Basophil activation test with progressively less heated forms of egg distinguishes egg allergic from tolerant children

BACKGROUND AND OBJECTIVE

Diagnosis of egg allergy through basophil activation testing (BAT) has been mainly performed with an egg white extract or individual egg allergens rather than clinically more representative whole-egg extracts. Impact of heating on whole-egg extract allergenicity remains unassessed.Validating BAT with gradually less heated whole-egg extracts in egg allergy diagnosis and as tolerance marker.

METHODS

CD63-based BAT was performed with five progressively less heated extracts from cake, hard-boiled egg, omelet, soft-boiled, and raw egg in 10 egg allergic (EA), 10 complete egg tolerant (ET) and 12 non-egg-sensitized non-allergic (NEA) children. Cutoffs and diagnostic accuracy measures were established through ROC analysis. Changes in basophil response were assessed in 12 baked egg tolerant children undergoing an 8-month gradual egg reintroduction protocol with BAT and oral food challenges prior to each reintroduction step.

RESULTS

Basophil responses to all egg extracts were increased in EA, but not in ET and NEA children. Responses decreased progressively with more heated egg extracts. Compared to ET children, EA children showed higher basophil sensitivity for all egg extracts. Negative BAT responses predicted clinical tolerance with a 90-100% sensitivity, 100% specificity, and false positive rate of 2.78%. In comparison, egg sIgE's (<0.35 kUA/L) had a lower specificity of 50-78% with a false positive rate of 40%. Basophil reactivity and sensitivity tended to decrease in baked egg tolerant children undergoing gradual egg reintroduction, concurrent with tolerance development.

CONCLUSION

BAT with progressively less heated egg preparations is a sensitive and highly specific tool to discriminate EA from ET children.

Conditionally unutilized proteins and their profound effects on growth and adaptation across microbial species

Protein synthesis is an important determinant of microbial growth and response that demands a high amount of metabolic and biosynthetic resources. Despite these costs, microbial species from different taxa and habitats massively synthesize proteins that are not utilized in the conditions they currently experience. Based on resource allocation models, recent studies have begun to reconcile the costs and benefits of these conditionally unutilized proteins (CUPs) in the context of varying environmental conditions. Such massive synthesis of CUPs is crucial to consider in different areas of modern microbiology, from the systematic investigation of cell physiology, via the prediction of evolution in laboratory and natural environments, to the rational design of strains in biotechnology applications.

Surgical Myocardial Revascularization with a Composite T-graft from the Left Internal Mammary Artery-Comparison of the Great Saphenous Vein with the Radial Artery

BACKGROUND

 Composite T-grafts between left internal mammary artery (LIMA) and radial artery (RA) are a common concept in complete arterial myocardial revascularization. The aim of the present study was to investigate whether the use of the great saphenous vein (SV) instead of RA leads to comparably good results in terms of outcome in this context.

METHODS

 Patients who underwent myocardial revascularization with a T-graft using RA or a segment of SV to the right coronary artery or circumflex artery between the beginning of 2014 and the end of 2019 at the Department of Cardiovascular Surgery, University Hospital Schleswig-Holstein, Campus Kiel were included. To minimize surgical variation, only patients were observed by a single senior surgeon in the department. Exclusion criteria were previous cardiac surgery, preoperative extracorporeal circulatory support, off-pump surgery, additional aortocoronary bypasses, and cardiac combination procedures.

