources.

The development of new treatments for heart failure lack animal models that encompass the increasingly heterogeneous disease profile of this patient population. This report provides evidence supporting the hypothesis that Western Diet-fed, aortic-banded Ossabaw swine display an integrated physiological, morphological, and genetic phenotype evocative of cardio-metabolic heart failure. This new preclinical animal model displays a distinctive constellation of findings that are conceivably useful to extending the understanding of how pre-existing cardio-metabolic syndrome can contribute to developing HF.

Many insects have triplets of camera type eyes, called ocelli, whose function remains unclear for most species. Here, we investigate the ocelli of the bumblebee, Bombus terrestris, using reconstructed 3D data from X-ray microtomography scans combined with computational ray-tracing simulations. This method enables us, not only to predict the visual fields of the ocelli, but to explore for the first time the effect that hair has on them as well as the difference between worker female and male ocelli. We find that bumblebee ocellar fields of view are directed forward and dorsally, incorporating the horizon as well as the sky. There is substantial binocular overlap between the median and lateral ocelli, but no overlap between the two lateral ocelli. Hairs in both workers and males occlude the ocellar field of view, mostly laterally in the worker median ocellus and dorsally in the lateral ocelli. There is little to no sexual dimorphism in the ocellar visual field, suggesting that in B. terrestris they confer no advantage to mating strategies. We compare our results with published observations for the visual fields of compound eyes in the same species as well as with the ocellar vision of other bee and insect species., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Right ventricular dysfunction is highly prevalent across cardiopulmonary diseases and independently predicts death in both heart failure (HF) and pulmonary hypertension (PH). Progression towards right ventricular failure (RVF) can occur in spite of optimal medical treatment of HF or PH, highlighting current insufficient understanding of RVF molecular pathophysiology. To identify molecular mechanisms that may distinctly underlie RVF, we investigated the cardiac ventricular transcriptome of advanced HF patients, with and without RVF. Using an integrated systems genomic and functional biology approach, we identified an RVF-specific gene module, for which WIPI1 served as a hub and HSPB6 and MAP4 as drivers, and confirmed the ventricular specificity of Wipi1, Hspb6, and Map4 transcriptional changes in adult murine models of pressure overload induced RV- versus LV- failure. We uncovered a shift towards non-canonical autophagy in the failing RV that correlated with RV-specific Wipi1 upregulation. In vitro siRNA silencing of Wipi1 in neonatal rat ventricular myocytes limited non-canonical autophagy and blunted aldosterone-induced mitochondrial superoxide levels. Our findings suggest that Wipi1 regulates mitochondrial oxidative signaling and non-canonical autophagy in cardiac myocytes. Together with our human transcriptomic analysis and corroborating studies in an RVF mouse model, these data render Wipi1 a potential target for RV-directed HF therapy.

The quality of visual information that is available to an animal is limited by the size of its eyes. Differences in eye size can be observed even between closely related individuals, yet we understand little about how this affects vision. Insects are good models for exploring the effects of size on visual systems because many insect species exhibit size polymorphism. Previous work has been limited by difficulties in determining the 3D structure of eyes. We have developed a novel method based on x-ray microtomography to measure the 3D structure of insect eyes and to calculate predictions of their visual capabilities. We used our method to investigate visual allometry in the bumblebee Bombus terrestris and found that size affects specific aspects of vision, including binocular overlap, optical sensitivity, and dorsofrontal visual resolution. This reveals that differential scaling between eye areas provides flexibility that improves the visual capabilities of larger bumblebees., Competing Interests: GT, PT, MS, AB, CR, EB No competing interests declared, (© 2019, Taylor et al.)

