Angiotensin II receptor inhibition ameliorates liver fibrosis and enhances hepatocellular carcinoma infiltration by effector T cells.

Although viral hepatocellular carcinoma (HCC) is declining, nonviral HCC, which often is the end stage of nonalcoholic or alcoholic steatohepatitis (NASH, ASH), is on an upward trajectory. Immune checkpoint inhibitors (ICIs) that block the T cell inhibitory receptor PD-1 were approved for treatment of all HCC types. However, only a minority of HCC patients show a robust and sustained response to PD-1 blockade, calling for improved understanding of factors that negatively impact response rate and duration and the discovery of new adjuvant treatments that enhance ICI responsiveness. Using a mouse model of NASH-driven HCC, we identified peritumoral fibrosis as a potential obstacle to T cell-mediated tumor regression and postulated that antifibrotic medications may increase ICI responsiveness. We now show that the angiotensin II receptor inhibitor losartan, a commonly prescribed and safe antihypertensive drug, reduced liver and peritumoral fibrosis and substantially enhanced anti-PD-1-induced tumor regression. Although losartan did not potentiate T cell reinvigoration, it substantially enhanced HCC infiltration by effector CD8+ T cells compared to PD-1 blockade alone. The beneficial effects of losartan correlated with blunted TGF-ß receptor signaling, reduced collagen deposition, and depletion of immunosuppressive fibroblasts.

SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes.

The SEVA platform (https://seva-plasmids.com) was launched one decade ago, both as a database (DB) and as a physical repository of plasmid vectors for genetic analysis and engineering of Gram-negative bacteria with a structure and nomenclature that follows a strict, fixed architecture of functional DNA segments. While the current update keeps the basic features of earlier versions, the platform has been upgraded not only with many more ready-to-use plasmids but also with features that expand the range of target species, harmonize DNA assembly methods and enable new applications. In particular, SEVA 4.0 includes (i) a sub-collection of plasmids for easing the composition of multiple DNA segments with MoClo/Golden Gate technology, (ii) vectors for Gram-positive bacteria and yeast and [iii] off-the-shelf constructs with built-in functionalities. A growing collection of plasmids that capture part of the standard-but not its entirety-has been compiled also into the DB and repository as a separate corpus (SEVAsib) because of its value as a resource for constructing and deploying phenotypes of interest. Maintenance and curation of the DB were accompanied by dedicated diffusion and communication channels that make the SEVA platform a popular resource for genetic analyses, genome editing and bioengineering of a large number of microorganisms.

A synthetic C2 auxotroph of Pseudomonas putida for evolutionary engineering of alternative sugar catabolic routes.

Acetyl-coenzyme A (AcCoA) is a metabolic hub in virtually all living cells, serving as both a key precursor of essential biomass components and a metabolic sink for catabolic pathways for a large variety of substrates. Owing to this dual role, tight growth-production coupling schemes can be implemented around the AcCoA node. Building on this concept, a synthetic C2 auxotrophy was implemented in the platform bacterium Pseudomonas putida through an in silico-informed engineering approach. A growth-coupling strategy, driven by AcCoA demand, allowed for direct selection of an alternative sugar assimilation route-the phosphoketolase (PKT) shunt from bifidobacteria. Adaptive laboratory evolution forced the synthetic P. putida auxotroph to rewire its metabolic network to restore C2 prototrophy via the PKT shunt. Large-scale structural chromosome rearrangements were identified as possible mechanisms for adjusting the network-wide proteome profile, resulting in improved PKT-dependent growth phenotypes. 13C-based metabolic flux analysis revealed an even split between the native Entner-Doudoroff pathway and the synthetic PKT bypass for glucose processing, leading to enhanced carbon conservation. These results demonstrate that the P. putida metabolism can be radically rewired to incorporate a synthetic C2 metabolism, creating novel network connectivities and highlighting the importance of unconventional engineering strategies to support efficient microbial production.

Machine Learning Enables Selection of Epistatic Enzyme Mutants for Stability Against Unfolding and Detrimental Aggregation.

