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.

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.

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.

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.

Core and auxiliary functions of one-carbon metabolism in Pseudomonas putida exposed by a systems-level analysis of transcriptional and physiological responses.

The soil bacterium Pseudomonas putida is a robust biomanufacturing host that assimilates a broad range of substrates while efficiently coping with adverse environmental conditions. P. putida is equipped with functions related to one-carbon (C1) compounds (e.g. methanol, formaldehyde, and formate) oxidation-yet pathways to assimilate these carbon sources are largely absent. In this work, we adopted a systems-level approach to study the genetic and molecular basis of C1 metabolism in P. putida. RNA sequencing identified two oxidoreductases, encoded by PP_0256 and PP_4596, transcriptionally active in the presence of formate. Quantitative physiology of deletion mutants revealed growth defects at high formate concentrations, pointing to an important role of these oxidoreductases in C1 tolerance. Moreover, we describe a concerted detoxification process for methanol and formaldehyde, the C1 intermediates upstream formate. Alcohol oxidation to highly-reactive formaldehyde by PedEH and other broad-substrate-range dehydrogenases underpinned the (apparent) suboptimal methanol tolerance of P. putida. Formaldehyde was mostly processed by a glutathione-dependent mechanism encoded in the frmAC operon, and thiol-independent FdhAB and AldB-II overtook detoxification at high aldehyde concentrations. Deletion strains were constructed and characterized towards unveiling these biochemical mechanisms, underscoring the worth of P. putida for emergent biotechnological applications-e.g. engineering synthetic formatotrophy and methylotrophy. IMPORTANCE C1 substrates continue to attract interest in biotechnology, as their use is both cost-effective and ultimately expected to mitigate the impact of greenhouse gas emissions. However, our current understanding of bacterial C1 metabolism remains relatively limited in species that cannot grow on (i.e., assimilate) these substrates. Pseudomonas putida, a model Gram-negative environmental bacterium, constitutes a prime example of this sort. The biochemical pathways active in response to methanol, formaldehyde, and formate have been largely overlooked-although the ability of P. putida to process C1 molecules has been previously alluded to in the literature. By using a systems-level strategy, this study bridges such knowledge gap through the identification and characterization of mechanisms underlying methanol, formaldehyde, and formate detoxification-including hitherto unknown enzymes that act on these substrates. The results reported herein both expand our understanding of microbial metabolism and lay a solid foundation for engineering efforts toward valorizing C1 feedstocks.

Sex-dependent deficits in associative learning across multiple LPS doses.

Activation of the immune system by administration of the bacterial endotoxin lipopolysaccharide (LPS) impairs cognitive and neural plasticity processes. For instance, acute LPS exposure has been reported to impair memory consolidation, spatial learning and memory, and associative learning. However, the inclusion of both males and females in basic research is limited. Whether LPS-induced cognitive deficits are comparable in males and females is currently unclear. Therefore, the present study evaluated sex differences in associative learning following administration of LPS at a dose (i.e., 0.25 mg/kg) that impairs learning in males and higher LPS doses (i.e., 0.325 - 1 mg/kg) across multiple experiments. Adult male and female C57BL/6J mice were trained in a two-way active avoidance conditioning task following their respective treatments. Results showed that LPS had sex-dependent effects on associative learning. The 0.25 mg/kg LPS dose impaired learning in males, consistent with prior work. However, LPS, at any of the doses employed across three experiments, did not disrupt associative learning in females. Female mice were resistant to learning deficits despite showing heightened levels of select proinflammatory cytokines in response to LPS. Collectively, these findings demonstrate that the learning impairments resulting from acute LPS exposure are sex-dependent.

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.

Successful Administration of Preoperative Botox for Giant Omphalocele Repair With Ultrasound Guidance.

We present a case of a four-year-old male with a history of giant omphalocele who underwent ultrasound-guided Botox injection to bilateral anterior abdominal wall musculature in preparation for definitive repair. Botox administration was successfully combined with preoperative subfascial tissue expanders to achieve definitive midline closure of the anterior abdominal wall defect. Our experience suggests that Botox can be safely used as part of the treatment plan for giant omphalocele repair.