Ptychographic X-ray computed tomography is a phase-contrast imaging technique capable of retrieving three-dimensional maps of the index of refraction of the imaged volumes with nanometric resolution. Despite its unmatched reach, its application remains prerogative of a limited number of laboratories at synchrotron sources. We present a detailed description of an experimental procedure and a data analysis pipeline which can be both exploited for ptychographic X-ray computed tomography experiments at any high-brilliance X-ray source. These have been validated at the I13-1 Coherence Branchline within the first experiment of its kind to be successfully carried out on a biological sample at Diamond Light Source.

Multiphase flow in permeable media is a complex pore-scale phenomenon, which is important in many natural and industrial processes. To understand the pore-scale dynamics of multiphase flow, we acquired time-series synchrotron X-ray micro-tomographic data at a voxel-resolution of 3.28 μm and time-resolution of 38 s during drainage and imbibition in a carbonate rock, under a capillary-dominated flow regime at elevated pressure. The time-series data library contains 496 tomographic images (gray-scale and segmented) for the complete drainage process, and 416 tomographic images (gray-scale and segmented) for the complete imbibition process. These datasets have been uploaded on the publicly accessible British Geological Survey repository, with the objective that the time-series information can be used by other groups to validate pore-scale displacement models such as direct simulations, pore-network and neural network models, as well as to investigate flow mechanisms related to the displacement and trapping of the non-wetting phase in the pore space. These datasets can also be used for improving segmentation algorithms for tomographic data with limited projections.

We describe a simple bioinformatics method for biomarker discovery that is based on the analysis of global transcript levels in a population of inbred mouse strains showing variation for disease-related traits. This method has advantages such as controlled environment and accessibility to heart and plasma tissue in the preclinical selection stage. We illustrate the approach by identifying candidate heart failure (HF) biomarkers by overlaying mouse transcriptome and clinical traits from 91 Hybrid Mouse Diversity Panel (HMDP) inbred strains and human HF transcriptome from the Myocardial Applied Genomics Network (MAGNet) consortium. We found that some of the top differentially expressed genes correlated with known human HF biomarkers, such as galectin-3 and tissue inhibitor of metalloproteinase 1. Using ELISA assays, we investigated one novel candidate, Glycoprotein NMB, in a mouse model of chronic β-adrenergic stimulation by isoproterenol (ISO) induced HF. We observed significantly lower GPNMB plasma levels in the ISO model compared to the control group (p-value = 0.007). In addition, we assessed GPNMB plasma levels among 389 HF cases and controls from the METabolic Syndrome In Men (METSIM) study. Lower levels of GPNMB were also observed in patients with HF from the METSIM study compared to non-HF controls (p-value < 0.0001). In summary, we have identified several candidate biomarkers for HF using the cardiac transcriptome data in a population of mice that may be directly relevant and applicable to human populations., (Copyright © 2018 Lin et al.)

An emerging method in the field of neural stimulation is the use of photons to activate neurons. The possible advantage of optical stimulation over electrical is attributable to its spatially selective activation of small neuron populations, which is promising in generating superior spatial resolution in neural interfaces. Two principal methods are explored for cochlear prostheses: direct stimulation of nerves with infrared light and optogenetics. This paper discusses basic requirements for developing a light delivery system (LDS) for the cochlea and provides examples for building such devices. The proposed device relies on small optical sources, which are assembled in an array to be inserted into the cochlea. The mechanical properties, the biocompatibility, and the efficacy of optrodes have been tested in animal models. The force required to insert optrodes into a model of the human scala tympani was comparable to insertion forces obtained for contemporary cochlear implant electrodes. Side-emitting diodes are powerful enough to evoke auditory responses in guinea pigs. Chronic implantation of the LDS did not elevate auditory brainstem responses over 26 weeks.