Machine learning (ML) has pervaded most areas of protein engineering, including stability and stereoselectivity. Using limonene epoxide hydrolase as the model enzyme and innov'SAR as the ML platform, comprising a digital signal process, we achieved high protein robustness that can resist unfolding with concomitant detrimental aggregation. Fourier transform (FT) allows us to take into account the order of the protein sequence and the nonlinear interactions between positions, and thus to grasp epistatic phenomena. The innov'SAR approach is interpolative, extrapolative and makes outside-the-box, predictions not found in other state-of-the-art ML or deep learning approaches. Equally significant is the finding that our approach to ML in the present context, flanked by advanced molecular dynamics simulations, uncovers the connection between epistatic mutational interactions and protein robustness.

Can we predict recurrence in WHO G1-G2 pancreatic neuroendocrine neoplasms? Results from a multi-institutional Spanish study.

INTRODUCTION: Pancreatic neuroendocrine neoplasms (PNEN) are rare tumours and well differentiated PNEN are associated with relatively indolent physiological behaviour. For this reason, only few studies have investigated those factors associated with recurrence in this group of patients. The aim of this study is to analyse whether it is possible to predict tumour recurrence in World Health Organization (WHO) 2017 G1-G2 PNEN patients. METHODS: This is a retrospective multi-institutional study. Patients submitted to pancreatic resection from 7 Spanish centres were reviewed. Only patients with WHO G1-G2 PNEN were included. Demographic and clinicopathological variables were analysed. RESULTS: Data from 137 patients were reviewed. Median age was 59.2 (25-84) years. Recurrence of disease occurred in 19 (13.9%) patients. Median DFS was 55 months. At multivariate analysis, tumour size >20 mm, lymphnode metastasis and a new tumour grade 2 incorporating Ki-67 labelling index (LI) > 5% and mitotic index (MI) > 2 were independently associated with recurrence. We developed a risk score model with these three factors. High-risk patients had a significantly lower 5-year disease-specific survival compared to low-risk patients (70% vs 100%). CONCLUSION: We propose a novel risk score for recurrence based on lymphnode metastasis, tumour size > 20 mm and a new grade 2 based on Ki-67 LI >5% and MI > 2. If 2 factors are present, patients have a higher risk for recurrence and a significantly poorer DSS, and therefore they should be closely monitored during follow-up. The role of adjuvant chemotherapy in these patients needs to be evaluated in clinical trials.

Novel Descriptors and Digital Signal Processing- Based Method for Protein Sequence Activity Relationship Study.

The work aiming to unravel the correlation between protein sequence and function in the absence of structural information can be highly rewarding. We present a new way of considering descriptors from the amino acids index database for modeling and predicting the fitness value of a polypeptide chain. This approach includes the following steps: (i) Calculating Q elementary numerical sequences (Ele_SEQ) depending on the encoding of the amino acid residues, (ii) determining an extended numerical sequence (Ext_SEQ) by concatenating the Q elementary numerical sequences, wherein at least one elementary numerical sequence is a protein spectrum obtained by applying fast Fourier transformation (FFT), and (iii) predicting a value of fitness for polypeptide variants (train and/or validation set). These new descriptors were tested on four sets of proteins of different lengths (GLP-2, TNF alpha, cytochrome P450, and epoxide hydrolase) and activities (cAMP activation, binding affinity, thermostability and enantioselectivity). We show that the use of multiple physicochemical descriptors coupled with the implementation of the FFT, taking into account the interactions between residues of amino amides within the protein sequence, could lead to very significant improvement in the quality of models and predictions. The choice of the descriptor or of the combination of descriptors and/or FFT is dependent on the couple protein/fitness. This approach can provide potential users with value added to existing mutant libraries where screening efforts have so far been unsuccessful in finding improved polypeptide mutants for useful applications.

MEX-3 proteins: recent insights on novel post-transcriptional regulators.

RNA-binding proteins of the evolutionarily-conserved MEX-3 family are mediators of post-transcriptional regulation in different organisms. Recent studies highlight their involvement in diverse physiological settings, including the maintenance of a balance between stem cell self-renewal and differentiation. Here, we draw attention to their putative role in tissue homeostasis and disease, particularly cancer.

