Phages overcome bacterial immunity via diverse anti-defence proteins.

It was recently shown that bacteria use, apart from CRISPR-Cas and restriction systems, a considerable diversity of phage resistance systems1-4, but it is largely unknown how phages cope with this multilayered bacterial immunity. Here we analysed groups of closely related Bacillus phages that showed differential sensitivity to bacterial defence systems, and discovered four distinct families of anti-defence proteins that inhibit the Gabija, Thoeris and Hachiman systems. We show that these proteins Gad1, Gad2, Tad2 and Had1 efficiently cancel the defensive activity when co-expressed with the respective defence system or introduced into phage genomes. Homologues of these anti-defence proteins are found in hundreds of phages that infect taxonomically diverse bacterial species. We show that the anti-Gabija protein Gad1 blocks the ability of the Gabija defence complex to cleave phage-derived DNA. Our data further reveal that the anti-Thoeris protein Tad2 is a 'sponge' that sequesters the immune signalling molecules produced by Thoeris TIR-domain proteins in response to phage infection. Our results demonstrate that phages encode an arsenal of anti-defence proteins that can disable a variety of bacterial defence mechanisms.

Phage anti-CBASS and anti-Pycsar nucleases subvert bacterial immunity.

The cyclic oligonucleotide-based antiphage signalling system (CBASS) and the pyrimidine cyclase system for antiphage resistance (Pycsar) are antiphage defence systems in diverse bacteria that use cyclic nucleotide signals to induce cell death and prevent viral propagation1,2. Phages use several strategies to defeat host CRISPR and restriction-modification systems3-10, but no mechanisms are known to evade CBASS and Pycsar immunity. Here we show that phages encode anti-CBASS (Acb) and anti-Pycsar (Apyc) proteins that counteract defence by specifically degrading cyclic nucleotide signals that activate host immunity. Using a biochemical screen of 57 phages in Escherichia coli and Bacillus subtilis, we discover Acb1 from phage T4 and Apyc1 from phage SBSphiJ as founding members of distinct families of immune evasion proteins. Crystal structures of Acb1 in complex with 3'3'-cyclic GMP-AMP define a mechanism of metal-independent hydrolysis 3' of adenosine bases, enabling broad recognition and degradation of cyclic dinucleotide and trinucleotide CBASS signals. Structures of Apyc1 reveal a metal-dependent cyclic NMP phosphodiesterase that uses relaxed specificity to target Pycsar cyclic pyrimidine mononucleotide signals. We show that Acb1 and Apyc1 block downstream effector activation and protect from CBASS and Pycsar defence in vivo. Active Acb1 and Apyc1 enzymes are conserved in phylogenetically diverse phages, demonstrating that cleavage of host cyclic nucleotide signals is a key strategy of immune evasion in phage biology.

Viruses inhibit TIR gcADPR signalling to overcome bacterial defence.

The Toll/interleukin-1 receptor (TIR) domain is a key component of immune receptors that identify pathogen invasion in bacteria, plants and animals1-3. In the bacterial antiphage system Thoeris, as well as in plants, recognition of infection stimulates TIR domains to produce an immune signalling molecule whose molecular structure remains elusive. This molecule binds and activates the Thoeris immune effector, which then executes the immune function1. We identified a large family of phage-encoded proteins, denoted here as Thoeris anti-defence 1 (Tad1), that inhibit Thoeris immunity. We found that Tad1 proteins are 'sponges' that bind and sequester the immune signalling molecule produced by TIR-domain proteins, thus decoupling phage sensing from immune effector activation and rendering Thoeris inactive. Tad1 can also efficiently sequester molecules derived from a plant TIR-domain protein, and a high-resolution crystal structure of Tad1 bound to a plant-derived molecule showed a unique chemical structure of 1 ''-2' glycocyclic ADPR (gcADPR). Our data furthermore suggest that Thoeris TIR proteins produce a closely related molecule, 1''-3' gcADPR, which activates ThsA an order of magnitude more efficiently than the plant-derived 1''-2' gcADPR. Our results define the chemical structure of a central immune signalling molecule and show a new mode of action by which pathogens can suppress host immunity.

Multiaxial pressure-strain analysis of regional myocardial work in the setting of graded coronary stenoses and dobutamine stress.