Background: Genetic diversity and the heterogeneous nature of cardiac fibroblasts (CFbs) have hindered characterization of the molecular mechanisms that regulate cardiac fibrosis. The Hybrid Mouse Diversity Panel offers a valuable tool to examine genetically diverse cardiac fibroblasts and their role in fibrosis., Methods: Three strains of mice (C57BL/6J, C3H/HeJ, and KK/HlJ) were selected from the Hybrid Mouse Diversity Panel and treated with either isoproterenol (ISO) or saline by an intraperitoneally implanted osmotic pump. After 21 days, cardiac function and levels of fibrosis were measured by echocardiography and trichrome staining, respectively. Activation and proliferation of CFbs were measured by in vitro and in vivo assays under normal and injury conditions. RNA sequencing was done on isolated CFbs from each strain. Results were analyzed by Ingenuity Pathway Analysis and validated by reverse transcription-qPCR, immunohistochemistry, and ELISA., Results: ISO treatment in C57BL/6J, C3H/HeJ, and KK/HlJ mice resulted in minimal, moderate, and extensive levels of fibrosis, respectively (n=7-8 hearts per condition). Isolated CFbs treated with ISO exhibited strain-specific increases in the levels of activation but showed comparable levels of proliferation. Similar results were found in vivo, with fibroblast activation, and not proliferation, correlating with the differential levels of cardiac fibrosis after ISO treatment. RNA sequencing revealed that CFbs from each strain exhibit unique gene expression changes in response to ISO. We identified Ltbp2 as a commonly upregulated gene after ISO treatment. Expression of LTBP2 was elevated and specifically localized in the fibrotic regions of the myocardium after injury in mice and in human heart failure patients., Conclusions: This study highlights the importance of genetic variation in cardiac fibrosis by using multiple inbred mouse strains to characterize CFbs and their response to ISO treatment. Our data suggest that, although fibroblast activation is a response that parallels the extent of scar formation, proliferation may not necessarily correlate with levels of fibrosis. In addition, by comparing CFbs from multiple strains, we identified pathways as potential therapeutic targets and LTBP2 as a marker for fibrosis, with relevance to patients with underlying myocardial fibrosis.

The success of ptychography and other imaging experiments at third-generation X-ray sources is apparent from their increasingly widespread application and the improving quality of the images they produce both for resolution and contrast and in terms of relaxation of experimental constraints. The wider availability of highly coherent X-rays stimulates the development of several complementary techniques which have seen limited mutual integration in recent years. This paper presents a framework in which some of the established imaging techniques - with particular regard for ptychography - are flexibly applied to tackle the variable requirements occurring at typical synchrotron experiments. In such a framework one can obtain low-resolution images of whole samples and smoothly zoom in on specific regions of interest as they are revealed by switching to a higher-resolution imaging mode. The techniques involved range from full-field microscopy, to reach the widest fields of view (>mm), to ptychography, to achieve the highest resolution (<100 nm), and have been implemented at the I13 Coherence Branchline at Diamond Light Source., (open access.)

The current advances in new generation X-ray sources are calling for the development and improvement of high-performance optics. Techniques for high-sensitivity phase sensing and wavefront characterisation, preferably performed at-wavelength, are increasingly required for quality control, optimisation and development of such devices. We here show that the recently proposed unified modulated pattern analysis (UMPA) can be used for these purposes. We characterised two polymer X-ray refractive lenses and quantified the effect of beam damage and shape errors on their refractive properties. Measurements were performed with two different setups for UMPA and validated with conventional X-ray grating interferometry. Due to its adaptability to different setups, the ease of implementation and cost-effectiveness, we expect UMPA to find applications for high-throughput quantitative optics characterisation and wavefront sensing.

Isoproterenol is used widely for inducing heart failure in mice. Isoproterenol is a nonselective beta-adrenergic agonist. The acute model mimics stress-induced cardiomyopathy. The chronic model mimics advanced heart failure in humans. In this chapter, we describe a protocol that we used to induce heart failure in 100+ strains of inbred mice. Techniques on surgical pump implantation and echocardiography are described in detail. We also discuss the impact of drug dosage, duration, mortality, age, gender, and strain on cardiac remodeling responses. The success of model creation may be assessed by echocardiogram or molecular markers. This chapter may be relevant to those who are interested in using this heart failure model.

