Quantitative mitochondrial DNA copy number determination using droplet digital PCR with single-cell resolution

Mitochondria are involved in a number of diverse cellular functions, including energy production, metabolic regulation, apoptosis, calcium homeostasis, cell proliferation, and motility, as well as free radical generation. Mitochondrial DNA (mtDNA) is present at hundreds to thousands of copies per cell in a tissue-specific manner. mtDNA copy number also varies during aging and disease progression and therefore might be considered as a biomarker that mirrors alterations within the human body. Here, we present a new quantitative, highly sensitive droplet digital PCR (ddPCR) method, droplet digital mitochondrial DNA measurement (ddMDM), to measure mtDNA copy number not only from cell populations but also from single cells. Our developed assay can generate data in as little as 3 h, is optimized for 96-well plates, and also allows the direct use of cell lysates without the need for DNA purification or nuclear reference genes. We show that ddMDM is able to detect differences between samples whose mtDNA copy number was close enough as to be indistinguishable by other commonly used mtDNA quantitation methods. By utilizing ddMDM, we show quantitative changes in mtDNA content per cell across a wide variety of physiological contexts including cancer progression, cell cycle progression, human T cell activation, and human aging.

Active transforming growth factor-beta in wound repair: determination using a new assay

Transforming growth factor (TGF)-beta regulates wound repair and scarring in an isoform-specific fashion. TGF-beta is produced in a latent form, and its activation is a critical regulatory step controlling the bioactivity of this growth factor. To date, it has been impossible to determine latent TGF-beta activation in vivo due to a lack of quantitative assays. We describe here a semiquantitative modification of the plasminogen activator inhibitor-1/luciferase bioassay (PAI/L assay) for TGF-beta, which we used to determine active and latent TGF-beta isoforms in frozen sections of rat wound tissue. We found that significant amounts of latent TGF-beta were rapidly activated upon wounding (38% of the total TGF-beta at 1 hour after wounding). A second peak of active TGF-beta (17% of total) occurred at 5 days after wounding. The predominant isoforms were TGF-beta1 and -2 with only minor amounts of TGF-beta3 present. This is the first TGF-beta bioassay allowing semiquantitative determination of active and latent isoforms present in vivo, and our results document the significance and temporal regulation of latent TGF-beta isoform activation in wound repair.

ESR1 mutations affect anti-proliferative responses to tamoxifen through enhanced cross-talk with IGF signaling

The purpose of this study was to address the role of ESR1 hormone-binding mutations in breast cancer. Soft agar anchorage-independent growth assay, Western blot, ERE reporter transactivation assay, proximity ligation assay (PLA), coimmunoprecipitation assay, silencing assay, digital droplet PCR (ddPCR), Kaplan-Meier analysis, and statistical analysis. It is now generally accepted that estrogen receptor (ESR1) mutations occur frequently in metastatic breast cancers; however, we do not yet know how to best treat these patients. We have modeled the three most frequent hormone-binding ESR1 (HBD-ESR1) mutations (Y537N, Y537S, and D538G) using stable lentiviral transduction in human breast cancer cell lines. Effects on growth were examined in response to hormonal and targeted agents, and mutation-specific changes were studied using microarray and Western blot analysis. We determined that the HBD-ESR1 mutations alter anti-proliferative effects to tamoxifen (Tam), due to cell-intrinsic changes in activation of the insulin-like growth factor receptor (IGF1R) signaling pathway and levels of PIK3R1/PIK3R3. The selective estrogen receptor degrader, fulvestrant, significantly reduced the anchorage-independent growth of ESR1 mutant-expressing cells, while combination treatments with the mTOR inhibitor everolimus, or an inhibitor blocking IGF1R, and the insulin receptor significantly enhanced anti-proliferative responses. Using digital drop (dd) PCR, we identified mutations at high frequencies ranging from 12 % for Y537N, 5 % for Y537S, and 2 % for D538G in archived primary breast tumors from women treated with adjuvant mono-tamoxifen therapy. The HBD-ESR1 mutations were not associated with recurrence-free or overall survival in response in this patient cohort and suggest that knowledge of other cell-intrinsic factors in combination with ESR1 mutation status will be needed determine anti-proliferative responses to Tam.