We present a detailed analysis of regional myocardial blood flow and work to better understand the effects of coronary stenoses and low-dose dobutamine stress. Our analysis is based on a unique open-chest model in anesthetized canines that features invasive hemodynamic monitoring, microsphere-based blood flow analysis, and an extensive three-dimensional (3-D) sonomicrometer array that provides multiaxial deformational assessments in the ischemic, border, and remote vascular territories. We use this model to construct regional pressure-strain loops for each territory and quantify the loop subcomponent areas that reflect myocardial work contributing to the ejection of blood and wasted work that does not. We demonstrate that reductions in coronary blood flow markedly alter the shapes and temporal relationships of pressure-strain loops, as well as the magnitudes of their total and subcomponent areas. Specifically, we show that moderate stenoses in the mid-left anterior descending coronary artery decrease regional midventricle myocardial work indices and substantially increase indices of wasted work. In the midventricle, these effects are most pronounced along the radial and longitudinal axes, with more modest effects along the circumferential axis. We further demonstrate that low-dose dobutamine can help to restore or even improve function, but often at the cost of increased wasted work. This detailed, multiaxial analysis provides unique insight into the physiology and mechanics of the heart in the presence of ischemia and low-dose dobutamine, with potential implications in many areas, including the detection and characterization of ischemic heart disease and the use of inotropic support for low cardiac output.NEW & NOTEWORTHY Our unique experimental model assesses cardiac pressure-strain relationships along multiple axes in multiple regions. We demonstrate that moderate coronary stenoses decrease regional myocardial work and increase wasted work and that low-dose dobutamine can help to restore myocardial function, but often with further increases in wasted work. Our findings highlight the significant directional variation of cardiac mechanics and demonstrate potential advantages of pressure-strain analyses over traditional, purely deformational measures, especially in characterizing physiological changes related to dobutamine.

Regional myocardial strain analysis via 2D speckle tracking echocardiography: validation with sonomicrometry and correlation with regional blood flow in the presence of graded coronary stenoses and dobutamine stress.

BACKGROUND: Quantitative regional strain analysis by speckle tracking echocardiography (STE) may be particularly useful in the assessment of myocardial ischemia and viability, although reliable measurement of regional strain remains challenging, especially in the circumferential and radial directions. We present an acute canine model that integrates a complex sonomicrometer array with microsphere blood flow measurements to evaluate regional myocardial strain and flow in the setting of graded coronary stenoses and dobutamine stress. We apply this unique model to rigorously evaluate a commercial 2D STE software package and explore fundamental regional myocardial flow-function relationships. METHODS: Sonomicrometers (16 crystals) were implanted in epicardial and endocardial pairs across the anterior myocardium of anesthetized open chest dogs (n = 7) to form three adjacent cubes representing the ischemic, border, and remote regions, as defined by their relative locations to a hydraulic occluder on the mid-left anterior descending coronary artery (LAD). Additional cardiac (n = 3) and extra-cardiac (n = 3) reference crystals were placed to define the cardiac axes and aid image registration. 2D short axis echocardiograms, sonometric data, and microsphere blood flow data were acquired at baseline and in the presence of mild and moderate LAD stenoses, both before and during low-dose dobutamine stress (5 µg/kg/min). Regional end-systolic 2D STE radial and circumferential strains were calculated with commercial software (EchoInsight) and compared to those determined by sonomicrometry and to microsphere blood flow measurements. Post-systolic indices (PSIs) were also calculated for radial and circumferential strains. RESULTS: Low-dose dobutamine augmented both strain and flow in the presence of mild and moderate stenoses. Regional 2D STE strains correlated moderately with strains assessed by sonomicrometry (Rradial = 0.56, p < 0.0001; Rcirc = 0.55, p < 0.0001) and with regional flow quantities (Rradial = 0.61, Rcirc = 0.63). Overall, correspondence between 2D STE and sonomicrometry was better in the circumferential direction (Bias ± 1.96 SD: - 1.0 ± 8.2% strain, p = 0.06) than the radial direction (5.7 ± 18.3%, p < 0.0001). Mean PSI values were greatest in low flow conditions and normalized with low-dose dobutamine. CONCLUSIONS: 2D STE identifies changes in regional end-systolic circumferential and radial strain produced by mild and moderate coronary stenoses and low-dose dobutamine stress. Regional 2D STE end-systolic strain measurements correlate modestly with regional sonomicrometer strain and microsphere flow measurements.

