Complete biosynthesis of QS-21 in engineered yeast.

QS-21 is a potent vaccine adjuvant and remains the only saponin-based adjuvant that has been clinically approved for use in humans1,2. However, owing to the complex structure of QS-21, its availability is limited. Today, the supply depends on laborious extraction from the Chilean soapbark tree or on low-yielding total chemical synthesis3,4. Here we demonstrate the complete biosynthesis of QS-21 and its precursors, as well as structural derivatives, in engineered yeast strains. The successful biosynthesis in yeast requires fine-tuning of the host's native pathway fluxes, as well as the functional and balanced expression of 38 heterologous enzymes. The required biosynthetic pathway spans seven enzyme families-a terpene synthase, P450s, nucleotide sugar synthases, glycosyltransferases, a coenzyme A ligase, acyl transferases and polyketide synthases-from six organisms, and mimics in yeast the subcellular compartmentalization of plants from the endoplasmic reticulum membrane to the cytosol. Finally, by taking advantage of the promiscuity of certain pathway enzymes, we produced structural analogues of QS-21 using this biosynthetic platform. This microbial production scheme will allow for the future establishment of a structure-activity relationship, and will thus enable the rational design of potent vaccine adjuvants.

Neural functional theory for inhomogeneous fluids: Fundamentals and applications.

We present a hybrid scheme based on classical density functional theory and machine learning for determining the equilibrium structure and thermodynamics of inhomogeneous fluids. The exact functional map from the density profile to the one-body direct correlation function is represented locally by a deep neural network. We substantiate the general framework for the hard sphere fluid and use grand canonical Monte Carlo simulation data of systems in randomized external environments during training and as reference. Functional calculus is implemented on the basis of the neural network to access higher-order correlation functions via automatic differentiation and the free energy via functional line integration. Thermal Noether sum rules are validated explicitly. We demonstrate the use of the neural functional in the self-consistent calculation of density profiles. The results outperform those from state-of-the-art fundamental measure density functional theory. The low cost of solving an associated Euler-Lagrange equation allows to bridge the gap from the system size of the original training data to macroscopic predictions upon maintaining near-simulation microscopic precision. These results establish the machine learning of functionals as an effective tool in the multiscale description of soft matter.

Anaerobic oxidation of ethane by archaea from a marine hydrocarbon seep.

Ethane is the second most abundant component of natural gas in addition to methane, and-similar to methane-is chemically unreactive. The biological consumption of ethane under anoxic conditions was suggested by geochemical profiles at marine hydrocarbon seeps1-3, and through ethane-dependent sulfate reduction in slurries4-7. Nevertheless, the microorganisms and reactions that catalyse this process have to date remained unknown8. Here we describe ethane-oxidizing archaea that were obtained by specific enrichment over ten years, and analyse these archaea using phylogeny-based fluorescence analyses, proteogenomics and metabolite studies. The co-culture, which oxidized ethane completely while reducing sulfate to sulfide, was dominated by an archaeon that we name 'Candidatus Argoarchaeum ethanivorans'; other members were sulfate-reducing Deltaproteobacteria. The genome of Ca. Argoarchaeum contains all of the genes that are necessary for a functional methyl-coenzyme M reductase, and all subunits were detected in protein extracts. Accordingly, ethyl-coenzyme M (ethyl-CoM) was identified as an intermediate by liquid chromatography-tandem mass spectrometry. This indicated that Ca. Argoarchaeum initiates ethane oxidation by ethyl-CoM formation, analogous to the recently described butane activation by 'Candidatus Syntrophoarchaeum'9. Proteogenomics further suggests that oxidation of intermediary acetyl-CoA to CO2 occurs through the oxidative Wood-Ljungdahl pathway. The identification of an archaeon that uses ethane (C2H6) fills a gap in our knowledge of microorganisms that specifically oxidize members of the homologous alkane series (CnH2n+2) without oxygen. Detection of phylogenetic and functional gene markers related to those of Ca. Argoarchaeum at deep-sea gas seeps10-12 suggests that archaea that are able to oxidize ethane through ethyl-CoM are widespread members of the local communities fostered by venting gaseous alkanes around these seeps.