RESULTS

 A total of 115 patients were studied. In 55 patients, the T-graft was placed between the LIMA and SV, and in 60 patients, the T-graft was placed between the LIMA and RA. Patients in the SV group were older (70.6 ± 7.8 vs. 58.5 ± 10.0 years; p < 0.001), suffered more frequently from non-ST elevation myocardial infarction (12.7 vs. 1.7%; p = 0.027), arterial hypertension (83.6 vs. 61.7%; p = 0.009), and atrial fibrillation (18.2 vs. 1.7%; p = 0.003). They were less likely to be active smokers (16.4 vs. 38.3%; p = 0.009) and less likely to have a history of variceal surgery (0 vs. 15.0%; p = 0.003). Calcification of the ascending aorta was also found more frequently in the saphenous group (18.2 vs. 3.3%, p = 0.009). Operative times and number of distal anastomoses did not differ significantly between the two groups. Postoperative deliriums (16.7 vs. 5.0%; p = 0.043) were observed more frequently in venous patients. Wound healing disorders of the leg (11.1 vs. 0%; p = 0.011) did only occur in SV group and wound infections of the arm only in the RA group. Complete follow-up was achieved in 74.8% of cases. Median follow-up was 60.3 (39.6; 73.2) months. Serious adverse cardiac-cerebral events (19.0 vs. 22.7%; p = 0.675) and mortality (14.5 vs. 6.7%; p = 0.167) did not differ significantly between the groups at follow-up. Myocardial infarction (0 vs. 2.5%; p = 1.000) and stroke (0 vs. 7.5%; p = 0.245) were observed exclusively in RA group. Percutaneous coronary intervention was required in single patients of RA group (0 vs. 15.0%; p = 0.028). No patient from either group underwent repeat coronary artery bypass grafting (CABG). The patients of SV group had angiographically competent grafts and open anastomoses. Graft failure was noted in a single patient in RA group, in which case both grafts and native coronary vessels were stented. Kaplan-Meier analysis revealed no significant survival disadvantage for SV group compared with RA group.

CONCLUSION

 CABG with a composite T-graft between LIMA and a segment of SV may be comparable to bypass surgery with a composite T-graft between LIMA and RA. This might be true in terms of morbidity and mortality over an intermediate-term observation period. The results of our studies give rise to the hypothesis that the decision not to perform aortic bypass anastomosis may be more important than the choice of graft material.

An optimal regulation of fluxes dictates microbial growth in and out of steady-state

Effective coordination of cellular processes is critical to ensure the competitive growth of microbial organisms. Pivotal to this coordination is the appropriate partitioning of cellular resources between protein synthesis via translation and the metabolism needed to sustain it. Here, we extend a low-dimensional allocation model to describe the dynamic regulation of this resource partitioning. At the core of this regulation is the optimal coordination of metabolic and translational fluxes, mechanistically achieved via the perception of charged- and uncharged-tRNA turnover. An extensive comparison with ≈ 60 data sets from Escherichia coli establishes this regulatory mechanism's biological veracity and demonstrates that a remarkably wide range of growth phenomena in and out of steady state can be predicted with quantitative accuracy. This predictive power, achieved with only a few biological parameters, cements the preeminent importance of optimal flux regulation across conditions and establishes low-dimensional allocation models as an ideal physiological framework to interrogate the dynamics of growth, competition, and adaptation in complex and ever-changing environments.

Changing Flows Balance Nutrient Absorption and Bacterial Growth along the Gut

Small intestine motility and its ensuing flow of luminal content impact both nutrient absorption and bacterial growth. To explore this interdependence we introduce a biophysical description of intestinal flow and absorption. Rooted in observations of mice we identify the average flow velocity as the key control of absorption efficiency and bacterial growth, independent of the exact contraction pattern. We uncover self-regulation of contraction and flow in response to nutrients and bacterial levels to promote efficient absorption while restraining detrimental bacterial overgrowth.

Coordination of gene expression with cell size enables Escherichia coli to efficiently maintain motility across conditions

To swim and navigate, motile bacteria synthesize a complex motility machinery involving flagella, motors, and a sensory system. A myriad of studies has elucidated the molecular processes involved, but less is known about the coordination of motility expression with cellular physiology: In Escherichia coli, motility genes are strongly up-regulated in nutrient-poor conditions compared to nutrient-replete conditions; yet a quantitative link to cellular motility has not been developed. Here, we systematically investigated gene expression, swimming behavior, cell growth, and available proteomics data across a broad spectrum of exponential growth conditions. Our results suggest that cells up-regulate the expression of motility genes at slow growth to compensate for reduction in cell size, such that the number of flagella per cell is maintained across conditions. The observed four or five flagella per cell is the minimum number needed to keep the majority of cells motile. This simple regulatory objective allows E. coli cells to remain motile across a broad range of growth conditions, while keeping the biosynthetic and energetic demands to establish and drive the motility machinery at the minimum needed. Given the strong reduction in flagella synthesis resulting from cell size increases at fast growth, our findings also provide a different physiological perspective on bacterial cell size control: A larger cell size at fast growth is an efficient strategy to increase the allocation of cellular resources to the synthesis of those proteins required for biomass synthesis and growth, while maintaining processes such as motility that are only needed on a per-cell basis.

