Disentangling the Gordian knot of local metabolic control of coronary blood flow.

Recognition that coronary blood flow is tightly coupled with myocardial metabolism has been appreciated for well over half a century. However, exactly how coronary microvascular resistance is tightly coupled with myocardial oxygen consumption (MV̇o2) remains one of the most highly contested mysteries of the coronary circulation to this day. Understanding the mechanisms responsible for local metabolic control of coronary blood flow has been confounded by continued debate regarding both anticipated experimental outcomes and data interpretation. For a number of years, coronary venous Po2 has been generally accepted as a measure of myocardial tissue oxygenation and thus the classically proposed error signal for the generation of vasodilator metabolites in the heart. However, interpretation of changes in coronary venous Po2 relative to MV̇o2 are quite nuanced, inherently circular in nature, and subject to confounding influences that remain largely unaccounted for. The purpose of this review is to highlight difficulties in interpreting the complex interrelationship between key coronary outcome variables and the arguments that emerge from prior studies performed during exercise, hemodilution, hypoxemia, and alterations in perfusion pressure. Furthermore, potential paths forward are proposed to help to facilitate further dialogue and study to ultimately unravel what has become the Gordian knot of the coronary circulation.

Inhibition of sodium-glucose cotransporter-2 preserves cardiac function during regional myocardial ischemia independent of alterations in myocardial substrate utilization.

The goal of the present study was to evaluate the effects of SGLT2i on cardiac contractile function, substrate utilization, and efficiency before and during regional myocardial ischemia/reperfusion injury in normal, metabolically healthy swine. Lean swine received placebo or canagliflozin (300 mg PO) 24 h prior to and the morning of an invasive physiologic study protocol. Hemodynamic and cardiac function measurements were obtained at baseline, during a 30-min complete occlusion of the circumflex coronary artery, and during a 2-h reperfusion period. Blood pressure, heart rate, coronary flow, and myocardial oxygen consumption were unaffected by canagliflozin treatment. Ventricular volumes remained unchanged in controls throughout the protocol. At the onset of ischemia, canagliflozin produced acute large increases in left ventricular end-diastolic and systolic volumes which returned to baseline with reperfusion. Canagliflozin-mediated increases in end-diastolic volume were directly associated with increases in stroke volume and stroke work relative to controls during ischemia. Canagliflozin also increased cardiac work efficiency during ischemia relative to control swine. No differences in myocardial uptake of glucose, lactate, free fatty acids or ketones, were noted between treatment groups at any time. In separate experiments using a longer 60 min coronary occlusion followed by 2 h of reperfusion, canagliflozin increased end-diastolic volume and stroke volume and significantly diminished myocardial infarct size relative to control swine. These data demonstrate that SGLT2i with canagliflozin preserves cardiac contractile function and efficiency during regional myocardial ischemia and provides ischemia protection independent of alterations in myocardial substrate utilization.

Local metabolic hypothesis is not sufficient to explain coronary autoregulatory behavior.

The local metabolic hypothesis proposes that myocardial oxygen tension determines the degree of autoregulation by increasing the production of vasodilator metabolites as perfusion pressure is reduced. Thus, normal physiologic levels of coronary venous PO2, an index of myocardial oxygenation, are proposed to be required for effective autoregulation. The present study challenged this hypothesis through determination of coronary responses to changes in coronary perfusion pressure (CPP 140-40 mmHg) in open-chest swine in the absence (n = 7) and presence of euvolemic hemodilution (~ 50% reduction in hematocrit), with (n = 5) and without (n = 6) infusion of dobutamine to augment MVO2. Coronary venous PO2 decreased over similar ranges (~ 28-15 mmHg) as CPP was lowered from 140 to 40 mmHg in each of the groups. However, coronary venous PO2 was not associated with changes in coronary blood flow (r = - 0.11; P = 0.29) or autoregulatory gain (r = - 0.29; P = 0.12). Coronary zero-flow pressure (Pzf) was measured in 20 mmHg increments and determined to be directly related to vascular resistance (r = 0.71; P < 0.001). Further analysis demonstrated that changes in coronary blood flow remained minimal at Pzf > 20 mmHg, but progressively increased as Pzf decreased below this threshold value (r = 0.68; P < 0.001). Coronary Pzf was also positively correlated with autoregulatory gain (r = 0.43; P = 0.001). These findings support that coronary autoregulatory behavior is predominantly dependent on an adequate degree of underlying vasomotor tone, independent of normal myocardial oxygen tension.

