Biosynthesis, Engineering, and Delivery of Selenoproteins.

Selenocysteine (Sec) was discovered as the 21st genetically encoded amino acid. In nature, site-directed incorporation of Sec into proteins requires specialized biosynthesis and recoding machinery that evolved distinctly in bacteria compared to archaea and eukaryotes. Many organisms, including higher plants and most fungi, lack the Sec-decoding trait. We review the discovery of Sec and its role in redox enzymes that are essential to human health and important targets in disease. We highlight recent genetic code expansion efforts to engineer site-directed incorporation of Sec in bacteria and yeast. We also review methods to produce selenoproteins with 21 or more amino acids and approaches to delivering recombinant selenoproteins to mammalian cells as new applications for selenoproteins in synthetic biology.

Delivery of the selenoprotein thioredoxin reductase 1 to mammalian cells.

Over-expression of genetically encoded thioredoxin reductase 1 (TrxR1) TrxR1 can be toxic to cells due to the formation of a truncated version of the enzyme. We developed a new mammalian cell-based model to investigate TrxR1 activity. Fusion of the HIV-derived cell penetrating peptide (TAT) enabled efficient cellular uptake of purified TrxR1 containing 21 genetically encoded amino acids, including selenocysteine. The TAT peptide did not significantly alter the catalytic activity of TrxR1 in vitro. We monitored TrxR1-dependent redox activity in human cells using a TrxR1-specific red fluorescent live-cell reporter. Using programmed selenocysteine incorporation in Escherichia coli, our approach allowed efficient production of active recombinant human selenoprotein TrxR1 for delivery to the homologous context of the mammalian cell. The delivered TAT-TrxR1 showed robust activity in live cells and provided a novel platform to study TrxR1 biology in human cells.

A novel fluorescent reporter sensitive to serine mis-incorporation.

High-fidelity translation was considered a requirement for living cells. The frozen accident theory suggested that any deviation from the standard genetic code should result in the production of so much mis-made and non-functional proteins that cells cannot remain viable. Studies in bacterial, yeast, and mammalian cells show that significant levels of mistranslation (1-10% per codon) can be tolerated or even beneficial under conditions of oxidative stress. Single tRNA mutants, which occur naturally in the human population, can lead to amino acid mis-incorporation at a codon or set of codons. The rate or level of mistranslation can be difficult or impossible to measure in live cells. We developed a novel red fluorescent protein reporter that is sensitive to serine (Ser) mis-incorporation at proline (Pro) codons. The mCherry Ser151Pro mutant is efficiently produced in Escherichia coli but non-fluorescent. We demonstrated in cells and with purified mCherry protein that the fluorescence of mCherry Ser151Pro is rescued by two different tRNASer gene variants that were mutated to contain the Pro (UGG) anticodon. Ser mis-incorporation was confirmed by mass spectrometry. Remarkably, E. coli tolerated mistranslation rates of ~10% per codon with negligible reduction in growth rate. Conformational sampling simulations revealed that the Ser151Pro mutant leads to significant changes in the conformational freedom of the chromophore precursor, which is indicative of a defect in chromophore maturation. Together our data suggest that the mCherry Ser151 mutants may be used to report Ser mis-incorporation at multiple other codons, further expanding the ability to measure mistranslation in living cells.

Acetylated Thioredoxin Reductase 1 Resists Oxidative Inactivation.

Thioredoxin Reductase 1 (TrxR1) is an enzyme that protects human cells against reactive oxygen species generated during oxidative stress or in response to chemotherapies. Acetylation of TrxR1 is associated with oxidative stress, but the function of TrxR1 acetylation in oxidizing conditions is unknown. Using genetic code expansion, we produced recombinant and site-specifically acetylated variants of TrxR1 that also contain the non-canonical amino acid, selenocysteine, which is essential for TrxR1 activity. We previously showed site-specific acetylation at three different lysine residues increases TrxR1 activity by reducing the levels of linked dimers and low activity TrxR1 tetramers. Here we use enzymological studies to show that acetylated TrxR1 is resistant to both oxidative inactivation and peroxide-induced multimer formation. To compare the effect of programmed acetylation at specific lysine residues to non-specific acetylation, we produced acetylated TrxR1 using aspirin as a model non-enzymatic acetyl donor. Mass spectrometry confirmed aspirin-induced acetylation at multiple lysine residues in TrxR1. In contrast to unmodified TrxR1, the non-specifically acetylated enzyme showed no loss of activity under increasing and strongly oxidating conditions. Our data suggest that both site-specific and general acetylation of TrxR1 regulate the enzyme's ability to resist oxidative damage.