New bounds on dark matter coupling from a global network of optical atomic clocks

We report on the first Earth-scale quantum sensor network based on optical atomic clocks aimed at dark matter (DM) detection. Exploiting differences in the susceptibilities to the fine-structure constant of essential parts of an optical atomic clock, i.e., the cold atoms and the optical reference cavity, we can perform sensitive searches for DM signatures without the need for real-time comparisons of the clocks. We report a two orders of magnitude improvement in constraints on transient variations of the fine-structure constant, which considerably improves the detection limit for the standard model (SM)-DM coupling. We use Yb and Sr optical atomic clocks at four laboratories on three continents to search for both topological defect and massive scalar field candidates. No signal consistent with a DM coupling is identified, leading to considerably improved constraints on the DM-SM couplings.

Activation of platelet-transforming growth factor beta-1 in the absence of thrombospondin-1

Thrombospondin-1 (TSP-1) has been shown to bind and activate transforming growth factor-beta1 (TGF-beta1). This observation raises the possibility that TSP-1 helps to sequester TGF-beta1 in platelet alpha granules and activates TGF-beta1 once both proteins are secreted. Herein, we evaluated the level of active and latent TGF-beta1 in the plasma and in the supernatant of thrombin-treated platelets from TSP-1 null and wild-type mice on two genetic backgrounds (C57BL/6 and 129Sv). The plasminogen activator inhibitor-1/luciferase bioassay and an immunological assay were used to determine active and latent TGF-beta1. No significant differences were observed in the levels of active and latent TGF-beta1 in the supernatant of thrombin-treated platelets from TSP-1 null and wild-type mice. Active and latent TGF-beta1 were significantly increased in the plasma and platelets of C57BL/6 mice as compared with 129Sv mice. In addition, there was an increase of plasma level of latent TGF-beta1 in TSP-1 null mice as compared with wild-type mice on the C57BL/6 background but not on the 129Sv background. No active TGF-beta1 was observed in the plasma of either TSP-1 null and wild-type mice. These data indicate that TSP-1 does not function as a chaperon for TGF-beta1 during platelet production and does not activate significant quantities of secreted TGF-beta1 despite a vast excess in the number of TSP-1 molecules as compared with TGF-beta1 molecules. Because platelet releasates from TSP-1 null mice contain active TGF-beta1, we suggest that other important mechanisms of physiological activation of TGF-beta1 probably exist in platelets.

Integrated analysis of telomerase enzymatic activity unravels an association with cancer stemness and proliferation

Active telomerase is essential for stem cells and most cancers to maintain telomeres. The enzymatic activity of telomerase is related but not equivalent to the expression of TERT, the catalytic subunit of the complex. Here we show that telomerase enzymatic activity can be robustly estimated from the expression of a 13-gene signature. We demonstrate the validity of the expression-based approach, named EXTEND, using cell lines, cancer samples, and non-neoplastic samples. When applied to over 9,000 tumors and single cells, we find a strong correlation between telomerase activity and cancer stemness. This correlation is largely driven by a small population of proliferating cancer cells that exhibits both high telomerase activity and cancer stemness. This study establishes a computational framework for quantifying telomerase enzymatic activity and provides new insights into the relationships among telomerase, cancer proliferation, and stemness.

Exercise reduces the protein abundance of TXNIP and its interacting partner REDD1 in skeletal muscle: potential role for a PKA-mediated mechanism