Computational Fluid Dynamics of Vascular Disease in Animal Models.

Recent applications of computational fluid dynamics (CFD) applied to the cardiovascular system have demonstrated its power in investigating the impact of hemodynamics on disease initiation, progression, and treatment outcomes. Flow metrics such as pressure distributions, wall shear stresses (WSS), and blood velocity profiles can be quantified to provide insight into observed pathologies, assist with surgical planning, or even predict disease progression. While numerous studies have performed simulations on clinical human patient data, it often lacks prediagnosis information and can be subject to large intersubject variability, limiting the generalizability of findings. Thus, animal models are often used to identify and manipulate specific factors contributing to vascular disease because they provide a more controlled environment. In this review, we explore the use of CFD in animal models in recent studies to investigate the initiating mechanisms, progression, and intervention effects of various vascular diseases. The first section provides a brief overview of the CFD theory and tools that are commonly used to study blood flow. The following sections are separated by anatomical region, with the abdominal, thoracic, and cerebral areas specifically highlighted. We discuss the associated benefits and obstacles to performing CFD modeling in each location. Finally, we highlight animal CFD studies focusing on common surgical treatments, including arteriovenous fistulas (AVF) and pulmonary artery grafts. The studies included in this review demonstrate the value of combining CFD with animal imaging and should encourage further research to optimize and expand upon these techniques for the study of vascular disease.

Regulation of myocardial oxygen delivery in response to graded reductions in hematocrit: role of K+ channels.

This study was designed to identify mechanisms responsible for coronary vasodilation in response to progressive decreases in hematocrit. Isovolemic hemodilution was produced in open-chest, anesthetized swine via concurrent removal of 500 ml of arterial blood and the addition of 500 ml of 37 °C saline or synthetic plasma expander (Hespan, 6% hetastarch in 0.9% sodium chloride). Progressive hemodilution with Hespan resulted in an increase in coronary flow from 0.39 ± 0.05 to 1.63 ± 0.16 ml/min/g (P < 0.001) as hematocrit was reduced from 32 ± 1 to 10 ± 1% (P < 0.001). Overall, coronary flow corresponded with the level of myocardial oxygen consumption, was dependent on arterial pressures ≥ ~ 60 mmHg, and occurred with little/no change in coronary venous PO2. Anemic coronary vasodilation was unaffected by the inhibition of nitric oxide synthase (L-NAME: 25 mg/kg iv; P = 0.92) or voltage-dependent K+ (K V) channels (4-aminopyridine: 0.3 mg/kg iv; P = 0.52). However, administration of the K ATP channel antagonist (glibenclamide: 3.6 mg/kg iv) resulted in an ~ 40% decrease in coronary blood flow (P < 0.001) as hematocrit was reduced to ~ 10%. These reductions in coronary blood flow corresponded with significant reductions in myocardial oxygen delivery at baseline and throughout isovolemic anemia (P < 0.001). These data indicate that vasodilator factors produced in response to isovolemic hemodilution converge on vascular smooth muscle glibenclamide-sensitive (K ATP) channels to maintain myocardial oxygen delivery and that this response is not dependent on endothelial-derived nitric oxide production or pathways that mediate dilation via K V channels.

Leptin augments coronary vasoconstriction and smooth muscle proliferation via a Rho-kinase-dependent pathway.