Suboptimal resource allocation in changing environments constrains response and growth in bacteria

To respond to fluctuating conditions, microbes typically need to synthesize novel proteins. As this synthesis relies on sufficient biosynthetic precursors, microbes must devise effective response strategies to manage depleting precursors. To better understand these strategies, we investigate the active response of Escherichia coli to changes in nutrient conditions, connecting transient gene expression to growth phenotypes. By synthetically modifying gene expression during changing conditions, we show how the competition by genes for the limited protein synthesis capacity constrains cellular response. Despite this constraint cells substantially express genes that are not required, trapping them in states where precursor levels are low and the genes needed to replenish the precursors are outcompeted. Contrary to common modeling assumptions, our findings highlight that cells do not optimize growth under changing environments but rather exhibit hardwired response strategies that may have evolved to promote fitness in their native environment. The constraint and the suboptimality of the cellular response uncovered provide a conceptual framework relevant for many research applications, from the prediction of evolution to the improvement of gene circuits in biotechnology.

A traveling-wave solution for bacterial chemotaxis with growth

Bacterial cells navigate their environment by directing their movement along chemical gradients. This process, known as chemotaxis, can promote the rapid expansion of bacterial populations into previously unoccupied territories. However, despite numerous experimental and theoretical studies on this classical topic, chemotaxis-driven population expansion is not understood in quantitative terms. Building on recent experimental progress, we here present a detailed analytical study that provides a quantitative understanding of how chemotaxis and cell growth lead to rapid and stable expansion of bacterial populations. We provide analytical relations that accurately describe the dependence of the expansion speed and density profile of the expanding population on important molecular, cellular, and environmental parameters. In particular, expansion speeds can be boosted by orders of magnitude when the environmental availability of chemicals relative to the cellular limits of chemical sensing is high. Analytical understanding of such complex spatiotemporal dynamic processes is rare. Our analytical results and the methods employed to attain them provide a mathematical framework for investigations of the roles of taxis in diverse ecological contexts across broad parameter regimes.

Cooperation in Microbial Populations: Theory and Experimental Model Systems

Cooperative behavior, the costly provision of benefits to others, is common across all domains of life. This review article discusses cooperative behavior in the microbial world, mediated by the exchange of extracellular products called public goods. We focus on model species for which the production of a public good and the related growth disadvantage for the producing cells are well described. To unveil the biological and ecological factors promoting the emergence and stability of cooperative traits we take an interdisciplinary perspective and review insights gained from both mathematical models and well-controlled experimental model systems. Ecologically, we include crucial aspects of the microbial life cycle into our analysis and particularly consider population structures where ensembles of local communities (subpopulations) continuously emerge, grow, and disappear again. Biologically, we explicitly consider the synthesis and regulation of public good production. The discussion of the theoretical approaches includes general evolutionary concepts, population dynamics, and evolutionary game theory. As a specific but generic biological example, we consider populations of Pseudomonas putida and its regulation and use of pyoverdines, iron scavenging molecules, as public goods. The review closes with an overview on cooperation in spatially extended systems and also provides a critical assessment of the insights gained from the experimental and theoretical studies discussed. Current challenges and important new research opportunities are discussed, including the biochemical regulation of public goods, more realistic ecological scenarios resembling native environments, cell-to-cell signaling, and multispecies communities.

A43 Translational research: NGS metagenomics into clinical diagnostics

As research next-generation sequencing (NGS) metagenomic pipelines transition to clinical diagnostics, the user-base changes from bioinformaticians to biologists, medical doctors, and lab-technicians. Besides the obvious need for benchmarking and assessment of diagnostic outcomes of the pipelines and tools, other focus points remain: reproducibility, data immutability, user-friendliness, portability/scalability, privacy, and a clear audit trail. We have a research metagenomics pipeline that takes raw fastq files and produces annotated contigs, but it is too complicated for non-bioinformaticians. Here, we present preliminary findings in adapting this pipeline for clinical diagnostics. We used information available on relevant fora (www.bioinfo-core.org) and experiences and publications from colleague bioinformaticians in other institutes (COMPARE, UBC, and LUMC). From this information, a robust and user-friendly storage and analysis workflow was designed for non-bioinformaticians in a clinical setting. Via Conda [https://conda.io] and Docker containers [http://www.docker.com], we made our disparate pipeline processes self-contained and reproducible. Furthermore, we moved all pipeline settings into a separate JSON file. After every analysis, the pipeline settings and virtual-environment recipes will be archived (immutably) under a persistent unique identifier. This allows long-term precise reproducibility. Likewise, after every run the raw data and final products will be automatically archived, complying with data retention laws/guidelines. All the disparate processes in the pipeline are parallelized and automated via Snakemake1 (i.e. end-users need no coding skills). In addition, interactive web-reports such as MultiQC [http://multiqc.info] and Krona2 are generated automatically. By combining Snakemake, Conda, and containers, our pipeline is highly portable and easily scaled up for outbreak situations, or scaled down to reduce costs. Since patient privacy is a concern, our pipeline automatically removes human genetic data. Moreover, all source code will be stored on an internal Gitlab server, and, combined with the archived data, ensures a clear audit trail. Nevertheless, challenges remain: (1) reproducible reference databases, e.g. being able to revert to an older version to reproduce old analyses. (2) A user-friendly GUI. (3) Connecting the pipeline and NGS data to in-house LIMS. (4) Efficient long-term storage, e.g. lossless compression algorithms. Nevertheless, this work represents a step forward in making user-friendly clinical diagnostic workflows.