Thioredoxin-interacting protein (TXNIP) negatively effects the redox state and growth signaling via its interactions with thioredoxin (TRX) and regulated in development and DNA damage response 1 (REDD1), respectively. TXNIP expression is downregulated by pathways activated during aerobic exercise (AE), via posttranslational modifications (PTMs; serine phosphorylation and ubiquitination). The purpose of this investigation was to determine the effects of acute AE on TXNIP expression, posttranslational modifications, and its interacting partners, REDD1 and TRX. Fifteen healthy adults performed 30 min of aerobic exercise (80% V̇o_2max) with muscle biopsies taken before, immediately following, and 3 h following the exercise bout. To explore potential mechanisms underlying our in vivo findings, primary human myotubes were exposed to two models of exercise, electrical pulse stimulation (EPS) and palmitate-forskolin-ionomycin (PFI). Immediately following exercise, TXNIP protein decreased, but returned to preexercise levels 3 h after exercise. These results were replicated in our PFI exercise model only. Although not statistically significant, there was a trending main effect in serine-phosphorylation status of TXNIP (P = 0.07) immediately following exercise. REDD1 protein decreased 3 h after exercise. AE had no effect on TRX protein expression, gene expression, or the activity of its reducing enzyme, thioredoxin reductase. Consequently, AE had no effect on the TRX: TXNIP interaction. Our results indicate that AE leads to acute reductions in TXNIP and REDD1 protein expression. However, these changes did not result in alterations in the TRX: TXNIP interaction and could not be entirely explained by alterations in TXNIP PTMs or changes in TRX expression or activity.NEW & NOTEWORTHY Aerobic exercise is an effective tool in the prevention and treatment of several chronic metabolic diseases. However, the mechanisms through which these benefits are conferred have yet to be fully elucidated. Our data reveal a novel effect of aerobic exercise on reducing the protein expression of molecular targets that negatively impact redox and insulin/growth signaling in skeletal muscle. These findings contribute to the expanding repository of molecular signatures provoked by aerobic exercise.

The experiences of new mothers accessing feeding support for infants with down syndrome during the COVID-19 pandemic

Infants with Down syndrome are more likely to experience feeding problems and mothers are likely to require more feeding support than mothers of typically developing infants. During the COVID-19 pandemic, many feeding support services changed from face-to-face to online, which impacted some maternal feeding experiences negatively, but no studies to date have explored the impact for mothers of infants with Down syndrome. Thematic analysis was conducted on semi-structured interviews from thirteen new mothers of infants (aged 8-17 months) with Down syndrome in the UK. Three superordinate themes were generated: (1) Every baby with Down syndrome has a unique journey, (2) There's no point asking, they won't know, (3) Lack of in-person support. Many mothers expressed frustrations over health professionals' lack of Down syndrome specific knowledge resulting in unmet needs, further magnified due to the nature of the virtual support being offered. Moreover, mothers struggled with reduced social support from other mothers when encountering feeding problems. These results hold real-world implications for health professionals who could provide more specialised face-to-face feeding support to mothers of infants with Down syndrome. This should be prioritised for children's overall development and mothers' wellbeing.

State-of-the-art RF signal generation from optical frequency division

We present the design of a novel, ultralow-phase-noise frequency synthesizer implemented with extremely-low-noise regenerative frequency dividers. This synthesizer generates eight outputs, viz. 1.6 GHz, 320 MHz, 160 MHz, 80 MHz, 40 MHz, 20 MHz, 10 MHz and 5 MHz for an 8 GHz input frequency. The residual single-sideband (SSB) phase noises of the synthesizer at 5 and 10 MHz outputs at 1 Hz offset from the carrier are -150 and -145 dBc/Hz, respectively, which are unprecedented phase noise levels. We also report the lowest values of phase noise to date for 5 and 10 MHz RF signals achieved with our synthesizer by dividing an 8 GHz signal generated from an ultra-stable optical-comb-based frequency division. The absolute SSB phase noises achieved for 5 and 10 MHz signals at 1 Hz offset are -150 and -143 dBc/Hz, respectively; at 100 kHz offset, they are -177 and -174 dBc/Hz, respectively. The phase noise of the 5 MHz signal corresponds to a frequency stability of approximately 7.6 × 10(-15) at 1 s averaging time for a measurement bandwidth (BW) of 500 Hz, and the integrated timing jitter over 100 kHz BW is 20 fs.