Suppression of Trapped Energetic Ions Driven Resistive Interchange Modes with Electron Cyclotron Heating in a Helical Plasma.

The resistive interchange mode destabilized by the resonant interaction with the trapped energetic ions is fully suppressed when the injected power of electron cyclotron heating exceeds a certain threshold. It is shown for the first time that the complete stabilization of the energetic-particle-driven mode without relaxing the energetic particle (EP) pressure gradient is possible by reducing the radial width of the eigenmodes δ_{w}, especially when δ_{w} narrows to a small enough value relative to the finite orbit width of EP.

Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments.

Live-cell imaging has opened an exciting window into the role cellular heterogeneity plays in dynamic, living systems. A major critical challenge for this class of experiments is the problem of image segmentation, or determining which parts of a microscope image correspond to which individual cells. Current approaches require many hours of manual curation and depend on approaches that are difficult to share between labs. They are also unable to robustly segment the cytoplasms of mammalian cells. Here, we show that deep convolutional neural networks, a supervised machine learning method, can solve this challenge for multiple cell types across the domains of life. We demonstrate that this approach can robustly segment fluorescent images of cell nuclei as well as phase images of the cytoplasms of individual bacterial and mammalian cells from phase contrast images without the need for a fluorescent cytoplasmic marker. These networks also enable the simultaneous segmentation and identification of different mammalian cell types grown in co-culture. A quantitative comparison with prior methods demonstrates that convolutional neural networks have improved accuracy and lead to a significant reduction in curation time. We relay our experience in designing and optimizing deep convolutional neural networks for this task and outline several design rules that we found led to robust performance. We conclude that deep convolutional neural networks are an accurate method that require less curation time, are generalizable to a multiplicity of cell types, from bacteria to mammalian cells, and expand live-cell imaging capabilities to include multi-cell type systems.

An assessment of existing risk stratification guidelines for the evaluation of patients with suspected choledocholithiasis.

BACKGROUND: Prior studies have demonstrated that existing risk stratification guidelines for the evaluation of suspected choledocholithiasis lack accuracy, leading to the overutilization of endoscopic retrograde cholangiopancreatography (ERCP). The aim of our study was to evaluate the performance characteristics of published guidelines in predicting choledocholithiasis and to determine the impact of laboratory trends on diagnostic accuracy. METHODS: We identified patients with suspected choledocholithiasis hospitalized over a 5-year period (2009-2014) at a tertiary care academic medical center. Among eligible patients, we assessed the performance characteristics of the American Society for Gastrointestinal Endoscopy (ASGE) guidelines predicting the presence of choledocholithiasis, confirmed by endoscopic ultrasound, magnetic resonance cholangiography, ERCP, or intra-operative cholangiography. We also evaluated whether a second set of liver function tests improved the accuracy of the guidelines. RESULTS: On presentation, 71 of the 173 eligible patients (41.4 %) met ASGE high-probability criteria for choledocholithiasis. Of these, only 39 (54.9 %) were found to have a choledocholithiasis on confirmatory testing. Conversely, of the 102 patients (58.6 %) who were classified as low or intermediate probability, 32 (31.4 %) had choledocholithiasis. Overall, the accuracy of the guidelines was 63 % (sensitivity 54.9 %; specificity 68.6 %). Incorporating a second set of laboratory tests did not improve accuracy (62.7 %), and a significant decline in liver function tests did not reliably predict spontaneous stone passage. CONCLUSIONS: Existing guidelines performed suboptimally for predicting choledocholithiasis in our patient population, similar to other validation studies. These findings further underscore the importance of developing alternate risk stratification tools for choledocholithiasis, aiming to minimize unnecessary diagnostic ERCP.

Sprouting of brainstem-spinal tracts in response to unilateral motor cortex stroke in mice.