Leptin has been implicated as a key upstream mediator of pathways associated with coronary vascular dysfunction and disease. The purpose of this investigation was to test the hypothesis that leptin modifies the coronary artery proteome and promotes increases in coronary smooth muscle contraction and proliferation via influences on Rho kinase signaling. Global proteomic assessment of coronary arteries from lean swine cultured with obese concentrations of leptin (30 ng/mL) for 3 days revealed significant alterations in the coronary artery proteome (68 proteins) and identified an association between leptin treatment and calcium signaling/contraction (four proteins) and cellular growth and proliferation (35 proteins). Isometric tension studies demonstrated that both acute (30 min) and chronic (3 days, serum-free media) exposure to obese concentrations of leptin potentiated depolarization-induced contraction of coronary arteries. Inhibition of Rho kinase significantly reduced leptin-mediated increases in coronary artery contractions. The effects of leptin on the functional expression of Rho kinase were time-dependent, as acute treatment increased Rho kinase activity while chronic (3 day) exposure was associated with increases in Rho kinase protein abundance. Proliferation assays following chronic leptin administration (8 day, serum-containing media) demonstrated that leptin augmented coronary vascular smooth muscle proliferation and increased Rho kinase activity. Inhibition of Rho kinase significantly reduced these effects of leptin. Taken together, these findings demonstrate that leptin promotes increases in coronary vasoconstriction and smooth muscle proliferation and indicate that these phenotypic effects are associated with alterations in the coronary artery proteome and dynamic effects on the Rho kinase pathway.

The LIFE-Adult-Study: objectives and design of a population-based cohort study with 10,000 deeply phenotyped adults in Germany.

BACKGROUND: The LIFE-Adult-Study is a population-based cohort study, which has recently completed the baseline examination of 10,000 randomly selected participants from Leipzig, a major city with 550,000 inhabitants in the east of Germany. It is the first study of this kind and size in an urban population in the eastern part of Germany. The study is conducted by the Leipzig Research Centre for Civilization Diseases (LIFE). Our objective is to investigate prevalences, early onset markers, genetic predispositions, and the role of lifestyle factors of major civilization diseases, with primary focus on metabolic and vascular diseases, heart function, cognitive impairment, brain function, depression, sleep disorders and vigilance dysregulation, retinal and optic nerve degeneration, and allergies. METHODS/DESIGN: The study covers a main age range from 40-79 years with particular deep phenotyping in elderly participants above the age of 60. The baseline examination was conducted from August 2011 to November 2014. All participants underwent an extensive core assessment programme (5-6 h) including structured interviews, questionnaires, physical examinations, and biospecimen collection. Participants over 60 underwent two additional assessment programmes (3-4 h each) on two separate visits including deeper cognitive testing, brain magnetic resonance imaging, diagnostic interviews for depression, and electroencephalography. DISCUSSION: The participation rate was 33 %. The assessment programme was accepted well and completely passed by almost all participants. Biomarker analyses have already been performed in all participants. Genotype, transcriptome and metabolome analyses have been conducted in subgroups. The first follow-up examination will commence in 2016.

TRPC3 regulates release of brain-derived neurotrophic factor from human airway smooth muscle.

Exogenous brain-derived neurotrophic factor (BDNF) enhances Ca(2+) signaling and cell proliferation in human airway smooth muscle (ASM), especially with inflammation. Human ASM also expresses BDNF, raising the potential for autocrine/paracrine effects. The mechanisms by which ASM BDNF secretion occurs are not known. Transient receptor potential channels (TRPCs) regulate a variety of intracellular processes including store-operated Ca(2+) entry (SOCE; including in ASM) and secretion of factors such as cytokines. In human ASM, we tested the hypothesis that TRPC3 regulates BDNF secretion. At baseline, intracellular BDNF was present, and BDNF secretion was detectable by enzyme linked immunosorbent assay (ELISA) of cell supernatants or by real-time fluorescence imaging of cells transfected with GFP-BDNF vector. Exposure to the pro-inflammatory cytokine tumor necrosis factor-alpha (TNFα) (20ng/ml, 48h) or a mixture of allergens (ovalbumin, house dust mite, Alternaria, and Aspergillus extracts) significantly enhanced BDNF secretion and increased TRPC3 expression. TRPC3 knockdown (siRNA or inhibitor Pyr3; 10µM) blunted BDNF secretion, and prevented inflammation effects. Chelation of extracellular Ca(2+) (EGTA; 1mM) or intracellular Ca(2+) (BAPTA; 5µM) significantly reduced secreted BDNF, as did the knockdown of SOCE proteins STIM1 and Orai1 or plasma membrane caveolin-1. Functionally, secreted BDNF had autocrine effects suggested by phosphorylation of high-affinity tropomyosin-related kinase TrkB receptor, prevented by chelating extracellular BDNF with chimeric TrkB-Fc. These data emphasize the role of TRPC3 and Ca(2+) influx in the regulation of BDNF secretion by human ASM and the enhancing effects of inflammation. Given the BDNF effects on Ca(2+) and cell proliferation, BDNF secretion may contribute to altered airway structure and function in diseases such as asthma.