Expanding Extender Substrate Selection for Unnatural Polyketide Biosynthesis by Acyltransferase Domain Exchange within a Modular Polyketide Synthase.

Modular polyketide synthases (PKSs) are polymerases that employ α-carboxyacyl-CoAs as extender substrates. This enzyme family contains several catalytic modules, where each module is responsible for a single round of polyketide chain extension. Although PKS modules typically use malonyl-CoA or methylmalonyl-CoA for chain elongation, many other malonyl-CoA analogues are used to diversify polyketide structures in nature. Previously, we developed a method to alter an extension substrate of a given module by exchanging an acyltransferase (AT) domain while maintaining protein folding. Here, we report in vitro polyketide biosynthesis by 13 PKSs (the wild-type PKS and 12 AT-exchanged PKSs with unusual ATs) and 14 extender substrates. Our ∼200 in vitro reactions resulted in 13 structurally different polyketides, including several polyketides that have not been reported. In some cases, AT-exchanged PKSs produced target polyketides by >100-fold compared to the wild-type PKS. These data also indicate that most unusual AT domains do not incorporate malonyl-CoA and methylmalonyl-CoA but incorporate various rare extender substrates that are equal to in size or slightly larger than natural substrates. We developed a computational workflow to predict the approximate AT substrate range based on active site volumes to support the selection of ATs. These results greatly enhance our understanding of rare AT domains and demonstrate the benefit of using the proposed PKS engineering strategy to produce novel chemicals in vitro.

Noether-Constrained Correlations in Equilibrium Liquids.

Liquid structure carries deep imprints of an inherent thermal invariance against a spatial transformation of the underlying classical many-body Hamiltonian. At first order in the transformation field Noether's theorem yields the local force balance. Three distinct two-body correlation functions emerge at second order, namely the standard two-body density, the localized force-force correlation function, and the localized force gradient. An exact Noether sum rule interrelates these correlators. Simulations of Lennard-Jones, Yukawa, soft-sphere dipolar, Stockmayer, Gay-Berne and Weeks-Chandler-Andersen liquids, of monatomic water and of a colloidal gel former demonstrate the fundamental role in the characterization of spatial structure.

The Impact of the COVID Pandemic on Adrenal Surgery at an Academic Endocrine Surgery Unit.

COVID-19 has severely affected the delivery of surgical care worldwide. The aim of the present study was to evaluate its impact on adrenal surgery at our academic endocrine center. All primary adrenal surgeries performed at the University Hospital of Cologne, Germany between 01.01.2019 and 31.07.2022 were included. This time frame was divided into pre-Covid (before 02/20), acute Covid (until 05/21), and post acute period (after 05/2021). Demographics, clinic-pathologic characteristics and treatment of these patients were analyzed. One hundred adrenalectomies were included: 22 before, 30 during, and 48 after the acute phase. The percentage of Conn adenomas and pheochromocytomas decreased during the acute phase (from 45.4 to 26.6% and from 18 to 10%, respectively) in favor of Cushing adenomas and suspicious tumors (from 4.5 to 20% and from 31.8 to 36.6%). About 90.9% of tumors resected for suspicion of malignancy were confirmed malignant by final histopathology, as opposed to 71.4% and 52.6% before and after the acute phase. The operative technique was similar during the three phases (63% retroperitoneoscopic, 34% laparoscopic and 2% open resections), with a significantly shorter operative time for retroperitoneoscopy (p=0.04). ICU monitoring demand increased during the acute phase (from 13.6% to 43.3%), according to the increase in Cushing adenomas and malignant tumors. During the acute phase of COVID-19 pandemic adrenal surgery for Cushing and malignant tumors increased, while a delay in pheochromocytoma surgery to the post acute phase was observed. The suspicion of malignancy formulated by the endocrine tumor board was accurate in 90.9% of cases.

Effect of sample height and particle elongation in the sedimentation of colloidal rods.