Imaging predictors of progression of lumbar spondylolysis to spondylolisthesis: a systematic review.

BACKGROUND CONTEXT: Isthmic spondylolisthesis (IS) is defined as the anterior translation of one lumbar vertebra relative to the next caudal segment as a result of a unilateral or bilateral fracture of the pars interarticularis. These fractures are interchangeably known as "pars defects" or "spondylolysis." Many risk factors have been proposed to explain the progression of a spondylolytic defect to IS, however, none are validated. PURPOSE: This systematic review provides an overview of various radiological and imaging parameters that can help predict the risk of progression of a spondylolytic defect into IS. STUDY DESIGN: Systematic review. METHODS: Medline, Embase and Cochrane online database were searched. The various correlations between imaging features with observed spondylolisthesis prevalence or severity or spondylolysis rates of spondylolisthesis were evaluated to provide a list of imaging risk factors to predict IS. Significance of the correlations in the original article was recorded to enable comparison of the collected evidence of separate image features. RESULTS: All searches combined generated a total of 431 results of which 26 articles were included into this study. Of the 22 potential risk factors identified, 5 were found to be statistically insignificant, 8 were found to be significant and 9 had mixed results. The following features were found to be significant risk factors in at least on study: disc degeneration, transverse process width, pelvic incidence, pelvic tilt, sacral slope, lumbar lordosis, lumbar index, thoracic kyphosis, facet joint angle above the level of defect, facet joint degeneration, facet tropism, multifidus size, lateral erector spinae size, mesenteric fat thickness, subcutaneous fat thickness and soft tissue calcification. CONCLUSION: Our research suggests that only disc degeneration had moderately strong evidence with consistent significant associations with development of IS in patients with spondylolysis. Transverse process width, pelvic incidence, pelvic tilt, sacral slope, lumbar lordosis, lumbar index, thoracic kyphosis, facet joint angle above the level of defect, facet joint degeneration, facet tropism, multifidus size, lateral erector spinae size, mesenteric fat thickness, subcutaneous fat thickness and soft tissue calcification had some evidence. All other radiological factors had weak evidence. The results of this study can be used to improve early clinical decision making for patients with spondylolysis.

The SARM1 TIR domain produces glycocyclic ADPR molecules as minor products.

Sterile alpha and TIR motif-containing 1 (SARM1) is a protein involved in programmed death of injured axons. Following axon injury or a drug-induced insult, the TIR domain of SARM1 degrades the essential molecule nicotinamide adenine dinucleotide (NAD+), leading to a form of axonal death called Wallerian degeneration. Degradation of NAD+ by SARM1 is essential for the Wallerian degeneration process, but accumulating evidence suggest that other activities of SARM1, beyond the mere degradation of NAD+, may be necessary for programmed axonal death. In this study we show that the TIR domains of both human and fruit fly SARM1 produce 1''-2' and 1''-3' glycocyclic ADP-ribose (gcADPR) molecules as minor products. As previously reported, we observed that SARM1 TIR domains mostly convert NAD+ to ADPR (for human SARM1) or cADPR (in the case of SARM1 from Drosophila melanogaster). However, we now show that human and Drosophila SARM1 additionally convert ~0.1-0.5% of NAD+ into gcADPR molecules. We find that SARM1 TIR domains produce gcADPR molecules both when purified in vitro and when expressed in bacterial cells. Given that gcADPR is a second messenger involved in programmed cell death in bacteria and likely in plants, we propose that gcADPR may play a role in SARM1-induced programmed axonal death in animals.

Three-dimensional brain growth abnormalities in childhood-onset schizophrenia visualized by using tensor-based morphometry.