Cigarette smoke-induced mitochondrial fragmentation and dysfunction in human airway smooth muscle.

The balance between mitochondrial fission and fusion is crucial for mitochondria to perform its normal cellular functions. We hypothesized that cigarette smoke (CS) disrupts this balance and enhances mitochondrial dysfunction in the airway. In nonasthmatic human airway smooth muscle (ASM) cells, CS extract (CSE) induced mitochondrial fragmentation and damages their networked morphology in a concentration-dependent fashion, via increased expression of mitochondrial fission protein dynamin-related protein 1 (Drp1) and decreased fusion protein mitofusin (Mfn) 2. CSE effects on Drp1 vs. Mfn2 and mitochondrial network morphology involved reactive oxygen species (ROS), activation of extracellular signal-regulated kinase (ERK), phosphatidylinositol 3-kinase (PI3K)/protein kinase B (Akt), protein kinase C (PKC) and proteasome pathways, as well as transcriptional regulation via factors such as NF-κB and nuclear erythroid 2-related factor 2. Inhibiting Drp1 prevented CSE effects on mitochondrial networks and ROS generation, whereas blocking Mfn2 had the opposite, detrimental effect. In ASM from asmatic patients, mitochondria exhibited substantial morphological defects at baseline and showed increased Drp1 but decreased Mfn2 expression, with exacerbating effects of CSE. Overall, these results highlight the importance of mitochondrial networks and their regulation in the context of cellular changes induced by insults such as inflammation (as in asthma) or CS. Altered mitochondrial fission/fusion proteins have a further potential to influence parameters such as ROS and cell proliferation and apoptosis relevant to airway diseases.

Observation of unusual molecular diffusion behaviour below the lower critical solution temperature of water/2-butoxyethanol mixtures by using fluorescence correlation spectroscopy.

The effect of solute affinity on solute diffusion in binary liquids well below the lower critical solution temperature (LCST) was studied by using fluorescence correlation spectroscopy. We measured the hydrodynamic radii of a hydrophobic and an amphiphilic fluorescent dye under systematic variation of the relative molar fractions of water/2-butoxyethanol and, for comparison, of water/methanol mixtures, which do not show phase separation. We found that the apparent hydrodynamic radius of the hydrophobic dye almost doubled in water/2-butoxyethanol, whereas it remained largely unchanged for the amphiphilic dye and in water/methanol mixtures. Our results indicate that the translational diffusion of solutes is influenced by transient local solution structures, even at temperatures well below the LCST. We conclude that, even far below LCST, different solutes can experience different environments in binary liquid mixtures depending on both the solute and solvent properties, all of which impact their reactivity.

The sample locator: A federated search tool for biosamples and associated data in Europe using HL7 FHIR.