Abstract 5102: Differential levels of mutated Kras drive lung cancer cell motility and morphology via a hypoxia-sensitive FAK/Erk/Myosin II signaling pathway

Kras controls many cellular processes such as cell migration and survival. Mutation of Kras to a constitutively active form is a common alteration in lung cancer. Being constantly active results in a hyper activation of downstream signaling cascades, which leads to enhanced tumorigenicity and high metastatic potential. How constitutive Kras activation translates into these different functions, however, remains unclear. Using patient-derived lung cancer cell lines expressing oncogenic KrasV12 we discovered that Kras expression, not transcription, gets up-regulated under long-term culture in 1% O2. We confirmed the in vivo relevance of this finding, staining mouse lung tumors for Kras and Hif1α, as an indicator for hypoxic areas, and found heterogeneous Kras levels throughout the tumors with hot-spots that overlaid with Hif1α expression. Up-regulation of KrasV12 also correlated with a significant increase in growth of tumor-like aggregates in soft-agar assays and a morphological change from adherent single-cells into sphere-like aggregates in cell culture. This morphology was reversible upon knock-down of Kras. Separation of single clones confirmed the relation between adherent and sphere-like morphologies and the level of KrasV12 expression. Interestingly, the expression level of Kras correlated with clonal migration behavior. Low Kras expressers were highly motile whereas high Kras expressers remained stationary in aggregates. In agreement, exogenous expression of KrasV12 in motile, low Kras expressers converted their morphology and migration behavior to sphere-like, stationary aggregates. Using Western blot analysis we found that these changes are due to differences in Erk activation down-stream of Kras. In high Kras expressers Erk is highly phosphorylated which leads to higher Myosin II activity and thus to a contractile, sphere-like morphology with low mobility. Low Kras levels result in less Erk activation and therefore lower Myosin II activity which leads to an adherent, motile phenotype. Using a specific Erk inhibitor, we could convert high Kras expressers into adherent, motile low Kras clones. At the same time we found an adhesion-dependent feedback mechanism which regulates cellular Kras levels. Protein analysis of cells cultured in low adhesion dishes formed spheres and dramatically increased their Kras content. Most interestingly, this increase was reversible by stimulation of adhesion. Additionally, blocking FAK activation in low Kras expressers resulted in up-regulation of Kras and Erk phosphorylation which went along with a switch to sphere-like morphology. Based on these findings we propose a novel mechanism for controlling cancer cell migration by a hypoxia-sensitive, adhesion-dependent Kras switch which makes the cell very adaptable to different environments during the whole process of metastasis.

Citation Format: Anette C. Schafer, Meghan Discoll, Ashwathi Mohan, Andrew Ludlow, Wesley Burford, Jerry W. Shay, Gaudenz Danuser. Differential levels of mutated Kras drive lung cancer cell motility and morphology via a hypoxia-sensitive FAK/Erk/Myosin II signaling pathway. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5102. doi:10.1158/1538-7445.AM2015-5102

Deployment of a transportable Yb optical lattice clock

We report on the first deployment of a ytterbium (Yb) transportable optical lattice clock (TOLC), commercially shipping the clock 3000 km from Boulder, Colorado, to Washington DC. The system, composed of a rigidly mounted optical reference cavity, an atomic physics package, and an optical frequency comb, fully realizes an independent frequency standard for comparisons in the optical and microwave domains. The shipped Yb TOLC was fully operational within 2 days of arrival, enabling frequency comparison with a rubidium (Rb) fountain at the United States Naval Observatory (USNO). To the best of our knowledge, this represents the first deployment of a fully independent TOLC, including the frequency comb, coherently uniting the optical stability of the Yb TOLC to the microwave output of the Rb fountain.

Using Human-Centred Design to Develop Innovative Approaches to Improve Delivery of Brief Interventions in Primary Care: The HealthEir Project

Introduction

A priority action of the Healthy Ireland implementation plan is the Making Every Contact Count initiative (MECC) that aims to leverage the 30 million annual contacts with the healthcare system by asking every health worker to deliver brief interventions [1]. Benefits of brief interventions are well established, but GPs and pharmacists report challenges implementing them in practice including limited training, time, and poor fit with existing practices [2].

Aim

This government-funded Sláintecare project aimed to develop a novel method for brief interventions in pharmacy/GP settings using human-centred design.

Methods

User research was carried out with twelve users, including patients (3), GPs (4), and pharmacists (5) to identify their needs and priorities. Participants were recruited via email using a purposive sampling approach and completed semi-structured interviews with a design researcher. All participants invited agreed to participate. Next, a series of design sprints were completed with the research team. Design sprints allowed the team to integrate insights from user research with findings from a literature review/secondary research to understand pain points, identify stakeholder and user goals, and develop a list of initial design specifications. This list was used to develop and iterate a series of prototype solutions. Prototype service blueprints and wireframes (simple, two-dimensional schematic illustrations of the digital interface) were developed and tested with users before final versions were agreed.