After a stroke to the motor cortex, sprouting of spared contralateral corticospinal fibers into the affected hemicord is one mechanism thought to mediate functional recovery. Little is known, however, about the role of the phylogenetically old, functionally very important brainstem-spinal systems. Adult mice were subjected to a unilateral photothrombotic stroke of the right motor cortex ablating 90% of the cross-projecting corticospinal cells. Unilateral retrograde tracing from the left cervical spinal hemicord devoid of its corticospinal input revealed widespread plastic responses in different brainstem nuclei 4 weeks after stroke. Whereas some nuclei showed no change or a decrease of their spinal projections, several parts of the medullary reticular formation as well as the spinally projecting raphe nuclei increased their projections to the cortically denervated cervical hemicord by 1.2- to 1.6-fold. The terminal density of corticobulbar fibers from the intact, contralesional cortex, which itself formed a fivefold expanded connection to the ipsilateral spinal cord, increased up to 1.6-fold specifically in these plastic, caudal medullary nuclei. A second stroke, ablating the originally spared motor cortex, resulted in the reappearance of the deficits that had partially recovered after the initial right-sided stroke, suggesting dependence of recovered function on the spared cortical hemisphere and its direct corticospinal and indirect corticobulbospinal connections.

Rewiring of the corticospinal tract in the adult rat after unilateral stroke and anti-Nogo-A therapy.

Adult Long Evans rats received a photothrombotic stroke that destroyed >90% of the sensorimotor cortex unilaterally; they were subsequently treated intrathecally for 2 weeks with a function blocking antibody against the neurite growth inhibitory central nervous system protein Nogo-A. Fine motor control of skilled forelimb grasping improved to 65% of intact baseline performance in the anti-Nogo-A treated rats, whereas control antibody treated animals recovered to only 20% of baseline scores. Bilateral retrograde tract tracing with two different tracers from the intact and the denervated side of the cervical spinal cord, at different time points post-lesion, indicated that the intact corticospinal tract had extensively sprouted across the midline into the denervated spinal hemicord. The original axonal arbours of corticospinal tract fibres that had recrossed the midline were subsequently withdrawn, leading to a complete side-switch in the projection of a subpopulation of contralesional corticospinal tract axons. Anterograde tracing from the contralesional cortex showed a 2-3-fold increase of midline crossing fibres and additionally a massive sprouting of the pre-existing ipsilateral ventral corticospinal tract fibres throughout the entire cervical enlargement of the anti-Nogo-A antibody-treated rats compared to the control group. The laminar distribution pattern of the ipsilaterally projecting corticospinal tract fibres was similar to that in the intact spinal cord. These plastic changes were paralleled by a somatotopic reorganization of the contralesional motor cortex where the formation of an ipsilaterally projecting forelimb area was observed. Intracortical microstimulation of the contralesional motor cortex revealed that low threshold currents evoked ipsilateral movements and electromyography responses at frequent cortical sites in the anti-Nogo-A, but not in the control antibody-treated animals. Subsequent transection of the spared corticospinal tract in chronically recovered animals, treated with anti-Nogo-A, led to a reappearance of the initial lesion deficit observed after the stroke lesion. These results demonstrate a somatotopic side switch anatomically and functionally in the projection of adult corticospinal neurons, induced by the destruction of one sensorimotor cortex and the neutralization of the CNS growth inhibitory protein Nogo-A.

CDX2 regulation by the RNA-binding protein MEX3A: impact on intestinal differentiation and stemness.

The homeobox transcription factor CDX2 plays a crucial role in intestinal cell fate specification, both during normal development and in tumorigenic processes involving intestinal reprogramming. The CDX2 regulatory network is intricate, but it has not yet been fully uncovered. Through genome-wide screening of a 3D culture system, the RNA-binding protein MEX3A was identified as putatively involved in CDX2 regulation; therefore, its biological relevance was addressed by setting up cell-based assays together with expression studies in murine intestine. We demonstrate here that MEX3A has a repressive function by controlling CDX2 levels in gastric and colorectal cellular models. This is dependent on the interaction with a specific binding determinant present in CDX2 mRNA 3'untranslated region. We have further determined that MEX3A impairs intestinal differentiation and cellular polarization, affects cell cycle progression and promotes increased expression of intestinal stem cell markers, namely LGR5, BMI1 and MSI1. Finally, we show that MEX3A is expressed in mouse intestine, supporting an in vivo context for interaction with CDX2 and modulation of stem cell properties. Therefore, we describe a novel CDX2 post-transcriptional regulatory mechanism, through the RNA-binding protein MEX3A, with a major impact in intestinal differentiation, polarity and stemness, likely contributing to intestinal homeostasis and carcinogenesis.