We study theoretically the effect of a gravitational field on the equilibrium behaviour of a colloidal suspension of rods with different length-to-width aspect ratios. The bulk phases of the system are described with analytical equations of state. The gravitational field is then incorporated via sedimentation path theory, which assumes a local equilibrium condition at each altitude of the sample. The bulk phenomenology is significantly enriched by the presence of the gravitational field. In a suspension of elongated rods with five stable phases in bulk, the gravitational field stabilizes up to fifteen different stacking sequences. The sample height has a non-trivial effect on the stable stacking sequence. New layers of distinct bulk phases appear either at the top, at the bottom, or simultaneously at the top and the bottom when increasing the sample height at constant colloidal concentration. We also study sedimentation in a mass-polydisperse suspension in which all rods have the same shape but different buoyant masses.

Inhomogeneous steady shear dynamics of a three-body colloidal gel former.

We investigate the stationary flow of a colloidal gel under an inhomogeneous external shear force using adaptive Brownian dynamics simulations. The interparticle forces are derived from the Stillinger-Weber potential, where the three-body term is tuned to enable network formation and gelation in equilibrium. When subjected to the shear force field, the system develops remarkable modulations in the one-body density profile. Depending on the shear magnitude, particles accumulate either in quiescent regions or in the vicinity of maximum net flow, and we deduce this strong non-equilibrium response to be characteristic of the gel state. Studying the components of the internal force parallel and perpendicular to the flow direction reveals that the emerging flow and structure of the stationary state are driven by significant viscous and structural superadiabatic forces. Thereby, the magnitude and nature of the observed non-equilibrium phenomena differ from the corresponding behavior of simple fluids. We demonstrate that a simple power functional theory reproduces accurately the viscous force profile, giving a rationale of the complex dynamical behavior of the system.

Iron corrosion by methanogenic archaea characterized by stable isotope effects and crust mineralogy.

Carbon and hydrogen stable isotope effects associated with methane formation by the corrosive archaeon Methanobacterium strain IM1 were determined during growth with hydrogen and iron. Isotope analyses were complemented by structural, elemental and molecular composition analyses of corrosion crusts. During growth with H2 , strain IM1 formed methane with average δ13 C of -43.5‰ and δ2 H of -370‰. Corrosive growth led to methane more depleted in 13 C, with average δ13 C ranging from -56‰ to -64‰ during the early and the late growth phase respectively. The corresponding δ2 H were less impacted by the growth phase, with average values ranging from -316 to -329‰. The stable isotope fractionation factors, α 13 C CO 2 / CH 4 , were 1.026 and 1.042 for hydrogenotrophic and corrosive growth respectively. Corrosion crusts formed by strain IM1 have a domed structure, appeared electrically conductive and were composed of siderite, calcite and iron sulfide, the latter formed by precipitation of sulfide (from culture medium) with ferrous iron generated during corrosion. Strain IM1 cells were found attached to crust surfaces and encrusted deep inside crust domes. Our results may assist to diagnose methanogens-induced corrosion in the field and suggest that intrusion of sulfide in anoxic settings may stimulate corrosion by methanogenic archaea via formation of semiconductive crusts.

Nitrogen Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing.

Pseudomonas putida KT2440 has long been studied for its diverse and robust metabolisms, yet many genes and proteins imparting these growth capacities remain uncharacterized. Using pooled mutant fitness assays, we identified genes and proteins involved in the assimilation of 52 different nitrogen containing compounds. To assay amino acid biosynthesis, 19 amino acid drop-out conditions were also tested. From these 71 conditions, significant fitness phenotypes were elicited in 672 different genes including 100 transcriptional regulators and 112 transport-related proteins. We divide these conditions into 6 classes, and propose assimilatory pathways for the compounds based on this wealth of genetic data. To complement these data, we characterize the substrate range of three promiscuous aminotransferases relevant to metabolic engineering efforts in vitro. Furthermore, we examine the specificity of five transcriptional regulators, explaining some fitness data results and exploring their potential to be developed into useful synthetic biology tools. In addition, we use manifold learning to create an interactive visualization tool for interpreting our BarSeq data, which will improve the accessibility and utility of this work to other researchers. IMPORTANCE Understanding the genetic basis of P. putida's diverse metabolism is imperative for us to reach its full potential as a host for metabolic engineering. Many target molecules of the bioeconomy and their precursors contain nitrogen. This study provides functional evidence linking hundreds of genes to their roles in the metabolism of nitrogenous compounds, and provides an interactive tool for visualizing these data. We further characterize several aminotransferases, lactamases, and regulators, which are of particular interest for metabolic engineering.

