Synthetic biology: advancing biological frontiers by building synthetic systems

Advances in synthetic biology are contributing to diverse research areas, from basic biology to biomanufacturing and disease therapy. We discuss the theoretical foundation, applications, and potential of this emerging field

Dynamically Reshaping Signaling Networks to Program Cell Fate via Genetic Controllers

Introduction: Engineering of cell fate through synthetic gene circuits requires methods to precisely implement control around native decision-making pathways and offers the potential to direct developmental programs and redirect aberrantly activated cell processes. We set out to develop molecular network diverters, a class of genetic control systems, to activate or attenuate signaling through a mitogen-activated protein kinase (MAPK) pathway, the yeast mating pathway, to conditionally route cells to one of three distinct fates. Methods: We used a combination of genetic elements—including pathway regulators, RNA-based transducers, and constitutive and pathway-responsive promoters—to build modular network diverters. We measured the impact of these genetic control systems on pathway activity by monitoring fluorescence from a transcriptional pathway reporter. Cell fate determination was measured through halo assays, in which mating-associated cell cycle arrest above a certain concentration of pheromone from wild-type cells results in a “halo” or cleared region around a disk saturated in pheromone. A phenomenological model of our system was built to elucidate design principles for dual diverters that integrate opposing functions while supporting independent routing to alternative fates. Results: We identified titratable positive (Ste4) and negative (Msg5) regulators of pathway activity that result in divergent cell fate decisions when controlled from network diverters. A positive diverter, controlling Ste4 through a feedback architecture, routed cells to the mating fate, characterized by pathway activation in the absence of pheromone. A negative diverter, controlling Msg5 through a nonfeedback architecture, routed cells to the nonmating fate, characterized by pathway inhibition in the presence of pheromone. When integrated into a dual-diverter architecture, the opposing functions of these positive and negative diverters resulted in antagonism, which prevented independent routing to the alternative fates. However, a modified architecture that incorporated both constitutive and feedback regulation over the pathway regulators enabled conditional routing of cells to one of three fates (wild type, mating, or nonmating) in response to specified environmental signals. Discussion: Our work identified design principles for networks that induce differentiation of cells in response to environmental signals and that enhance the robust performance of integrated mutually antagonistic genetic programs. For example, integrated negative regulators can buffer a system against noise amplification mediated through positive-feedback loops by providing a resistance to amplification. Negative feedback can play an important role by reducing population heterogeneity and mediating robust, long-term cell fate decisions. The dual-diverter configuration enables routing to alternative fates and minimizes impact on the opposing diverter by integrating differential regulatory strategies on functionally redundant genes. Molecular network diverters provide a foundation for robustly programming spatial and temporal control over cell fate

A World of Cobenefits: Solving the Global Nitrogen Challenge

Nitrogen is a critical component of the economy, food security, and planetary health. Many of the world\u27s sustainability targets hinge on global nitrogen solutions, which, in turn, contribute lasting benefits for (i) world hunger; (ii) soil, air, and water quality; (iii) climate change mitigation; and (iv) biodiversity conservation. Balancing the projected rise in agricultural nitrogen demands while achieving these 21st century ideals will require policies to coordinate solutions among technologies, consumer choice, and socioeconomic transformation

The sound of silence:Transgene silencing in mammalian cell engineering

To elucidate principles operating in native biological systems and to develop novel biotechnologies, synthetic biology aims to build and integrate synthetic gene circuits within native transcriptional networks. The utility of synthetic gene circuits for cell engineering relies on the ability to control the expression of all constituent transgene components. Transgene silencing, defined as the loss of expression over time, persists as an obstacle for engineering primary cells and stem cells with transgenic cargos. In this review, we highlight the challenge that transgene silencing poses to the robust engineering of mammalian cells, outline potential molecular mechanisms of silencing, and present approaches for preventing transgene silencing. We conclude with a perspective identifying future research directions for improving the performance of synthetic gene circuits.ISSN:2405-472

Real-world predictors of survival in patients with limited-stage small-cell lung cancer in Manitoba, Canada