Anaerobic glucose uptake in Pseudomonas putida KT2440 in a bioelectrochemical system.

Providing an anodic potential in a bio-electrochemical system to the obligate aerobe Pseudomonas putida enables anaerobic survival and allows the cells to overcome redox imbalances. In this setup, the bacteria could be exploited to produce chemicals via oxidative pathways at high yield. However, the absence of anaerobic growth and low carbon turnover rates remain as obstacles for the application of such an electro-fermentation technology. Growth and carbon turnover start with carbon uptake into the periplasm and cytosol. P. putida KT2440 has three native transporting systems for glucose, each differing in energy and redox demand. This architecture previously led to the hypothesis that internal redox and energy constraints ultimately limit cytoplasmic carbon utilization in a bio-electrochemical system. However, it remains largely unclear which uptake route is predominantly used by P. putida under electro-fermentative conditions. To elucidate this, we created three gene deletion mutants of P. putida KT2440, forcing the cells to exclusively utilize one of the routes. When grown in a bio-electrochemical system, the pathway mutants were heavily affected in terms of sugar consumption, current output and product formation. Surprisingly, however, we found that about half of the acetate formed in the cytoplasm originated from carbon that was put into the system via the inoculation biomass, while the other half came from the consumption of substrate. The deletion of individual sugar uptake routes did not alter significantly the secreted acetate concentrations among different strains even with different carbon sources. This means that the stoichiometry of the sugar uptake routes is not a limiting factor during electro-fermentation and that the low rates might be caused by other reasons, for example energy limitations or a yet-to-be-identified oxygen-dependent regulatory mechanism.

Literature review and robotic management of a rare case of primary retroperitoneal mucinous cystadenoma.

Primary retroperitoneal mucinous cystic tumors (PRMCT) are divided into 3 groups: benign, borderline malignancy, and malignant. We report a rare case of benign retroperitoneal mucinous cystadenoma of a 59-year-old Caucasian female who presented to our clinic with moderate intermittent left upper quadrant abdominal pain for several months, accompanied by early satiety, and unintentional weight loss of 10 pounds. An abdominal contrast-enhanced computed tomography (CT) scan indicated the presence of a 6.5 × 8.8 cm multilobulated mass in the left upper quadrant, characterized by a homogenous appearance with smooth margins. Upper endoscopic ultrasound and fine needle aspiration were performed. Cytology and histology results yielded rare inflammatory cells and debris with no cytological evidence of malignancy. The case was discussed at the hepatopancreatobiliary conference; the patient underwent a robotic resection of the mass with a gastric rim. Primary retroperitoneal mucinous cystadenomas are commonly managed by complete surgical excision. Robotic excision presents an alternative approach for handling this uncommon neoplastic lesion.

Development of an engineered extracellular vesicles-based vaccine platform for combined delivery of mRNA and protein to induce functional immunity.

mRNA incorporated in lipid nanoparticles (LNPs) became a new class of vaccine modality for induction of immunity against COVID-19 and ushered in a new era in vaccine development. Here, we report a novel, easy-to-execute, and cost effective engineered extracellular vesicles (EVs)-based combined mRNA and protein vaccine platform (EVX-M+P vaccine) and explore its utility in proof-of-concept immunity studies in the settings of cancer and infectious disease. As a first example, we engineered EVs, natural nanoparticle carriers shed by all cells, to contain ovalbumin mRNA and protein (EVOvaM+P vaccine) to serve as cancer vaccine against ovalbumin-expressing melanoma tumors. EVOvaM+P administration to mice with established melanoma tumors resulted in tumor regression associated with effective humoral and adaptive immune responses. As a second example, we generated engineered EVs that contain Spike (S) mRNA and protein to serve as a combined mRNA and protein vaccine (EVSpikeM+P vaccine) against SARS-CoV-2 infection. EVSpikeM+P vaccine administration in mice and baboons elicited robust production of neutralizing IgG antibodies against RBD (receptor binding domain) of S protein and S protein specific T cell responses. Our proof-of-concept study describes a new platform with an ability for rapid development of combination mRNA and protein vaccines employing EVs for deployment against cancer and other diseases.