Spatiotemporal establishment of dense bacterial colonies growing on hard agar

The physical interactions of growing bacterial cells with each other and with their surroundings significantly affect the structure and dynamics of biofilms. Here a 3D agent-based model is formulated to describe the establishment of simple bacterial colonies expanding by the physical force of their growth. With a single set of parameters, the model captures key dynamical features of colony growth by non-motile, non EPS-producing E. coli cells on hard agar. The model, supported by experiment on colony growth in different types and concentrations of nutrients, suggests that radial colony expansion is not limited by nutrients as commonly believed, but by mechanical forces. Nutrient penetration instead governs vertical colony growth, through thin layers of vertically oriented cells lifting up their ancestors from the bottom. Overall, the model provides a versatile platform to investigate the influences of metabolic and environmental factors on the growth and morphology of bacterial colonies.

Bacterial growth, flow, and mixing shape human gut microbiota density and composition

The human gut microbiota is highly dynamic, and host physiology and diet exert major influences on its composition. In our recent study, we integrated new quantitative measurements on bacterial growth physiology with a reanalysis of published data on human physiology to build a comprehensive modeling framework. This can generate predictions of how changes in different host factors influence microbiota composition. For instance, hydrodynamic forces in the colon, along with colonic water absorption that manifests as transit time, exert a major impact on microbiota density and composition. This can be mechanistically explained by their effect on colonic pH which directly affects microbiota competition for food. In this addendum, we describe the underlying analysis in more detail. In particular, we discuss the mixing dynamics of luminal content by wall contractions and its implications for bacterial growth and density, as well as the broader implications of our insights for the field of gut microbiota research.

Extracorporeal Membrane Oxygenation (Ecmo): Extended Indications for Artificial Support of Both Heart and Lungs

Extracorporeal membrane oxygenation (ECMO) was used to achieve temporary artificial support in cardiac and pulmonary function in 22 patients from 1987 to September 1990. Standard indications were postcardiotomy cardiogenic shock (n=4), neonatal (n=1) and adult respiratory distress syndrome (n=4). ECMO was also used for extended indications, such as graft failure following heart (n=11) or lung transplantation (n=2). In six of these cases ECMO was instituted as a bridge device to subsequent retransplantation of either the heart (n=4) or one lung (n=2). One out of nine patients supported by ECMO for standard indications, and two out of 13 patients supported for extended indications are long-term survivors. This series illustrates the results with ECMO in emergency situations, in patients under immunosuppressive protocols, or in patients with advanced lung failure requiring almost complete artificial gas exchange. In such complex situations, ECMO does provide stabilization until additional therapeutic measures are in effect. ECMO cannot be recommended for postoperative cardiogenic shock but short-term ECMO support is an accepted method in most cases with graft failure or pulmonary failure or other origin.

Szintigraphischer Nachweis einer stillen Aspiration nach beidseitiger Lungentransplantation

Vorgestellt wird der Fall einer 25jährigen Patientin nach beidseitiger Lungentransplantation und rezidivierenden Pneumonien. Klinisch bestand der Verdacht auf eine stille Aspiration. Szintigraphisch gelang sowohl der Aspirationsnachweis als auch eine Differenzierung hinsichtlich der Genese: direkte oro-pulmonale Aspiration versus Aspiration nach gastro-öspohagealem Reflux.