Results

Findings from the interviews and literature review indicated (1) the main barrier to adoption was time, (2) patients and pharmacists were very positive about brief interventions with GPs more hesitant, (3) an approach blending technology with a consultation was preferred, and (4) having a specific list of local supports was important. Prototyping and evaluation processes identified that a simple interface with a clear indication of progress were preferred.

A blended intervention combining a tablet-based digital tool and structured interaction was developed. The interface was designed to maximise use of patient and healthcare professional time, and mapped to the 5As approach (which is underpinned by principles of motivational interviewing, shared-decision making, and readiness to change frameworks). The HealthEir digital tool enables patients to self-complete the Ask, Advise, and Assess phases of a brief intervention using a tablet device while waiting to see their pharmacist/GP. The pharmacist or GP then review the patient’s responses, risk level, and importance confidence and readiness scores. They complete the Assist and Arrange elements during the consultation, supported by a directory of local/national patient support services before printing information tickets for the patient to keep. The HealthEir intervention has been successfully rolled out at eight pilot pharmacy sites nationally, with a mix of urban/rural sites, and independent/chain pharmacies.

Conclusions

Adopting an interdisciplinary approach based on human-centred design principles led to the development of a blended brief intervention that has been successfully introduced in pilot sites across Ireland. While the implementation has been smooth despite COVID-19 challenges, and initial feedback has been very positive, the impact cannot yet be fully evaluated as research is ongoing. Future work will involve extending the intervention to include other healthcare professionals.

References

1. Making Every Contact Count Framework https://www.hse.ie/eng/about/who/healthwellbeing/making-every-contact-count/framework/framework.html (accessed Oct 10, 2020)

2. Keyworth C, Epton T, Goldthorpe J, Calam R, Armitage CJ. ‘It's difficult, I think it's complicated’: Health care professionals’ barriers and enablers to providing opportunistic behaviour change interventions during routine medical consultations. British journal of health psychology. 2019 Sep;24(3):571–92.

The psychological impact of the secondary school transition on families of autistic children

The transition from primary to secondary school is a stressful period for autistic individuals. However, less is known about parental experiences of the school transition, and its impact on the family. This study explored mothers' perspectives on the psychological impact of the transition to secondary school for their autistic children and their families. Using Interpretative Phenomenological Analysis, semi-structured interviews were analysed to explore the experiences of eight mothers of autistic children at the end of their child's first year in secondary school. The analysis revealed two superordinate themes: lack of available support and detrimental psychological impact on the family. Mothers reported the negative impact the transition had on themselves, their child, and the wider family. The importance of pre- and ongoing transition support was highlighted to reduce the concerns of children and their parents throughout the transition process. The findings highlighted the need for autism-specific individualized guidance, as well as considering the potential for transition issues to impact on siblings.

Optical-Clock-Based Time Scale

A time scale is a procedure for accurately and continuously marking the passage of time. It is exemplified by Coordinated Universal Time (UTC) and provides the backbone for critical navigation tools such as the Global Positioning System. Present time scales employ microwave atomic clocks, whose attributes can be combined and averaged in a manner such that the composite is more stable, accurate, and reliable than the output of any individual clock. Over the past decade, clocks operating at optical frequencies have been introduced that are orders of magnitude more stable than any microwave clock. However, in spite of their great potential, these optical clocks cannot be operated continuously, which makes their use in a time scale problematic. We report the development of a hybrid microwave-optical time scale, which only requires the optical clock to run intermittently while relying upon the ensemble of microwave clocks to serve as the flywheel oscillator. The benefit of using a clock ensemble as the flywheel oscillator instead of a single clock can be understood by the Dick-effect limit. This time scale demonstrates for the first time subnanosecond accuracy over a few months, attaining a fractional frequency stability of 1.45 × 10-16 at 30 days and reaching the 10-17 decade at 50 days, with respect to UTC. This time scale significantly improves the accuracy in timekeeping and could change the existing time-scale architectures.