BACKGROUND: This study outlines the development of a highly interoperable federated IT infrastructure for academic biobanks located at the major university hospital sites across Germany. High-quality biosamples linked to clinical data, stored in biobanks are essential for biomedical research. We aimed to facilitate the findability of these biosamples and their associated data. Networks of biobanks provide access to even larger pools of samples and data even from rare diseases and small disease subgroups. The German Biobank Alliance (GBA) established in 2017 under the umbrella of the German Biobank Node (GBN), has taken on the mission of a federated data discovery service to make biosamples and associated data available to researchers across Germany and Europe. METHODS: In this context, we identified the requirements of researchers seeking human biosamples from biobanks and the needs of biobanks for data sovereignty over their samples and data in conjunction with the sample donor's consent. Based on this, we developed a highly interoperable federated IT infrastructure using standards such as Fast Healthcare Interoperability Resources (HL7 FHIR) and Clinical Quality Language (CQL). RESULTS: The infrastructure comprises two major components enabling federated real-time access to biosample metadata, allowing privacy-compliant queries and subsequent project requests. It has been in use since 2019, connecting 16 German academic biobanks, with additional European biobanks joining. In production since 2019 it has run 4941 queries over the span of one year on more than 900,000 biosamples collected from more than 170,000 donors. CONCLUSION: This infrastructure enhances the visibility and accessibility of biosamples for research, addressing the growing demand for human biosamples and associated data in research. It also underscores the need for improvements in processes beyond IT infrastructure, aiming to advance biomedical research and similar infrastructure development in other fields.

Generation of a Fast Healthcare Interoperability Resources (FHIR)-based Ontology for Federated Feasibility Queries in the Context of COVID-19: Feasibility Study.

BACKGROUND: The COVID-19 pandemic highlighted the importance of making research data from all German hospitals available to scientists to respond to current and future pandemics promptly. The heterogeneous data originating from proprietary systems at hospitals' sites must be harmonized and accessible. The German Corona Consensus Dataset (GECCO) specifies how data for COVID-19 patients will be standardized in Fast Healthcare Interoperability Resources (FHIR) profiles across German hospitals. However, given the complexity of the FHIR standard, the data harmonization is not sufficient to make the data accessible. A simplified visual representation is needed to reduce the technical burden, while allowing feasibility queries. OBJECTIVE: This study investigates how a search ontology can be automatically generated using FHIR profiles and a terminology server. Furthermore, it describes how this ontology can be used in a user interface (UI) and how a mapping and a terminology tree created together with the ontology can translate user input into FHIR queries. METHODS: We used the FHIR profiles from the GECCO data set combined with a terminology server to generate an ontology and the required mapping files for the translation. We analyzed the profiles and identified search criteria for the visual representation. In this process, we reduced the complex profiles to code value pairs for improved usability. We enriched our ontology with the necessary information to display it in a UI. We also developed an intermediate query language to transform the queries from the UI to federated FHIR requests. Separation of concerns resulted in discrepancies between the criteria used in the intermediate query format and the target query language. Therefore, a mapping was created to reintroduce all information relevant for creating the query in its target language. Further, we generated a tree representation of the ontology hierarchy, which allows resolving child concepts in the process. RESULTS: In the scope of this project, 82 (99%) of 83 elements defined in the GECCO profile were successfully implemented. We verified our solution based on an independently developed test patient. A discrepancy between the test data and the criteria was found in 6 cases due to different versions used to generate the test data and the UI profiles, the support for specific code systems, and the evaluation of postcoordinated Systematized Nomenclature of Medicine (SNOMED) codes. Our results highlight the need for governance mechanisms for version changes, concept mapping between values from different code systems encoding the same concept, and support for different unit dimensions. CONCLUSIONS: We developed an automatic process to generate ontology and mapping files for FHIR-formatted data. Our tests found that this process works for most of our chosen FHIR profile criteria. The process established here works directly with FHIR profiles and a terminology server, making it extendable to other FHIR profiles and demonstrating that automatic ontology generation on FHIR profiles is feasible.

The Architecture of a Feasibility Query Portal for Distributed COVID-19 Fast Healthcare Interoperability Resources (FHIR) Patient Data Repositories: Design and Implementation Study.