Expanded FDA regulation of health and wellness apps.

This paper argues that the Food and Drug Administration's (FDA) policy for health and wellness apps is ethically problematic. Currently, the FDA does not regulate health and wellness apps that are not intended for medical use. As a result of this hands-off policy, preventing harm to consumers is left primarily to developers and app marketplaces. We argue that the FDA's duties to prevent harm and maintain accountability to the American public require that they play a much stronger role. We also discuss concerns about efficiency and fostering innovation, and argue that while they should help shape FDA regulation of health and wellness apps, they do not justify complete absence of FDA involvement.

The Molecular Architecture of Unnatural Amino Acid Translation Systems.

Expanding the genetic code using non-canonical amino acids has revolutionized synthetic biology. In a recent issue of Cell Chemical Biology, Yanagisawa et al. (2019) expanded our knowledge of orthogonal translation systems by presenting a tour de force structural characterization of multiple genetic code expansion systems based on pyrrolysyl-tRNA synthetase.

Acetylation Regulates Thioredoxin Reductase Oligomerization and Activity.

AIMS: Thioredoxin reductase 1 (TrxR1) is a cancer target and essential selenoprotein that defends the cell against reactive oxygen species and regulates cellular signaling and redox pathways. Previous cell-based studies correlated TrxR1 acetylation with modulated cellular reduction activity, yet the function of specific acetylation sites on TrxR1 remains unknown. INNOVATION: We produced site-specifically acetylated TrxR1 variants that also contain selenocysteine (Sec). We demonstrated efficient high-fidelity protein synthesis with 22 different amino acids by simultaneous UAG codon reassignment to Nɛ-acetyl-lysine and UGA codon recoding to Sec. RESULTS: We characterized TrxR1 variants acetylated at physiologically relevant sites and found that single acetylation sites increased TrxR1 activity, enhancing the apparent catalytic rate up to 2.7-fold. The activity increase in acetylated TrxR1 (acTrxR1) is reversible and is reduced following deacetylation with histone deacetylase. CONCLUSION: Here we present a novel mechanism through which acetylation increases TrxR1 activity by destabilizing low-activity TrxR1 multimers, increasing the population of active dimeric TrxR1. Antioxid. Redox Signal. 29, 377-388.

A systematic review of biomarkers for disease progression in Alzheimer's disease.

BACKGROUND: Using surrogate biomarkers for disease progression as endpoints in neuroprotective clinical trials may help differentiate symptomatic effects of potential neuroprotective agents from true slowing of the neurodegenerative process. A systematic review was undertaken to determine what biomarkers for disease progression in Alzheimer's disease exist and how well they perform. METHODS: MEDLINE and Embase (1950-2011) were searched using five search strategies. Abstracts were assessed to identify papers meriting review in full. Studies of participants with probable Alzheimer's disease diagnosed by formal criteria were included. We made no restriction on age, disease duration, or drug treatment. We only included studies with a longitudinal design, in which the putative biomarker and clinical measure were both measured at least twice, as this is the only appropriate study design to use when developing a disease progression biomarker. We included studies which attempted to draw associations between the changes over time in the biomarker used to investigate disease progression and a clinical measure of disease progression. RESULTS: Fifty-nine studies were finally included. The commonest biomarker modality examined was brain MRI (17/59, 29% of included studies). Median follow-up in included studies was only 1.0 (IQR 0.8-1.7) year and most studies only measured the putative biomarker and clinical measure twice. Included studies were generally of poor quality with small numbers of participants (median 31 (IQR 17 to 64)), applied excessively restrictive study entry criteria, had flawed methodologies and conducted overly simplistic statistical analyses without adjusting for confounding factors. CONCLUSIONS: We found insufficient evidence to recommend the use of any biomarker as an outcome measure for disease progression in Alzheimer's disease trials. However, further investigation into the efficacy of using MRI measurements of ventricular volume and whole brain volume appeared to be merited. A provisional 'roadmap' to improve the quality of future disease progression biomarker studies is presented.

The emergence of the Responsible Conduct of Research (RCR) in PHS policy and practice.

