Study of Secondary Metabolite Gene Expression in Marine Microbial Co-Cultures Using Quantitative Real-Time PCR

Interactions among microbial organisms often cannot be observed directly, but they can be inferred genetically using new molecular techniques. The analysis of secondary metabolite gene expression produced by co-cultured marine microbial species allows us to see how these organisms interact with one another when kept in the same environment. Co-cultures of three different strains of marine bacteria, P. aeruginosa PAO1, Roseobacter denitrificans OCH114, and Salinispora arenicola CNS-205 were grown in a laboratory setting, and using the Real-Time qPCR method gene expression levels of two different secondary metabolite producing genes from each organism was accessed across three time points. P. aeruginosa PAO1’s secondary metabolite genes RdhA and PhzH stayed repressed through all co-cultures and time points in this study, and Roseobacter denitrificans OCH-114’s secondary metabolite genes metallo-beta-lactamase and DMSP lyase were up-regulated after the 30 minute time point in the P. aeruginosa-R. denitrificans co-culture and at the 0 minute time point in the R. denitrificans-S. arenicola co-culture

Co-Cultures of Pseudomonas aeruginosa and Roseobacter denitrificans Reveal Shifts in Gene Expression Levels Compared to Solo Cultures

Consistent biosynthesis of desired secondary metabolites (SMs) from pure microbial cultures is often unreliable. In a proof-of-principle study to induce SM gene expression and production, we describe mixed “co-culturing” conditions and monitoring of messages via quantitative real-time PCR (qPCR). Gene expression of model bacterial strains (Pseudomonas aeruginosa PAO1 and Roseobacter denitrificans Och114) was analyzed in pure solo and mixed cocultures to infer the effects of interspecies interactions on gene expression in vitro, Two P. aeruginosa genes (PhzH coding for portions of the phenazine antibiotic pathway leading to pyocyanin (PCN) and the RhdA gene for thiosulfate: cyanide sulfurtransferase (Rhodanese)) and two R. denitrificans genes (BetaLact for metallo-beta-lactamase and the DMSP gene for dimethylpropiothetin dethiomethylase) were assessed for differential expression. Results showed that R. denitrificans DMSP and BetaLact gene expression became elevated in a mixed culture. In contrast, P. aeruginosa co-cultures with R. denitrificans or a third species did not increase target gene expression above control levels. This paper provides insight for better control of target SM gene expression in vitro and bypass complex genetic engineering manipulations

Pathologic response rates after neoadjuvant therapy for sarcoma: A single institution study

(1) Background: Pathologic necrosis of soft tissue sarcomas (STS) has been used to determine treatment response, but its relationship to neoadjuvant treatments remains indeterminate. In this retrospective, single institution study, we hypothesized that neoadjuvant chemoradiation (NA-CRT) yields higher rates of pathologic complete response (pCR) than neoadjuvant radiation (NA-XRT) or chemotherapy (NA-CT) alone. (2) Methods: Patients with extremity STS between 2011–2020 who received neoadjuvant treatment were included. pCR was defined as percent necrosis of the surgical specimen greater than or equal to 90%. (3) Results: 79 patients were analyzed. 51.9% of the population were male with a mean age of 58.4 years. 49.4% identified as Non-Hispanic White. Twenty-six (32.9%) patients achieved pCR while 53 (67.1%) did not. NA-CT (OR 15.82, 95% CI = 2.58–96.9, p = 0.003 in univariate (UVA) and OR 24.7, 95% CI = 2.88–211.2, p = 0.003 in multivariate (MVA), respectively) and NA-XRT (OR 5.73, 95% CI = 1.51–21.8, p = 0.010 in UVA and OR 7.95, 95% CI = 1.87–33.7, p = 0.005 in MVA, respectively) was significantly associated with non-pCR when compared to NA-CRT. The analysis also demonstrated that grade 3 tumors, when using grade 2 as reference, also had significantly higher odds of achieving pCR (OR 0.23, 95% CI = 0.06–0.80, p = 0.022 in UVA and OR 0.16, 95% CI = 0.04–0.70, p = 0.015 in MVA, respectively). (4) Conclusion: NA-CRT yields superior pCR compared to other neoadjuvant regimens. This extends to higher grade tumors