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

Although viral hepatocellular carcinoma (HCC) is declining, non-viral HCC, which often is the end-stage of non-alcoholic or alcoholic steatohepatitis (NASH, ASH), is on an upward trajectory. Immune checkpoint inhibitors (ICI) that block the T cell inhibitory receptor PD-1 were approved for treatment of all HCC types. However, only a small portion 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 anti-fibrotic 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 inhibition of TGF-ß receptor signaling, collagen deposition and depletion of immunosuppressive fibroblasts. Significance: Immune checkpoint inhibitors are used in HCC treatment but overall response rates for single agent PD-1/PD-L1 blockers have remained stubbornly low. Using a mouse model of NASH-driven HCC, we show that co-treatment with the safe and inexpensive angiotensin II receptor inhibitor losartan substantially enhanced anti-PD-1 triggered HCC regression. Although losartan did not influence the reinvigoration of exhausted CD8 + T cells it considerably enhanced their intratumoral invasion, which we postulated to be compromised by peritumoral fibrosis. Indeed, the beneficial effect of losartan correlated with inhibition of TGF-ß signaling and collagen deposition, and depletion of immunosuppressive fibroblasts. Losartan should be evaluated for its adjuvant activity in HCC patients undergoing PD-1/PD-L1 blocking therapy.

Infections by entomopathogenic fungi in common green iguanas (Iguana iguana) in captivity in Brazil.

Entomopathogenic fungi, widely available biological agents used to control agricultural pests, are sporadically reported to cause focal or disseminated infection in reptiles and mammals, including humans. This study summarizes the clinical presentation, histopathological and molecular findings by panfungal polymerase chain reaction and sequencing of four cases of hypocrealean fungal infections in captive common green iguanas (Iguana, iguana). One case of granulomatous pneumonia, hepatitis and serositis was related to Metarhizium flavoviride complex infection. Two disseminated fungal infection cases, with scarce inflammatory cell infiltration, were caused by Beauveria bassiana while there was one case of multifocal granulomatous and necrotizing pneumonia by Purpureocillium spp. To the best of our knowledge, this is the first report of fatal mycosis infection due to entomopathogenic fungi in captive common green iguanas.

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.

Additive Manufacturing of Degradable Materials via Ring-Opening Metathesis Polymerization (ROMP).

Thermoset materials comprise a significant proportion of high-performance plastics due to their shape permanence and excellent thermal and mechanical properties. However, these properties come at the expense of degradability. Here, we show for the first time that the industrial thermoset polydicyclopentadiene (PDCPD) can be additively manufactured (AM) with degradable 2,3-dihydrofuran (DHF) linkages using a photochemical approach. Treatment of the manufactured objects with acid results in rapid degradation to soluble byproducts. This work highlights the potential of ring-opening metathesis polymerization (ROMP) chemistry to create degradable materials amenable to advanced manufacturing processes.

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.

Standardization of regulatory nodes for engineering heterologous gene expression: a feasibility study.

The potential of LacI/Ptrc , XylS/Pm , AlkS/PalkB , CprK/PDB3 and ChnR/PchnB regulatory nodes, recruited from both Gram-negative and Gram-positive bacteria, as the source of parts for formatting expression cargoes following the Standard European Vector Architecture (SEVA) has been examined. The five expression devices, which cover most known regulatory configurations in bacteria were assembled within exactly the same plasmid backbone and bearing the different functional segments arrayed in an invariable DNA scaffold. Their performance was then analysed in an Escherichia coli strain of reference through the readout of a fluorescence reporter gene that contained strictly identical translation signal elements. This approach allowed us to describe and compare the cognate expression systems with quantitative detail. The constructs under scrutiny diverged considerably in their capacity, expression noise, inducibility and ON/OFF ratios. Inspection of such a variance exposed the different constraints that rule the optimal arrangement of functional DNA segments in each case. The data highlighted also the ease of standardizing inducer-responsive devices subject to transcriptional activation as compared to counterparts based on repressors. The study resulted in a defined collection of formatted expression cargoes lacking any cross talk while offering a panoply of choices to potential users and help interoperability of the specific constructs.

Continuous Additive Manufacturing using Olefin Metathesis.