The Responsible Conduct of Research (RCR) is now an established academic field taught at virtually every major American research university and generates a growing volume of research and pedagogical literature. Paradoxically, it is a field without a consensually agreed upon definition, goals, foundational theories, research agenda, and pedagogical methodology. It has been suggested that RCR as currently being taught is ineffective in preventing misconduct and improving the quality of research. The following short history of RCR, focused mainly on Federal policy and practice, explains how this curious state of affairs developed and persists and concludes with some suggestions for the future of RCR instruction.

A systematic review of biomarkers for disease progression in Parkinson's disease.

BACKGROUND: Using surrogate biomarkers for disease progression as endpoints in neuroprotective clinical trials may help differentiate symptomatic effects of potential neuroprotective agents from true disease-modifying effects. A systematic review was undertaken to determine what biomarkers for disease progression in Parkinson's disease (PD) exist. METHODS: MEDLINE and EMBASE (1950-2010) were searched using five search strategies. Abstracts were assessed to identify papers meriting review in full. Studies of participants with idiopathic PD diagnosed by formal criteria or clearly described clinical means were included. We made no restriction on age, disease duration, drug treatment, or study design. We included studies which attempted to draw associations between any tests used to investigate disease progression and any clinical measures of disease progression. The electronic search was validated by hand-searching the two journals from which most included articles came. RESULTS: 183 studies were included: 163 (89%) cross-sectional, 20 (11%) longitudinal. The electronic search strategy had a sensitivity of 71.4% (95% CI 51.1-86.0) and a specificity of 97.1% (95% CI 96.5-97.7). In longitudinal studies median follow-up was 2.0 years (IQR 1.1-3.5). Included studies were generally poor quality--cross-sectional with small numbers of participants, applying excessive inclusion/exclusion criteria, with flawed methodologies and simplistic statistical analyses. CONCLUSION: We found insufficient evidence to recommend the use of any biomarker for disease progression in PD clinical trials, which may simply reflect the poor quality of research in this area. We therefore present a provisional 'roadmap' for conducting future disease progression biomarker studies, and recommend new quality criteria by which future studies may be judged.

Preparing whistleblowers for reporting research misconduct.

Making an allegation of research misconduct can be stressful for a whistleblower. The Research Integrity Officer (RIO) can play an important role in helping reduce the stress by thoroughly discussing what whistleblowers can expect if they make an allegation. Through interviews with 77 RIOs who had recently handled a research misconduct case, we found that RIOs who addressed more topics as well as specific aspects of the topics were more likely to have used some type of memory aide in their initial contact with whistleblowers, talked with ORI staff or other RIOs about "hypothetical" research misconduct cases, or attended a RIO boot camp training. We believe that RIOs who more fully inform whistleblowers are providing timely preparation and building whistleblowers' confidence so they can make a more informed decision about reporting and experience less stress.

Assessing the preparedness of research integrity officers (RIOs) to appropriately handle possible research misconduct cases.

Institutions receiving federal funding for research from the U.S.Public Health Service need to have policies and procedures to both prevent research misconduct and to adjudicate it when it occurs. The person who is designated to handle research misconduct is typically referred to as the research integrity officer (RIO). In this interview study we report on 79 RIOs who describe how they would handle allegations of research misconduct. Their responses were compared to two expert RIOs. The responses to the allegations in the scenarios demonstrated that RIOs are not uniformly well prepared to handle activities associated with reported allegations of research misconduct. We recommend greater preparation through directed training, use of check lists of possible behaviors necessary to consider when situations arise, being involved in a network of RIOs so one can discuss options, and the possible need to certify RIOs.

Mentoring and research misconduct: an analysis of research mentoring in closed ORI cases.

We are reporting on how involved the mentor was in promoting responsible research in cases of research misconduct. We reviewed the USPHS misconduct files of the Office of Research Integrity. These files are created by Institutions who prosecute a case of possible research misconduct; ORI has oversight review of these investigations. We explored the role of the mentor in the cases of trainee research misconduct on three specific behaviors that we believe mentors should perform with their trainee: (1) review source data, (2) teach specific research standards and (3) minimize stressful work situations. We found that almost three quarters of the mentors had not reviewed the source data and two thirds had not set standards. These two behaviors are positively correlated. We did not see convincing evidence in the records that mentors were causing stress, but it was apparent in the convicted trainees' confessions that over 50% experienced some kind of stress. Secondary data, while not created for this research purpose, allows us to look at concrete research behaviors that are otherwise not very researchable. We believe it is important for mentors and institutions to devote more attention to teaching mentors about the process of education and their responsibilities in educating the next generation of scientists. This becomes a critical issue for large research groups who need to determine who is in charge educating, supervising and assuring data integrity.