Cardioembolic Stroke in Atrial Fibrillation-Rationale for Preventive Closure of the Left Atrial Appendage

Atrial fibrillation is the most common cardiac arrhythmias, and a major cause of morbidity and mortality due to cardioembolic stroke. The left atrial appendage is the major site of thrombus formation in non-valvular atrial fibrillation. Loss of atrial systole in atrial fibrillation and increased relative risk of associated stroke point strongly toward a role for stasis of blood in left atrial thrombosis, although thrombus formation is multifactorial, and much more than blood flow irregularities are implicated. Oral anticoagulation with vitamin-K-antagonists is currently the most effective prophylaxis for stroke in atrial fibrillation. Unfortunately, this treatment is often contraindicated, particularly in the elderly, in whom risk of stroke is high. Moreover, given the risk of major bleeding, there is reason to be skeptical of the net benefit when warfarin is used in those patients. This work reviews the pathophysiology of cardioembolic stroke and critically spotlights the current status of preventive anticoagulation therapy. Various techniques to exclude the left atrial appendage from circulation were discussed as a considerable alternative for stroke prophylaxis

Peripheral temperature gradient screening of high-Z impurities in optimised 'hybrid' scenario H-mode plasmas in JET-ILW

Screening of high-Z (W) impurities from the confined plasma by the temperature gradient at the plasma periphery of fusion-grade H-mode plasmas has been demonstrated in the JET-ILW (ITER-like wall) tokamak. Through careful optimisation of the hybrid-scenario, deuterium plasmas with sufficient heating power (greater than or similar to 32 MW), high enough ion temperature gradients at the H-mode pedestal top can be achieved for the collisional, neo-classical convection of the W impurities to be directed outwards, expelling them from the confined plasma. Measurements of the W impurity fluxes between and during edge-localised modes (ELMs) based on fast bolometry measurements show that in such plasmas there is a net efflux (loss) between ELMs but that ELMs often allow some W back into the confined plasma. Provided steady, high-power heating is maintained, this mechanism allows such plasmas to sustain high performance, with an average D-D neutron rate of similar to 3.2 x 10(16) s(-1) over a period of similar to 3 s, after an initial overshoot (equivalent to a D-T fusion power of similar to 9.4 MW), without an uncontrolled rise in W impurity radiation, giving added confidence that impurity screening by the pedestal may also occur in ITER, as has previously been predicted (Dux et al 2017 Nucl. Mater. Energy 12 28-35)

Overview of JET results for optimising ITER operation

The JET 2019–2020 scientific and technological programme exploited the results of years of concerted scientific and engineering work, including the ITER-like wall (ILW: Be wall and W divertor) installed in 2010, improved diagnostic capabilities now fully available, a major neutral beam injection upgrade providing record power in 2019–2020, and tested the technical and procedural preparation for safe operation with tritium. Research along three complementary axes yielded a wealth of new results. Firstly, the JET plasma programme delivered scenarios suitable for high fusion power and alpha particle (α) physics in the coming D–T campaign (DTE2), with record sustained neutron rates, as well as plasmas for clarifying the impact of isotope mass on plasma core, edge and plasma-wall interactions, and for ITER pre-fusion power operation. The efficacy of the newly installed shattered pellet injector for mitigating disruption forces and runaway electrons was demonstrated. Secondly, research on the consequences of long-term exposure to JET-ILW plasma was completed, with emphasis on wall damage and fuel retention, and with analyses of wall materials and dust particles that will help validate assumptions and codes for design and operation of ITER and DEMO. Thirdly, the nuclear technology programme aiming to deliver maximum technological return from operations in D, T and D–T benefited from the highest D–D neutron yield in years, securing results for validating radiation transport and activation codes, and nuclear data for ITER