BackgroundAlthough therapy for limited-stage small-cell lung cancer (LS-SCLC) is administered with curative intent, most patients relapse and eventually die of recurrent disease. Chemotherapy (CT) with concurrent radiotherapy (RT) remains the standard of care for LS-SCLC; however, this could evolve in the near future. Therefore, understanding the current prognostic factors associated with survival is essential.ObjectiveThis real-world analysis examines factors associated with long-term survival in patients with LS-SCLC treated with CT in Manitoba, Canada.MethodsA retrospective cohort study was conducted using Manitoba Cancer Registry and CancerCare Manitoba records. Eligible patients were aged >18 years and had cytologically confirmed LS-SCLC diagnosed between January 1, 2004, and December 31, 2018, for which they received CT ± RT. Baseline patient, disease, and treatment characteristics and survival duration, characterized as short (<6 months), medium (6−24 months), and long term (>24 months), were extracted. Overall survival (OS) was estimated at one, two, and five years and assessed using Kaplan-Meier methods and Cox proportional hazards models.ResultsOver the 15-year study period, 304 patients met the eligibility criteria. Long-term survivors comprised 39.1% of the cohort; at diagnosis, this subgroup was younger, more likely to have Eastern Cooperative Oncology Group Performance Status (ECOG PS) 0, and have normal lactate dehydrogenase, sodium, and hemoglobin levels. OS estimates for the entire cohort at one, two, and five years were 66%, 38%, and 18%, respectively. In the ECOG PS 0 subgroup, OS estimates at one, two, and five years were 85%, 52%, and 24%, respectively; OS estimates were 60%, 35%, and 17%, respectively, for ECOG PS 1−2 and were 47%, 23%, and 10%, respectively, for ECOG PS 3−4. OS was significantly higher among patients with normal serum sodium and hemoglobin levels than those with abnormal levels. Univariable hazard regression models found that ECOG PS, age at diagnosis, receipt of prophylactic cranial irradiation (PCI), and thoracic RT were associated with survival. On multivariable hazard regression, ECOG PS and receipt of PCI were associated with survival.ConclusionSurvival for greater than two years in patients with LS-SCLC treated with CT ± RT was associated with ECOG PS and receipt of PCI

Real-world predictors of survival in patients with extensive-stage small-cell lung cancer in Manitoba, Canada: a retrospective cohort study

BackgroundExtensive-stage small-cell lung cancer (ES-SCLC) is an incurable cancer with poor prognosis in which characteristics predictive of long-term survival are debated. The utility of agents such as immune checkpoint inhibitors highlights the importance of identifying key characteristics and treatment strategies that contribute to long-term survival and could help guide therapeutic decisions.ObjectiveThis real-world analysis examines the characteristics, treatment patterns, and clinical outcomes of patients receiving chemotherapy without immunotherapy for ES-SCLC in Manitoba, Canada.MethodsA retrospective cohort study assessed patient characteristics, treatment, and survival duration (short: <6 months; medium: 6–24 months; long: >24 months) using the Manitoba Cancer Registry and CancerCare Manitoba records. Eligible patients were aged >18 years with cytologically confirmed ES-SCLC diagnosed between January 1, 2004, and December 31, 2018, and received cytotoxic chemotherapy (CT). The one-, two-, and five-year probabilities of overall survival (OS) were assessed relative to patient, disease, and treatment characteristics using Kaplan-Meier methods and Cox proportional hazards models.ResultsThis analysis included 537 patients. Cisplatin was used in 56.1% of patients, 45.6% received thoracic radiotherapy (RT), and few received prophylactic cranial irradiation (PCI). In the overall cohort, one-, two- and five-year OS rates were 26%, 8%, and 3%, respectively. For patients with Eastern Cooperative Oncology Group Performance Status (ECOG PS) 0, OS rates at one, two, and five years were 43%, 17%, and 10%, respectively, vs. 27%, 8%, and 2% for those with ECOG PS 1–2, and 16%, 3%, and 3% for those with ECOG PS 3–4. In long-term survivors, ECOG PS scores were lower and abnormal laboratory test results were less frequent. Overall, 74.4% of long-term survivors received thoracic RT and 53.5% received PCI. Known poor prognostic factors – including brain/liver metastases, high lactate dehydrogenase (LDH), abnormal sodium, and low hemoglobin levels – were less common but still seen in long-term survivors.ConclusionAlthough rare, patients with ES-SCLC may experience long-term survival with CT ± thoracic RT ± PCI. Factors predicting long-term survival include traditional prognostic factors such as ECOG PS, LDH level, and receipt of thoracic RT or PCI. These findings support current treatment algorithms for ES-SCLC and provide baseline survival estimates to assess the real-world impact of adding immune checkpoint inhibitors in the future

An idiographic analysis of women's accounts of living with mental health conditions in Haredi Jewish communities.