BACKGROUND: An essential step in any medical research project after identifying the research question is to determine if there are sufficient patients available for a study and where to find them. Pursuing digital feasibility queries on available patient data registries has proven to be an excellent way of reusing existing real-world data sources. To support multicentric research, these feasibility queries should be designed and implemented to run across multiple sites and securely access local data. Working across hospitals usually involves working with different data formats and vocabularies. Recently, the Fast Healthcare Interoperability Resources (FHIR) standard was developed by Health Level Seven to address this concern and describe patient data in a standardized format. The Medical Informatics Initiative in Germany has committed to this standard and created data integration centers, which convert existing data into the FHIR format at each hospital. This partially solves the interoperability problem; however, a distributed feasibility query platform for the FHIR standard is still missing. OBJECTIVE: This study described the design and implementation of the components involved in creating a cross-hospital feasibility query platform for researchers based on FHIR resources. This effort was part of a large COVID-19 data exchange platform and was designed to be scalable for a broad range of patient data. METHODS: We analyzed and designed the abstract components necessary for a distributed feasibility query. This included a user interface for creating the query, backend with an ontology and terminology service, middleware for query distribution, and FHIR feasibility query execution service. RESULTS: We implemented the components described in the Methods section. The resulting solution was distributed to 33 German university hospitals. The functionality of the comprehensive network infrastructure was demonstrated using a test data set based on the German Corona Consensus Data Set. A performance test using specifically created synthetic data revealed the applicability of our solution to data sets containing millions of FHIR resources. The solution can be easily deployed across hospitals and supports feasibility queries, combining multiple inclusion and exclusion criteria using standard Health Level Seven query languages such as Clinical Quality Language and FHIR Search. Developing a platform based on multiple microservices allowed us to create an extendable platform and support multiple Health Level Seven query languages and middleware components to allow integration with future directions of the Medical Informatics Initiative. CONCLUSIONS: We designed and implemented a feasibility platform for distributed feasibility queries, which works directly on FHIR-formatted data and distributed it across 33 university hospitals in Germany. We showed that developing a feasibility platform directly on the FHIR standard is feasible.

APERITIF - Automatic Patient Recruiting for Clinical Trials Based on HL7 FHIR.

Clinical trials are carried out to prove the safety and effectiveness of new interventions and therapies. As diseases and their causes continue to become more specific, so do inclusion and exclusion criteria for trials. Patient recruitment has always been a challenge, but with medical progress, it becomes increasingly difficult to achieve the necessary number of cases. In Germany, the Medical Informatics Initiative is planning to use the central application and registration office to conduct feasibility analyses at an early stage and thus to identify suitable project partners. This approach aims to technically adapt/integrate the envisioned infrastructure in such a way that it can be used for trial case number estimation for the planning of multicenter clinical trials. We have developed a fully automated solution called APERITIF that can identify the number of eligible patients based on free-text eligibility criteria, taking into account the MII core data set and based on the FHIR standard. The evaluation showed a precision of 62.64 % for inclusion criteria and a precision of 66.45 % for exclusion criteria.

Desiderata for a Synthetic Clinical Data Generator.

The current movement in Medical Informatics towards comprehensive Electronic Health Records (EHRs) has enabled a wide range of secondary use cases for this data. However, due to a number of well-justified concerns and barriers, especially with regards to information privacy, access to real medical records by researchers is often not possible, and indeed not always required. An appealing alternative to the use of real patient data is the employment of a generator for realistic, yet synthetic, EHRs. However, we have identified a number of shortcomings in prior works, especially with regards to the adaptability of the projects to the requirements of the German healthcare system. Based on three case studies, we define a non-exhaustive list of requirements for an ideal generator project that can be used in a wide range of localities and settings, to address and enable future work in this regard.

Oncology on FHIR: A Data Model for Distributed Cancer Research.

In the field of oncology, a close integration of cancer research and patient care is indispensable. Although an exchange of data between health care providers and other institutions such as cancer registries has already been established in Germany, it does not take advantage of internationally coordinated health data standards. Translational cancer research would also benefit from such standards in the context of secondary data use. This paper employs use cases from the German Cancer Consortium (DKTK) to show how this gap can be closed using a harmonised FHIR-based data model, and how to apply it to an existing federated data platform.