Predictive JET current ramp-up modelling using QuaLiKiz-neural-network

This work applies the coupled JINTRAC and QuaLiKiz-neural-network (QLKNN) model on the ohmic current ramp-up phase of a JET D discharge. The chosen scenario exhibits a hollow T-e profile attributed to core impurity accumulation, which is observed to worsen with the increasing fuel ion mass from D to T. A dynamic D simulation was validated, evolving j, n(e), T-e, T-i, n(Be), n(Ni), and n(W) for 7.25 s along with self-consistent equilibrium calculations, and was consequently extended to simulate a pure T plasma in a predict-first exercise. The light impurity (Be) accounted for Z(eff) while the heavy impurities (Ni, W) accounted for Prad. This study reveals the role of transport on the Te hollowing, which originates from the isotope effect on the electron-ion energy exchange affecting T-i. This exercise successfully affirmed isotopic trends from previous H experiments and provided engineering targets used to recreate the D q-profile in T experiments, demonstrating the potential of neural network surrogates for fast routine analysis and discharge design. However, discrepancies were found between the impurity transport behaviour of QuaLiKiz and QLKNN, which lead to notable T-e hollowing differences. Further investigation into the turbulent component of heavy impurity transport is recommended

Testing a prediction model for the H-mode density pedestal against JET-ILW pedestals

The neutral ionisation model proposed by Groebner et al (2002 Phys. Plasmas 9 2134) to determine the plasma density profile in the H-mode pedestal, is extended to include charge exchange processes in the pedestal stimulated by the ideas of Mahdavi et al (2003 Phys. Plasmas 10 3984). The model is then tested against JET H-mode pedestal data, both in a 'standalone' version using experimental temperature profiles and also by incorporating it in the Europed version of EPED. The model is able to predict the density pedestal over a wide range of conditions with good accuracy. It is also able to predict the experimentally observed isotope effect on the density pedestal that eludes simpler neutral ionization models

Overview of JET results for optimising ITER operation

The JET 2019–2020 scientific and technological programme exploited the results of years of concerted scientific and engineering work, including the ITER-like wall (ILW: Be wall and W divertor) installed in 2010, improved diagnostic capabilities now fully available, a major neutral beam injection upgrade providing record power in 2019–2020, and tested the technical and procedural preparation for safe operation with tritium. Research along three complementary axes yielded a wealth of new results. Firstly, the JET plasma programme delivered scenarios suitable for high fusion power and alpha particle (α) physics in the coming D–T campaign (DTE2), with record sustained neutron rates, as well as plasmas for clarifying the impact of isotope mass on plasma core, edge and plasma-wall interactions, and for ITER pre-fusion power operation. The efficacy of the newly installed shattered pellet injector for mitigating disruption forces and runaway electrons was demonstrated. Secondly, research on the consequences of long-term exposure to JET-ILW plasma was completed, with emphasis on wall damage and fuel retention, and with analyses of wall materials and dust particles that will help validate assumptions and codes for design and operation of ITER and DEMO. Thirdly, the nuclear technology programme aiming to deliver maximum technological return from operations in D, T and D–T benefited from the highest D–D neutron yield in years, securing results for validating radiation transport and activation codes, and nuclear data for ITER

First-Principles Density Limit Scaling in Tokamaks Based on Edge Turbulent Transport and Implications for ITER

A first-principles scaling law, based on turbulent transport considerations, and a multimachine database of density limit discharges from the ASDEX Upgrade, JET, and TCV tokamaks, show that the increase of the boundary turbulent transport with the plasma collisionality sets the maximum density achievable in tokamaks. This scaling law shows a strong dependence on the heating power, therefore predicting for ITER a significantly larger safety margin than the Greenwald empirical scaling [Greenwald et al., Nucl. Fusion, 28, 2199 (1988)] in case of unintentional high-to-low confinement transition