This research examines the reported experiences of women who developed mental health conditions while they were members of Haredi Jewish communities. The research focuses on how their communities responded and how these responses affected their self-evaluations and relationships with their communities. A qualitative, idiographic approach was used. Four women were recruited through mental health charities and an online group for former community members. The women were interviewed and transcripts were subjected to Interpretative Phenomenological Analysis. Three cross-case themes were developed: "The negative evaluation of mental health conditions in Haredi communities", "'Cloak and dagger': Secrecy and consequences of mental health problems in Haredi communities" and "Going and staying: Mental health experiences and changed relationships with Haredism/Judaism". The themes are discussed in terms of stigma and the threat posed to Haredi communities' self-understanding and self-presentation by the women voicing their mental health status within and outside the communities

Model evaluation in relation to soil N2O emissions: An algorithmic method which accounts for variability in measurements and possible time lags

AbstractThe loss of nitrogen from fertilised soils in the form of nitrous oxide (N2O) is a side effect of modern agriculture and the focus of many model-based studies. Due to the spatial and temporal heterogeneity of soil N2O emissions, the measured data can introduce limitations to the use of those statistical methods that are most commonly employed in the evaluation of model performance. In this paper, we describe these limitations and present an algorithm developed to address them. We implement the algorithm using simulated and measured N2O data from two UK arable sites. We show that possible time lags between the measured and simulated data can affect model evaluation and that their consideration in the evaluation process can reduce measures such as the Mean Squared Error (MSE) by 30%. We also analyse the algorithm's results to identify patterns in the estimated lags and to narrow down their possible causes

BHPR research: qualitative1. Complex reasoning determines patients' perception of outcome following foot surgery in rheumatoid arhtritis

Background: Foot surgery is common in patients with RA but research into surgical outcomes is limited and conceptually flawed as current outcome measures lack face validity: to date no one has asked patients what is important to them. This study aimed to determine which factors are important to patients when evaluating the success of foot surgery in RA Methods: Semi structured interviews of RA patients who had undergone foot surgery were conducted and transcribed verbatim. Thematic analysis of interviews was conducted to explore issues that were important to patients. Results: 11 RA patients (9 ♂, mean age 59, dis dur = 22yrs, mean of 3 yrs post op) with mixed experiences of foot surgery were interviewed. Patients interpreted outcome in respect to a multitude of factors, frequently positive change in one aspect contrasted with negative opinions about another. Overall, four major themes emerged. Function: Functional ability & participation in valued activities were very important to patients. Walking ability was a key concern but patients interpreted levels of activity in light of other aspects of their disease, reflecting on change in functional ability more than overall level. Positive feelings of improved mobility were often moderated by negative self perception ("I mean, I still walk like a waddling duck”). Appearance: Appearance was important to almost all patients but perhaps the most complex theme of all. Physical appearance, foot shape, and footwear were closely interlinked, yet patients saw these as distinct separate concepts. Patients need to legitimize these feelings was clear and they frequently entered into a defensive repertoire ("it's not cosmetic surgery; it's something that's more important than that, you know?”). Clinician opinion: Surgeons' post operative evaluation of the procedure was very influential. The impact of this appraisal continued to affect patients' lasting impression irrespective of how the outcome compared to their initial goals ("when he'd done it ... he said that hasn't worked as good as he'd wanted to ... but the pain has gone”). Pain: Whilst pain was important to almost all patients, it appeared to be less important than the other themes. Pain was predominately raised when it influenced other themes, such as function; many still felt the need to legitimize their foot pain in order for health professionals to take it seriously ("in the end I went to my GP because it had happened a few times and I went to an orthopaedic surgeon who was quite dismissive of it, it was like what are you complaining about”). Conclusions: Patients interpret the outcome of foot surgery using a multitude of interrelated factors, particularly functional ability, appearance and surgeons' appraisal of the procedure. While pain was often noted, this appeared less important than other factors in the overall outcome of the surgery. Future research into foot surgery should incorporate the complexity of how patients determine their outcome Disclosure statement: All authors have declared no conflicts of interes

A search for resonances decaying into a Higgs boson and a new particle X in the XH → qqbb final state with the ATLAS detector

A search for heavy resonances decaying into a Higgs boson (H) and a new particle (X) is reported, utilizing 36.1 fb−1 of proton–proton collision data at collected during 2015 and 2016 with the ATLAS detector at the CERN Large Hadron Collider. The particle X is assumed to decay to a pair of light quarks, and the fully hadronic final state is analysed. The search considers the regime of high XH resonance masses, where the X and H bosons are both highly Lorentz-boosted and are each reconstructed using a single jet with large radius parameter. A two-dimensional phase space of XH mass versus X mass is scanned for evidence of a signal, over a range of XH resonance mass values between 1 TeV and 4 TeV, and for X particles with masses from 50 GeV to 1000 GeV. All search results are consistent with the expectations for the background due to Standard Model processes, and 95% CL upper limits are set, as a function of XH and X masses, on the production cross-section of the resonance