Wavefront errors of rotationally parabolic refractive X-ray lenses made of beryllium (Be CRLs) have been recovered for various lens sets and X-ray beam configurations. Due to manufacturing via an embossing process, aberrations of individual lenses within the investigated ensemble are very similar. By deriving a mean single-lens deformation for the ensemble, aberrations of any arbitrary lens stack can be predicted from the ensemble with \bar{\sigma} = 0.034λ. Using these findings the expected focusing performance of current Be CRLs are modeled for relevant X-ray energies and bandwidths and it is shown that a correction of aberrations can be realised without prior lens characterization but simply based on the derived lens deformation. The performance of aberration-corrected Be CRLs is discussed and the applicability of aberration-correction demonstrated over wide X-ray energy ranges.

Reconstructing tomographic images of high resolution, as in x-ray microscopy or transmission electron microscopy, is often limited by the stability of the stages or sample drifts, which requires an image alignment prior to reconstruction. Feature-based image registration is routinely used to align images, but this technique relies on strong features in the sample or the application of gold tracer particles, for example. In this Letter, we present an analytic approach for achieving the vertical registration based on the inherent properties of the data acquired for tomographic reconstruction. It is computationally cheap to implement and can be easily integrated into existing reconstruction pipelines.

Adult mammalian cardiomyocyte regeneration after injury is thought to be minimal. Mononuclear diploid cardiomyocytes (MNDCMs), a relatively small subpopulation in the adult heart, may account for the observed degree of regeneration, but this has not been tested. We surveyed 120 inbred mouse strains and found that the frequency of adult mononuclear cardiomyocytes was surprisingly variable (>7-fold). Cardiomyocyte proliferation and heart functional recovery after coronary artery ligation both correlated with pre-injury MNDCM content. Using genome-wide association, we identified Tnni3k as one gene that influences variation in this composition and demonstrated that Tnni3k knockout resulted in elevated MNDCM content and increased cardiomyocyte proliferation after injury. Reciprocally, overexpression of Tnni3k in zebrafish promoted cardiomyocyte polyploidization and compromised heart regeneration. Our results corroborate the relevance of MNDCMs in heart regeneration. Moreover, they imply that intrinsic heart regeneration is not limited nor uniform in all individuals, but rather is a variable trait influenced by multiple genes.

Background: The implantation of mechanical circulatory support devices in heart failure patients is associated with a systemic inflammatory response, potentially leading to death from multiple organ dysfunction syndrome. Previous studies point to the involvement of many mechanisms, but an integrative hypothesis does not yet exist. Using time-dependent whole-genome mRNA expression in circulating leukocytes, we constructed a systems-model to improve mechanistic understanding and prediction of adverse outcomes., Methods: We sampled peripheral blood mononuclear cells from 22 consecutive patients undergoing mechanical circulatory support device (MCS) surgery, at 5 timepoints: day -1 preoperative, and postoperative days 1, 3, 5, and 8. Clinical phenotyping was performed using 12 clinical parameters, 2 organ dysfunction scoring systems, and survival outcomes. We constructed a strictly phenotype-driven time-dependent non-supervised systems-representation using weighted gene co-expression network analysis, and annotated eigengenes using gene ontology, pathway, and transcription factor binding site enrichment analyses. Genes and eigengenes were mapped to the clinical phenotype using a linear mixed-effect model, with Cox models also fit at each timepoint to survival outcomes., Results: We inferred a 19-module network, in which most module eigengenes correlated with at least one aspect of the clinical phenotype. We observed a response of advanced heart failure patients to surgery orchestrated into stages: first, activation of the innate immune response, followed by anti-inflammation, and finally reparative processes such as mitosis, coagulation, and apoptosis. Eigengenes related to red blood cell production and extracellular matrix degradation became predictors of survival late in the timecourse corresponding to multiorgan dysfunction and disseminated intravascular coagulation., Conclusions: Our model provides an integrative representation of leukocyte biology during the systemic inflammatory response following MCS device implantation. It demonstrates consistency with previous hypotheses, identifying a number of known mechanisms. At the same time, it suggests novel hypotheses about time-specific targets.