Ontological Modelling and Execution of Phenotypic Queries in the Leipzig Health Atlas.

Sharing data is of great importance for research in medical sciences. It is the basis for reproducibility and reuse of already generated outcomes in new projects and in new contexts. FAIR data principles are the basics for sharing data. The Leipzig Health Atlas (LHA) platform follows these principles and provides data, describing metadata, and models that have been implemented in novel software tools and are available as demonstrators. LHA reuses and extends three different major components that have been previously developed by other projects. The SEEK management platform is the foundation providing a repository for archiving, presenting and secure sharing a wide range of publication results, such as published reports, (bio)medical data as well as interactive models and tools. The LHA Data Portal manages study metadata and data allowing to search for data of interest. Finally, PhenoMan is an ontological framework for phenotype modelling. This paper describes the interrelation of these three components. In particular, we use the PhenoMan to, firstly, model and represent phenotypes within the LHA platform. Then, secondly, the ontological phenotype representation can be used to generate search queries that are executed by the LHA Data Portal. The PhenoMan generates the queries in a novel domain specific query language (SDQL), which is specific for data management systems based on CDISC ODM standard, such as the LHA Data Portal. Our approach was successfully applied to represent phenotypes in the Leipzig Health Atlas with the possibility to execute corresponding queries within the LHA Data Portal.

Fluorescent probes and delivery methods for single-molecule experiments.

The recent explosion in papers utilising single-molecule experiments pushes the envelope further for increased spatial and temporal resolution. In order to achieve this, a combination of novel fluorescent probes and spectroscopy techniques are required. Herein, we provide an overview on our contribution to developments in the field of fluorescent probes along with a palette of alternative delivery methods for introducing the probes into living cells. We discuss probe requirements arising from the use of single-molecule spectroscopy methods and the customisation of probes that depends on the target molecule, the chemical state of the molecule as well as the distance and the type of interaction between sensor and ligand. We explain how Förster resonance energy transfer (FRET) and photon-induced electron transfer (PET) can increase the probe customisation. We also discuss additional requirements that arise when performing experiments in living cells like toxicity and cell permeability. Regarding the latter, we devote a special paragraph on the different ways to introduce the desired probe into the cell and how the different properties of each probe and cell type may require different delivery methods. We offer insights based on our experience working with a variety of single-molecule methods, fluorescent probes and delivery systems. Overall, we encompass the latest developments on probe design and delivery and illustrate that the wealth of information provided by single-molecule studies goes along with increased complexity.

Experimental approach to extend the range for counting fluorescent molecules based on photon-antibunching.

In single-molecule fluorescence spectroscopy photon-antibunching is frequently used to prove the occurrence of single fluorophores. Furthermore, the relative frequency of coincident photon pairs was also used to determine the number of fluorophores in the diffraction limited observation volume of a confocal microscope. However, the ability to count fluorophores is so far limited to approximately 3 molecules due to saturation of the calibration curve with increasing number of fluorophores. Recently, we introduced a novel theoretical framework for counting the number of emitting molecules by analyzing photon-distributions acquired with a confocal microscope using four single-photon detectors. Here, we present the experimental realization of the proposed scheme in a confocal setup using novel multi-channel photon-counting electronics and DNA constructs that were labelled with five fluorophores. Our experimental results give a clear correlation between the number of estimated fluorophores and the number of bleaching steps for DNA probes conjugated with five ATTO647N labels with an error of approximately 20%. Moreover, we could acquire experimental data for up to 15 fluorophores indicating the simultaneous occurrence of three DNA probes. Our experiments put into perspective that the analysis of photon-distributions acquired with four detection channels is suited to count the number of fluorescently labelled molecules in larger aggregates or clusters with potential for applications in molecular and cell biology and for time-resolved analysis of multi-chromophoric compounds in material sciences.