Shear and Bulk Acceleration Viscosities in Simple Fluids.

Inhomogeneities in the velocity field of a moving fluid are dampened by the inherent viscous behavior of the system. Both bulk and shear effects, related to the divergence and the curl of the velocity field, are relevant. On molecular time scales, beyond the Navier-Stokes description, memory plays an important role. Using molecular and overdamped Brownian dynamics many-body simulations, we demonstrate that analogous viscous effects act on the acceleration field. This acceleration viscous behavior is associated with the divergence and the curl of the acceleration field, and it can be quantitatively described using simple exponentially decaying memory kernels. The simultaneous use of velocity and acceleration fields enables the description of fast dynamics on molecular scales.

Adrenal Surgery in the Era of Multidisciplinary Endocrine Tumor Boards.

Work up of adrenal masses includes assessment of endocrine activity and malignancy risk. There is no indication for surgical removal of nonfunctional adrenal adenomas, according to the guidelines. In the present study, we aimed at evaluating the impact of a university endocrine tumor board on the quality of the indications for adrenal surgery at our institution. One hundred consecutive patients receiving primary adrenal surgery at the University Hospital of Cologne, Germany were included. Their demographics, clinic-pathologic characteristics, treatment and outcome were analyzed. In 55 (55%) cases, indication for surgery consisted in functional benign tumors, including Conn, Cushing adenomas and pheochromocytomas. Forty (40%) tumors were referred to surgery for malignancy suspicion and 5 (5%) myelolipomas were removed due to their size. Eighty-nine percent of surgeries were performed as minimally invasive procedures. Overall morbidity included two (2%) self-limiting pancreatic fistulas after left laparoscopic adrenalectomy for pheochromocytoma. All functional tumors were confirmed benign by final histology. Only 33 (82.5%) of 40 suspicious cases turned out to be malignant. Consequently, nonfunctional benign adenomas were "unnecessarily" removed in only 7 (7%) patients, with 6 (85.7%) of them having a history of extra-adrenal cancer and all of them fulfilling criteria for surgery, according to the international guidelines. In conclusion, the endocrine tumor board provided an excellent adherence to the guidelines with most surgeries being performed either for functional or malignant tumors. In nonfunctional tumors with history of extra adrenal cancer, CT guided biopsy might be considered for obviating surgery.

Sedimentation path theory for mass-polydisperse colloidal systems.

Both polydispersity and the presence of a gravitational field are inherent to essentially any colloidal experiment. While several theoretical works have focused on the effect of polydispersity on the bulk phase behavior of a colloidal system, little is known about the effect of a gravitational field on a polydisperse colloidal suspension. We extend here the sedimentation path theory to study sedimentation-diffusion-equilibrium of a mass-polydisperse colloidal system: the particles possess different buoyant masses but they are otherwise identical. The model helps to understand the interplay between gravity and polydispersity on sedimentation experiments. Since the theory can be applied to any parent distribution of buoyant masses, it can also be used to study the sedimentation of monodisperse colloidal systems. We find that mass-polydispersity has a strong influence in colloidal systems near density matching for which the bare density of the colloidal particles equals the solvent density. To illustrate the theory, we study crystallization in sedimentation-diffusion-equilibrium of a suspension of mass-polydisperse hard spheres.

Subacute thyroiditis after SARS-Cov2 vaccination: A review of the cases being described and personal experience.