Understanding the pore-scale dynamics of two-phase fluid flow in permeable media is important in many processes such as water infiltration in soils, oil recovery, and geo-sequestration of CO 2 . The two most important processes that compete during the displacement of a non-wetting fluid by a wetting fluid are pore-filling or piston-like displacement and snap-off; this latter process can lead to trapping of the non-wetting phase. We present a three-dimensional dynamic visualization study using fast synchrotron X-ray micro-tomography to provide new insights into these processes by conducting a time-resolved pore-by-pore analysis of the local curvature and capillary pressure. We show that the time-scales of interface movement and brine layer swelling leading to snap-off are several minutes, orders of magnitude slower than observed for Haines jumps in drainage. The local capillary pressure increases rapidly after snap-off as the trapped phase finds a position that is a new local energy minimum. However, the pressure change is less dramatic than that observed during drainage. We also show that the brine-oil interface jumps from pore-to-pore during imbibition at an approximately constant local capillary pressure, with an event size of the order of an average pore size, again much smaller than the large bursts seen during drainage.

Background: Chronic myocardial infarction (MI) triggers pathological remodeling in the heart and cardiac nervous system. Abnormal function of the autonomic nervous system (ANS), including stellate ganglia (SG) and dorsal root ganglia (DRG) contribute to increased sympathoexcitation, cardiac dysfunction and arrythmogenesis. ANS modulation is a therapeutic target for arrhythmia associated with cardiac injury. However, the molecular mechanism involved in the pathological remodeling in ANS following cardiac injury remains to be established., Methods and Results: In this study, we performed transcriptome analysis by RNA-sequencing in thoracic SG and (T1-T4) DRG obtained from Yorkshire pigs following either acute (3 to 5 hours) or chronic (8 weeks) myocardial infarction. By differential expression and weighted gene co-expression network analysis (WGCNA), we identified significant transcriptome changes and specific gene modules in the ANS tissues in response to myocardial infarction at either acute or chronic phases. Both differential expressed genes and the member genes of the WGCNA gene module associated with post-infarct condition were significantly enriched for inflammatory signaling and apoptotic cell death. Targeted validation analysis supported a significant induction of inflammatory and apoptotic signal in both SG and DRG following myocardial infarction, along with cellular evidence of apoptosis induction based on TUNEL analysis. Importantly, these molecular changes were observed specifically in the thoracic segments but not in their counterparts obtained from lumbar sections., Conclusion: Myocardial injury leads to time-dependent global changes in gene expression in the innervating ANS. Induction of inflammatory gene expression and loss of neuron cell viability in SG and DRG are potential novel mechanisms contributing to abnormal ANS function which can promote cardiac arrhythmia and pathological remodeling in myocardium.

Background: Diffusion tensor imaging (DTI) is widely used to assess tissue microstructure non-invasively. Cardiac DTI enables inference of cell and sheetlet orientations, which are altered under pathological conditions. However, DTI is affected by many factors, therefore robust validation is critical. Existing histological validation is intrinsically flawed, since it requires further tissue processing leading to sample distortion, is routinely limited in field-of-view and requires reconstruction of three-dimensional volumes from two-dimensional images. In contrast, synchrotron radiation imaging (SRI) data enables imaging of the heart in 3D without further preparation following DTI. The objective of the study was to validate DTI measurements based on structure tensor analysis of SRI data., Methods: One isolated, fixed rat heart was imaged ex vivo with DTI and X-ray phase contrast SRI, and reconstructed at 100 μm and 3.6 μm isotropic resolution respectively. Structure tensors were determined from the SRI data and registered to the DTI data., Results: Excellent agreement in helix angles (HA) and transverse angles (TA) was observed between the DTI and structure tensor synchrotron radiation imaging (STSRI) data, where HA DTI-STSRI  = -1.4° ± 23.2° and TA DTI-STSRI  = -1.4° ± 35.0° (mean ± 1.96 standard deviation across all voxels in the left ventricle). STSRI confirmed that the primary eigenvector of the diffusion tensor corresponds with the cardiomyocyte long-axis across the whole myocardium., Conclusions: We have used STSRI as a novel and high-resolution gold standard for the validation of DTI, allowing like-with-like comparison of three-dimensional tissue structures in the same intact heart free of distortion. This represents a critical step forward in independently verifying the structural basis and informing the interpretation of cardiac DTI data, thereby supporting the further development and adoption of DTI in structure-based electro-mechanical modelling and routine clinical applications.