The development of chemistry is reported to implement selective dual-wavelength olefin metathesis polymerization for continuous additive manufacturing (AM). A resin formulation based on dicyclopentadiene is produced using a latent olefin metathesis catalyst, various photosensitizers (PSs) and photobase generators (PBGs) to achieve efficient initiation at one wavelength (e.g., blue light) and fast catalyst decomposition and polymerization deactivation at a second (e.g., UV-light). This process enables 2D stereolithographic (SLA) printing, either using photomasks or patterned, collimated light. Importantly, the same process is readily adapted for 3D continuous AM, with printing rates of 36 mm h-1 for patterned light and up to 180 mm h-1 using un-patterned, high intensity light.

Synthetic metabolism for biohalogenation.

The pressing need for novel bioproduction approaches faces a limitation in the number and type of molecules accessed through synthetic biology. Halogenation is widely used for tuning physicochemical properties of molecules and polymers, but traditional halogenation chemistry often lacks specificity and generates harmful by-products. Here, we pose that deploying synthetic metabolism tailored for biohalogenation represents an unique opportunity towards economically attractive and environmentally friendly organohalide production. On this background, we discuss growth-coupled selection of functional metabolic modules that harness the rich repertoire of biosynthetic and biodegradation capabilities of environmental bacteria for in vivo biohalogenation. By rationally combining these approaches, the chemical landscape of living cells can accommodate bioproduction of added-value organohalides which, as of today, are obtained by traditional chemistry.

The effect of squash domestication on a belowground tritrophic interaction.

The domestication of plants has commonly resulted in the loss of plant defense metabolites, with important consequences for the plants' interactions with herbivores and their natural enemies. Squash domestication started 10'000 years ago and has led to the loss of cucurbitacins, which are highly toxic triterpenes. The banded cucumber beetle (Diabrotica balteata), a generalist herbivore, is adapted to feed on plants from the Cucurbitaceae and is known to sequester cucurbitacins, supposedly for its own defense. However, the evidence for this is inconclusive. In this study we tested the impact of squash domestication on the chemical protection of D. balteata larvae against a predatory rove beetle (Dalotia coriaria). We found that cucurbitacins do not defend the larvae against this common soil dwelling predator. In fact, D. balteata larvae were less attacked when they fed on cucurbitacin-free roots of domesticated varieties compared to high-cucurbitacin roots of wild plants. This study appears to be the first to look at the consequences of plant domestication on belowground tritrophic interactions. Our results challenge the generalized assumption that sequestered cucurbitacins protect this herbivore against natural enemies, and instead reveals an opposite effect that may be due to a tradeoff between coping with cucurbitacins and avoiding predation.

Cooling Anesthesia for Intravitreal Injection: Results of the Prospective Open-Label, Dose-Ranging COOL-1 Trial.

PURPOSE: To evaluate the safety and efficacy of a novel medical device to provide cooling anesthesia to the eye as local anesthesia for intravitreal injections. STUDY DESIGN: First in human, open-label study of 43 subjects assessed at three different doses: -10°C for 20 seconds (group 1), -15°C for 15 seconds (group 2), and -15°C for 20 seconds (group 3). Main outcome measures were safety and pain of injection using a numeric rating scale (NRS). RESULTS: Cooling anesthesia did not result in any serious ocular adverse events. One grade 1 adverse event was a vasovagal response during cooling administration which resolved immediately after cooling. Mean NRS scores at the time of injection for each group ranged from 2.5 to 4.3 There was a statistically significant difference between pain scores of the 3 groups at injection in aggregate but not in pairwise comparisons (P value = 0.047). There was a statistically significant decrease in pain from injection to 5 minutes post injection in all groups (P value = 0.00008, 0.003, 0.0005 for groups 1, 2, 3, respectively) as well as from 5 minutes to 24-48 hours (P value = 0.00001, 0.018, and 0.0545 for groups 1, 2, 3, respectively). CONCLUSION: The rapid cooling anesthesia device was well tolerated for achieving local anesthesia among patients receiving intravitreal injections with no serious ocular adverse events.

Pathology in Practice.

In collaboration with the American College of Veterinary Pathologists.