Objective. The present study evaluates the occurrence of subacute thyroiditis in temporal connection with SARS-Cov2 vaccinations described in the literature last year and confirmed by our clinical routine. Methods. Systematic literature search in Medline for studies reporting diagnosis of subacute thyroiditis in temporal connection with vaccinations against Covid 19. Results. The literature search yielded 24 relevant references out of which 22 were "case reports" and two "Letters to the Editor" and encompassed 37 patient cases, in total. They had received a SARS-Cov2 vaccination shortly before the diagnosis (median interval to vaccination six days). In none of these cases, infection of the upper respiratory tract had previously been identified as a classic trigger of the disease. Newly occurring hyperthyroidism and increased laboratory signs of inflammation were described in 78% and 74% of cases, respectively. Atypical clinical pictures (asymptomatic, euthyroid, no inflammation marks) have been observed in both the literature and our patients suspected of thyroid cancer referred to surgery. Conclusions. In times of pandemics and the resulting vaccination, new rapidly occurring sonographic changes in the thyroid gland should be revaluated after 2-3 weeks, or recommended to undergo a fine-needle biopsy, in order to avoid unnecessary surgical interventions.

Feasibility and Oncologic Outcome of Salvage Surgery in Isolated Seminal Vesicle Remnants after Radical Prostatectomy.

BACKGROUND: To demonstrate the feasibility of resecting isolated locally relapsing seminal vesicle remnants after primary radical prostatectomy and radiotherapy. Early oncologic outcomes and prognostic risk factors for relapse are demonstrated. OBJECTIVES AND METHODS: A total of 32 patients underwent open resection of locoregional prostate cancer recurrence in seminal vesicles, as documented on either MRI, 11C-choline, or 68Ga-PSMA PET/CT scans. Age, PSA-DT, PSA, and time to recurrence after primary treatment resection status were used in a uni- and multivariate Cox regression analysis for biochemical relapse after surgery. RESULTS: Median patient age at time of salvage surgery was 70 (57-77) years. Median PSA and PSA-DT was 2.79 (0.4-61.54) ng/mL and 5.4 (1.6-20.1) months, respectively. Median surgical time and hospital stay was 132 (75-313) min and 5.5 (4-13) days, respectively. After a mean follow-up of 29 (2-92) months, 3 patients died at 8, 14, and 40 months after salvage surgery, and 6 (18.75%) patients remain without biochemical relapse and further treatment. Median progression-free survival was 12 (1-81) months. In the univariable Cox regression analysis, age at time of surgery, preoperative PSA, and the time from primary treatment to salvage surgery were identified as significant parameters for biochemical relapse. Only the interval from primary to salvage surgery was significant in the multivariate analysis with a hazard ratio of 1.008 (95% CI: 1.001-1.015, p = 0.018). In the entire cohort, 4 adjunctive surgeries (3 ureteroneocystostomies and 1 nephrectomy) were needed due to local progressive disease. CONCLUSION: Seminal vesicle resection is feasible with no significant intra- or postoperative complications. Almost all patients progressed to biochemical or systemic relapse. Salvage surgery must be seen as a preventive for local symptoms, in our experience most often postrenal ipsilateral obstruction.

Design, Synthesis and Biological Characterization of Histone Deacetylase 8 (HDAC8) Proteolysis Targeting Chimeras (PROTACs) with Anti-Neuroblastoma Activity.

In addition to involvement in epigenetic gene regulation, histone deacetylases (HDACs) regulate multiple cellular processes through mediating the activity of non-histone protein substrates. The knockdown of HDAC8 isozyme is associated with the inhibition of cell proliferation and apoptosis enhancement in several cancer cell lines. As shown in several studies, HDAC8 can be considered a potential target in the treatment of cancer forms such as childhood neuroblastoma. The present work describes the development of proteolysis targeting chimeras (PROTACs) of HDAC8 based on substituted benzhydroxamic acids previously reported as potent and selective HDAC8 inhibitors. Within this study, we investigated the HDAC8-degrading profiles of the synthesized PROTACs and their effect on the proliferation of neuroblastoma cells. The combination of in vitro screening and cellular testing demonstrated selective HDAC8 PROTACs that show anti-neuroblastoma activity in cells.

Hochaufgelöste Mikrobenporträts mit hoher Tiefenschärfe.