Earlier studies revealed progressive cortical gray matter (GM) loss in childhood-onset schizophrenia (COS) across both lateral and medial surfaces of the developing brain. Here, we use tensor-based morphometry to visualize white matter (WM) growth abnormalities in COS throughout the brain. Using high-dimensional elastic image registration, we compared 3D maps of local WM growth rates in COS patients and healthy children over a 5-year period, based on analyzing longitudinal brain MRIs from 12 COS patients and 12 healthy controls matched for age, gender, and scan interval. COS patients showed up to 2.2% slower growth rates per year than healthy controls in WM (P = 0.02, all P values corrected). The greatest differences were in the right hemisphere (P = 0.006). This asymmetry was attributable to a right slower than left hemisphere growth rate mapped in COS patients (P = 0.037) but not in healthy controls. WM growth rates reached 2.6% per year in healthy controls (P = 0.0002). COS patients showed only a 1.3% per year trend for growth in the left hemisphere (P = 0.066). In COS, WM growth rates were associated with improvement in the Children's Global Assessment Scale (R = 0.64, P = 0.029). Growth rates were reduced throughout the brain in COS, but this process appeared to progress in a front-to-back (frontal-parietal) fashion, and this effect was not attributable to lower IQ. Growth rates were correlated with functional prognosis and were visualized as detailed 3D maps. Finally, these findings also confirm that the progressive GM deficits seen in schizophrenia are not the result of WM overgrowth.

Learning-Based Regularization for Cardiac Strain Analysis via Domain Adaptation.

Reliable motion estimation and strain analysis using 3D+ time echocardiography (4DE) for localization and characterization of myocardial injury is valuable for early detection and targeted interventions. However, motion estimation is difficult due to the low-SNR that stems from the inherent image properties of 4DE, and intelligent regularization is critical for producing reliable motion estimates. In this work, we incorporated the notion of domain adaptation into a supervised neural network regularization framework. We first propose a semi-supervised Multi-Layered Perceptron (MLP) network with biomechanical constraints for learning a latent representation that is shown to have more physiologically plausible displacements. We extended this framework to include a supervised loss term on synthetic data and showed the effects of biomechanical constraints on the network's ability for domain adaptation. We validated the semi-supervised regularization method on in vivo data with implanted sonomicrometers. Finally, we showed the ability of our semi-supervised learning regularization approach to identify infarct regions using estimated regional strain maps with good agreement to manually traced infarct regions from postmortem excised hearts.

Unsupervised Motion Tracking of Left Ventricle in Echocardiography.

Accurate motion tracking of the left ventricle is critical in detecting wall motion abnormalities in the heart after an injury such as a myocardial infarction. We propose an unsupervised motion tracking framework with physiological constraints to learn dense displacement fields between sequential pairs of 2-D B-mode echocardiography images. Current deep-learning motion-tracking algorithms require large amounts of data to provide ground-truth, which is difficult to obtain for in vivo datasets (such as patient data and animal studies), or are unsuccessful in tracking motion between echocardiographic images due to inherent ultrasound properties (such as low signal-to-noise ratio and various image artifacts). We design a U-Net inspired convolutional neural network that uses manually traced segmentations as a guide to learn displacement estimations between a source and target image without ground-truth displacement fields by minimizing the difference between a transformed source frame and the original target frame. We then penalize divergence in the displacement field in order to enforce incompressibility within the left ventricle. We demonstrate the performance of our model on synthetic and in vivo canine 2-D echocardiography datasets by comparing it against a non-rigid registration algorithm and a shape-tracking algorithm. Our results show favorable performance of our model against both methods.

A SEMI-SUPERVISED JOINT LEARNING APPROACH TO LEFT VENTRICULAR SEGMENTATION AND MOTION TRACKING IN ECHOCARDIOGRAPHY.

Accurate interpretation and analysis of echocardiography is important in assessing cardiovascular health. However, motion tracking often relies on accurate segmentation of the myocardium, which can be difficult to obtain due to inherent ultrasound properties. In order to address this limitation, we propose a semi-supervised joint learning network that exploits overlapping features in motion tracking and segmentation. The network simultaneously trains two branches: one for motion tracking and one for segmentation. Each branch learns to extract features relevant to their respective tasks and shares them with the other. Learned motion estimations propagate a manually segmented mask through time, which is used to guide future segmentation predictions. Physiological constraints are introduced to enforce realistic cardiac behavior. Experimental results on synthetic and in vivo canine 2D+t echocardiographic sequences outperform some competing methods in both tasks.

Molecular basis of force-from-lipids gating in the mechanosensitive channel MscS.