Multicentre prospective observational study on professional wound care using honey (Medihoney™).

In recent years, the treatment of wounds with honey has received an increasing amount of attention from healthcare professionals in Germany and Austria. We conducted a prospective observational multicentre study using Medihoney™ dressings in 10 hospitals - nine in Germany and one in Austria. Wound-associated parameters were monitored systematically at least three times in all patients. Data derived from the treatment of 121 wounds of various aetiologies over a period of 2 years were analysed. Almost half of the patients were younger than 18 years old, and 32% of the study population was oncology patients. Overall, wound size decreased significantly during the study period and many wounds healed after relatively short time periods. Similarly, perceived pain levels decreased significantly, and the wounds showed noticeably less slough/necrosis. In general, our findings show honey to be an effective and feasible treatment option for professional wound care. In addition, our study showed a relationship between pain and slough/necrosis at the time of recruitment and during wound healing. Future comparative trials are still needed to evaluate the extent to which the positive observations made in this and other studies can definitely be attributed to the effects of honey in wound care.

Simulation of Electrowetting-Induced Droplet Detachment: A Study of Droplet Oscillations on Solid Surfaces.

The electrowetting-induced detachment of droplets from solid surfaces is important for numerous applications in the fields of heat transfer and fluid mechanics. The forced oscillations of droplets on solid surfaces and their ability to detach are studied. In this study, the process is efficiently simulated by implementing a powerful methodology developed by our team. Our results agree with experiments showing that optimal detachment, in terms of actuation energy, is achieved when the application of voltage is synchronized with the spreading time of the droplet. Under these conditions, the droplet oscillates with a period close to that of a mirrored Rayleigh droplet. The relationship between the droplet's oscillation period and its physical properties is examined. During voltage-droplet synchronization, the droplet's ability to detach depends mostly on its contact angle, its viscosity, and the applied voltage. An energy analysis is also conducted, revealing how energy is supplied to the droplet by electrowetting-induced detachment.

Inference to the best action and its basis in clinical expertise.

Can contemporary cognitive science explain clinical expertise? We argue that the answer could be "no." In support of this, we provide an analysis of two of the most essential expressions of clinical expertise in nursing and medicine, the ability to run a code blue and the ability to diagnose congestive heart failure. We show how it makes sense to treat both as examples of what we call inference to the best action, and we then argue that two of the standard explanatory paradigms of cognitive science - the Humean and Bayesian paradigms - are unable to provide a plausible analysis of inference to the best action.

Recursive genome engineering decodes the evolutionary origin of an essential thymidylate kinase activity in Pseudomonas putida KT2440.

IMPORTANCE: Investigating fundamental aspects of metabolism is vital for advancing our understanding of the diverse biochemical capabilities and biotechnological applications of bacteria. The origin of the essential thymidylate kinase function in the model bacterium Pseudomonas putida KT2440, seemingly interrupted due to the presence of a large genomic island that disrupts the cognate gene, eluded a satisfactory explanation thus far. This is a first-case example of an essential metabolic function, likely acquired by horizontal gene transfer, which "landed" in a locus encoding the same activity. As such, foreign DNA encoding an essential dNMPK could immediately adjust to the recipient host-instead of long-term accommodation and adaptation. Understanding how these functions evolve is a major biological question, and the work presented here is a decisive step toward this direction. Furthermore, identifying essential and accessory genes facilitates removing those deemed irrelevant in industrial settings-yielding genome-reduced cell factories with enhanced properties and genetic stability.