Assessing newborn body composition using principal components analysis: differences in the determinants of fat and skeletal size.

BACKGROUND: Birth weight is a composite of skeletal size and soft tissue. These components are likely to have different growth patterns. The aim of this paper is to investigate the association between established determinants of birth weight and these separate components. METHODS: Weight, length, crown-rump, knee-heel, head circumference, arm circumference, and skinfold thicknesses were measured at birth in 699 healthy, term, UK babies recruited as part of the Exeter Family Study of Childhood Health. Corresponding measurements were taken on both parents. Principal components analysis with varimax rotation was used to reduce these measurements to two independent components each for mother, father and baby: one highly correlated with measures of fat, the other with skeletal size. RESULTS: Gestational age was significantly related to skeletal size, in both boys and girls (r = 0.41 and 0.52), but not fat. Skeletal size at birth was also associated with parental skeletal size (maternal: r = 0.24 (boys), r = 0.39 (girls) ; paternal: r = 0.16 (boys), r = 0.25 (girls)), and maternal smoking (0.4 SD reduction in boys, 0.6 SD reduction in girls). Fat was associated with parity (first borns smaller by 0.45 SD in boys; 0.31 SD in girls), maternal glucose (r = 0.18 (boys); r = 0.27 (girls)) and maternal fat (r = 0.16 (boys); r = 0.36 (girls)). CONCLUSION: Principal components analysis with varimax rotation provides a useful method for reducing birth weight to two more meaningful components: skeletal size and fat. These components have different associations with known determinants of birth weight, suggesting fat and skeletal size may have different regulatory mechanisms, which would be important to consider when studying the associations of birth weight with later adult disease.

Repeated measurement of pregnancy-associated plasma protein-A (PAPP-A) in Down syndrome screening: a validation study.

OBJECTIVES: To confirm that measuring pregnancy-associated plasma protein-A (PAPP-A) in both first- and second-trimester serum samples improves Down syndrome screening. METHODS: We selected paired first- and second-trimester stored serum samples from 34 Down syndrome pregnancies (cases) and 514 unaffected pregnancies (controls) and tested the second-trimester samples for PAPP-A and dimeric inhibin-A (DIA). First-trimester PAPP-A measurements were already available, as were second-trimester measurements of alpha-fetoprotein, unconjugated estriol (uE3), and human chorionic gonadotrophin (hCG). RESULTS: PAPP-A was lower among cases than controls (0.47 MoM) in the first trimester (at an average of 12.5 weeks); in the second trimester, it was not different (0.91 MoM). Using repeated measures of PAPP-A alone, 21 of 34 cases were detected (62%, 95%CI 44% to 78%) with 5% false positives. At an observed 2% false-positive rate, the detection rates (DR) for the quadruple (69%) and serum integrated (69%) tests were lower than for the repeated measures test (75%). Modelled performance at 12 weeks was similar to these observed findings (70, 75, and 82%, respectively). If the first-trimester samples were collected at 10 weeks, however, DR would be higher (70, 81, and 91%, respectively). CONCLUSIONS: Adding a repeated measure of PAPP-A to existing serum markers improves Down syndrome screening to levels that are currently obtainable only by including ultrasound measurement of nuchal translucency (NT). Serum-based screening has the advantages of higher availability and reliability at a lower cost, resulting in a more effective screening strategy. A serum-based repeated measures test has a place in routine Down syndrome screening.

Repeated measures screening for Down's Syndrome.

OBJECTIVE: To demonstrate the potential value of screening for Down's Syndrome using highly correlated repeated measures of serum markers taken in the first and second trimesters of pregnancy. DESIGN: A Monte Carlo simulation study. POPULATION: Detection rates and false positive rates relating to the maternal age distribution of England and Wales for the period 1996 to 1998 were obtained using marker distributions from the SURUSS study. RESULTS: Screening using first trimester nuchal translucency and repeated measures of uE3 and PAPP-A in the first and second trimester has an estimated false positive rate of 0.3% for an 85% detection rate. This should be compared with the integrated test with an estimated false positive rate of 1.2% for the same detection rate. CONCLUSIONS: The performance of repeated measures screening tests, and their acceptability to women, should be assessed in further prospective studies.