Prokaryotic mechanosensitive (MS) channels open by sensing the physical state of the membrane. As such, lipid-protein interactions represent the defining molecular process underlying mechanotransduction. Here, we describe cryo-electron microscopy (cryo-EM) structures of the E. coli small-conductance mechanosensitive channel (MscS) in nanodiscs (ND). They reveal a novel membrane-anchoring fold that plays a significant role in channel activation and establish a new location for the lipid bilayer, shifted ~14 Å from previous consensus placements. Two types of lipid densities are explicitly observed. A phospholipid that 'hooks' the top of each TM2-TM3 hairpin and likely plays a role in force sensing, and a bundle of acyl chains occluding the permeation path above the L105 cuff. These observations reshape our understanding of force-from-lipids gating in MscS and highlight the key role of allosteric interactions between TM segments and phospholipids bound to key dynamic components of the channel.

Flow network tracking for spatiotemporal and periodic point matching: Applied to cardiac motion analysis.

The accurate quantification of left ventricular (LV) deformation/strain shows significant promise for quantitatively assessing cardiac function for use in diagnosis and therapy planning. However, accurate estimation of the displacement of myocardial tissue and hence LV strain has been challenging due to a variety of issues, including those related to deriving tracking tokens from images and following tissue locations over the entire cardiac cycle. In this work, we propose a point matching scheme where correspondences are modeled as flow through a graphical network. Myocardial surface points are set up as nodes in the network and edges define neighborhood relationships temporally. The novelty lies in the constraints that are imposed on the matching scheme, which render the correspondences one-to-one through the entire cardiac cycle, and not just two consecutive frames. The constraints also encourage motion to be cyclic, which an important characteristic of LV motion. We validate our method by applying it to the estimation of quantitative LV displacement and strain estimation using 8 synthetic and 8 open-chested canine 4D echocardiographic image sequences, the latter with sonomicrometric crystals implanted on the LV wall. We were able to achieve excellent tracking accuracy on the synthetic dataset and observed a good correlation with crystal-based strains on the in-vivo data.

Efficient Two-Pass 3-D Speckle Tracking for Ultrasound Imaging.

Speckle tracking based on block matching is the most common method for multi-dimensional motion estimation in ultrasound elasticity imaging. Extension of two-dimensional (2-D) methods to three dimensions (3-D) has been problematic because of the large computational load of 3-D tracking, as well as performance issues related to the low frame (volume) rates of 3-D images. To address both of these problems, we have developed an efficient two-pass tracking method suited to cardiac elasticity imaging. PatchMatch, originally developed for image editing, has been adapted for ultrasound to provide first-pass displacement estimates. Second-pass estimation uses conventional block matching within a much smaller search region. 3-D displacements are then obtained using correlation filtering previously shown to be effective against speckle decorrelation. Both simulated and in vivo canine cardiac results demonstrate that the proposed two-pass method reduces computational cost compared to conventional 3-D exhaustive search by a factor of 10. Moreover, it outperforms one-pass tracking by a factor of about 3 in terms of root-mean-square error relative to available ground-truth displacements.

Statistical shape modeling of the left ventricle: myocardial infarct classification challenge.

Statistical shape modeling is a powerful tool for visualizing and quantifying geometric and functional patterns of the heart. After myocardial infarction (MI), the left ventricle typically remodels in response to physiological challenges. Several methods have been proposed in the literature to describe statistical shape changes. Which method best characterizes left ventricular remodeling after MI is an open research question. A better descriptor of remodeling is expected to provide a more accurate evaluation of disease status in MI patients. We therefore designed a challenge to test shape characterization in MI given a set of three-dimensional left ventricular surface points. The training set comprised 100 MI patients, and 100 asymptomatic volunteers (AV). The challenge was initiated in 2015 at the Statistical Atlases and Computational Models of the Heart workshop, in conjunction with the MICCAI conference. The training set with labels was provided to participants, who were asked to submit the likelihood of MI from a different (validation) set of 200 cases (100 AV and 100 MI). Sensitivity, specificity, accuracy and area under the receiver operating characteristic curve were used as the outcome measures. The goals of this challenge were to (1) establish a common dataset for evaluating statistical shape modeling algorithms in MI, and (2) test whether statistical shape modeling provides additional information characterizing MI patients over standard clinical measures. Eleven groups with a wide variety of classification and feature extraction approaches participated in this challenge. All methods achieved excellent classification results with accuracy ranges from 0.83 to 0.98. The areas under the receiver operating characteristic curves were all above 0.90. Four methods showed significantly higher performance than standard clinical measures. The dataset and software for evaluation are available from the Cardiac Atlas Project website1.