Due to their short wavelength, X-rays can in principle be focused down to a few nanometres and below. At the same time, it is this short wavelength that puts stringent requirements on X-ray optics and their metrology. Both are limited by today's technology. In this work, we present accurate at wavelength measurements of residual aberrations of a refractive X-ray lens using ptychography to manufacture a corrective phase plate. Together with the fitted phase plate the optics shows diffraction-limited performance, generating a nearly Gaussian beam profile with a Strehl ratio above 0.8. This scheme can be applied to any other focusing optics, thus solving the X-ray optical problem at synchrotron radiation sources and X-ray free-electron lasers.

Underground storage permanence is a major concern for carbon capture and storage. Pumping CO2 into carbonate reservoirs has the potential to dissolve geologic seals and allow CO2 to escape. However, the dissolution processes at reservoir conditions are poorly understood. Thus, time-resolved experiments are needed to observe and predict the nature and rate of dissolution at the pore scale. Synchrotron fast tomography is a method of taking high-resolution time-resolved images of complex pore structures much more quickly than traditional µ-CT. The Diamond Lightsource Pink Beam was used to dynamically image dissolution of limestone in the presence of CO2-saturated brine at reservoir conditions. 100 scans were taken at a 6.1 µm resolution over a period of 2 hours. The images were segmented and the porosity and permeability were measured using image analysis and network extraction. Porosity increased uniformly along the length of the sample; however, the rate of increase of both porosity and permeability slowed at later times.

The high-throughput 3D visualisation of biological specimens is essential for studying diseases and developmental disorders. It requires imaging methods that deliver high-contrast, high-resolution volumetric information at short sample preparation and acquisition times. Here we show that X-ray phase-contrast tomography using a single grating can provide a powerful alternative to commonly employed techniques, such as high-resolution episcopic microscopy (HREM). We present the phase tomography of a mouse embryo in paraffin obtained with an X-ray single-grating interferometer at I13-2 Beamline at Diamond Light Source and discuss the results in comparison with HREM measurements. The excellent contrast and quantitative density information achieved non-destructively and without staining using a simple, robust setup make X-ray single-grating interferometry an optimum candidate for high-throughput imaging of biological specimens as an alternative for existing methods like HREM.

We previously reported a genetic analysis of heart failure traits in a population of inbred mouse strains treated with isoproterenol to mimic catecholamine-driven cardiac hypertrophy. Here, we apply a co-expression network algorithm, wMICA, to perform a systems-level analysis of left ventricular transcriptomes from these mice. We describe the features of the overall network but focus on a module identified in treated hearts that is strongly related to cardiac hypertrophy and pathological remodeling. Using the causal modeling algorithm NEO, we identified the gene Adamts2 as a putative regulator of this module and validated the predictive value of NEO using small interfering RNA-mediated knockdown in neonatal rat ventricular myocytes. Adamts2 silencing regulated the expression of the genes residing within the module and impaired isoproterenol-induced cellular hypertrophy. Our results provide a view of higher order interactions in heart failure with potential for diagnostic and therapeutic insights., (Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.)