The past decade has seen the advent of a new imaging technique in the life sciences that is ideal for microbiological applications: the helium ion microscope (HIM). Its lateral resolution is better than one nanometre, it has a large depth-of-field and can image non-conductive specimens which renders the tool ideal for studying microbiological objects such as microbes attached to surfaces, microbial biofilms and viruses. Here we compare HIM with electron microscopy techniques and highlight selected examples that demonstrate the new possibilities for microbiology opened up by this technique.

Methods to study the structure of misfolded protein states in systemic amyloidosis.

Systemic amyloidosis is defined as a protein misfolding disease in which the amyloid is not necessarily deposited within the same organ that produces the fibril precursor protein. There are different types of systemic amyloidosis, depending on the protein constructing the fibrils. This review will focus on recent advances made in the understanding of the structural basis of three major forms of systemic amyloidosis: systemic AA, AL and ATTR amyloidosis. The three diseases arise from the misfolding of serum amyloid A protein, immunoglobulin light chains or transthyretin. The presented advances in understanding were enabled by recent progress in the methodology available to study amyloid structures and protein misfolding, in particular concerning cryo-electron microscopy (cryo-EM) and nuclear magnetic resonance (NMR) spectroscopy. An important observation made with these techniques is that the structures of previously described in vitro formed amyloid fibrils did not correlate with the structures of amyloid fibrils extracted from diseased tissue, and that in vitro fibrils were typically more protease sensitive. It is thus possible that ex vivo fibrils were selected in vivo by their proteolytic stability.

Universality in Driven and Equilibrium Hard Sphere Liquid Dynamics.

We demonstrate that the time evolution of the van Hove dynamical pair correlation function is governed by adiabatic forces that arise from the free energy and by superadiabatic forces that are induced by the flow of the van Hove function. The superadiabatic forces consist of drag, viscous, and structural contributions, as occur in active Brownian particles, in liquids under shear and in lane forming mixtures. For hard sphere liquids, we present a power functional theory that predicts these universal force fields in quantitative agreement with our Brownian dynamics simulation results.

Toward individualized prediction of seizure recurrence: Hippocampal neuroimaging features in a cohort of patients from a first seizure clinic.

PURPOSE: We performed an exploratory analysis of electroencephalography (EEG) and neuroimaging data from a cohort of 51 patients with first seizure (FS) and new-onset epilepsy (NOE) to identify variables, or combinations of variables, that might discriminate between clinical trajectories over a one-year period and yield potential biomarkers of epileptogenesis. METHODS: Patients underwent EEG, hippocampal and whole brain structural magnetic resonance imaging (MRI), diffusion tensor imaging (DTI), and magnetic resonance spectroscopy (MRS) within six weeks of the index seizure, and repeat neuroimaging one year later. We classified patients with FS as having had a single seizure (FS-SS) or having converted to epilepsy (FS-CON) after one year and performed logistic regression to identify combinations of variables that might discriminate between FS-SS and FS-CON, and between FS-SS and the combined group FS-CON + NOE. We performed paired t-tests to assess changes in quantitative variables over time. RESULTS: Several combinations of variables derived from hippocampal structural MRI, DTI, and MRS provided excellent discrimination between FS-SS and FS-CON in our sample, with areas under the receiver operating curve (AUROC) ranging from 0.924 to 1. They also provided excellent discrimination between FS-SS and the combined group FS-CON + NOE in our sample, with AUROC ranging from 0.902 to 1. After one year, hippocampal fractional anisotropy (FA) increased bilaterally, hippocampal radial diffusivity (RD) decreased on the side with the larger initial measurement, and whole brain axial diffusivity (AD) increased in patients with FS-SS; hippocampal volume decreased on the side with the larger initial measurement, hippocampal FA increased bilaterally, hippocampal RD decreased bilaterally and whole brain AD, FA and mean diffusivity increased in the combined group FS-CON + NOE (corrected threshold for significance, q = 0.017). CONCLUSION: We propose a prospective, multicenter study to develop and test models for the prediction of seizure recurrence in patients after a first seizure, based on hippocampal neuroimaging. Further longitudinal neuroimaging studies in patients with a first seizure and new-onset epilepsy may provide clues to the microstructural changes occurring at the earliest stages of epilepsy and yield biomarkers of epileptogenesis.