Statistical properties of Jacobian maps and the realization of unbiased large-deformation nonlinear image registration.

Maps of local tissue compression or expansion are often computed by comparing magnetic resonance imaging (MRI) scans using nonlinear image registration. The resulting changes are commonly analyzed using tensor-based morphometry to make inferences about anatomical differences, often based on the Jacobian map, which estimates local tissue gain or loss. Here, we provide rigorous mathematical analyses of the Jacobian maps, and use themto motivate a new numerical method to construct unbiased nonlinear image registration. First, we argue that logarithmic transformation is crucial for analyzing Jacobian values representing morphometric differences. We then examine the statistical distributions of log-Jacobian maps by defining the Kullback-Leibler (KL) distance on material density functions arising in continuum-mechanical models. With this framework, unbiased image registration can be constructed by quantifying the symmetric KL-distance between the identity map and the resulting deformation. Implementation details, addressing the proposed unbiased registration as well as the minimization of symmetric image matching functionals, are then discussed and shown to be applicable to other registration methods, such as inverse consistent registration. In the results section, we test the proposed framework, as well as present an illustrative application mapping detailed 3-D brain changes in sequential magnetic resonance imaging scans of a patient diagnosed with semantic dementia. Using permutation tests, we show that the symmetrization of image registration statistically reduces skewness in the log-Jacobian map.

Autologous osteochondral transplantation for simple cyst in the patella.

Treatment options for chondral and osteochondral defects of the patella have been few and results have been inconsistent at best. Autologous osteochondral transplantation presents a new way to revisit these patellar defects. We report the case of a young female softball player with a simple cyst in the patella and an osteochondral defect that serves as the indication for autograft osteochondral transplantation.

Arthodesis of the infected ankle and subtalar joint.

Arthrodesis of the ankle or subtalar joint for limb salvage in joint sepsis is extremely complicated, and produces a protracted course of management. A successful outcome is founded on the diligence of the surgeon in the preoperative evaluation, intraoperative technique, and postoperative care of the patient. Liberal consultation with infectious disease specialists, vascular, and plastic surgeons is recommended. Recognition of patient-specific comorbidities is essential to the selection of appropriate limb salvage candidates.

The regulatory subunits of PI3K, p85alpha and p85beta, interact with XBP-1 and increase its nuclear translocation.

Despite the fact that X-box binding protein-1 (XBP-1) is one of the main regulators of the unfolded protein response (UPR), the modulators of XBP-1 are poorly understood. Here, we show that the regulatory subunits of phosphotidyl inositol 3-kinase (PI3K), p85alpha (encoded by Pik3r1) and p85beta (encoded by Pik3r2) form heterodimers that are disrupted by insulin treatment. This disruption of heterodimerization allows the resulting monomers of p85 to interact with, and increase the nuclear translocation of, the spliced form of XBP-1 (XBP-1s). The interaction between p85 and XBP-1s is lost in ob/ob mice, resulting in a severe defect in XBP-1s translocation to the nucleus and thus in the resolution of endoplasmic reticulum (ER) stress. These defects are ameliorated when p85alpha and p85beta are overexpressed in the liver of ob/ob mice. Our results define a previously unknown insulin receptor signaling pathway and provide new mechanistic insight into the development of ER stress during obesity.

Endoplasmic reticulum stress plays a central role in development of leptin resistance.

Leptin has not evolved as a therapeutic modality for the treatment of obesity due to the prevalence of leptin resistance in a majority of the obese population. Nevertheless, the molecular mechanisms of leptin resistance remain poorly understood. Here, we show that increased endoplasmic reticulum (ER) stress and activation of the unfolded protein response (UPR) in the hypothalamus of obese mice inhibits leptin receptor signaling. The genetic imposition of reduced ER capacity in mice results in severe leptin resistance and leads to a significant augmentation of obesity on a high-fat diet. Moreover, we show that chemical chaperones, 4-phenyl butyric acid (PBA), and tauroursodeoxycholic acid (TUDCA), which have the ability to decrease ER stress, act as leptin-sensitizing agents. Taken together, our results may provide the basis for a novel treatment of obesity.