CD3ζ ITAMs enable ligand discrimination and antagonism by inhibiting TCR signaling in response to low-affinity peptides

The T cell antigen receptor (TCR) contains ten immunoreceptor tyrosine-based activation motif (ITAM) signaling sequences distributed within six CD3 subunits; however, the reason for such structural complexity and multiplicity is unclear. Here we evaluated the effect of inactivating the three CD3ζ chain ITAMs on TCR signaling and T cell effector responses using a conditional 'switch' mouse model. Unexpectedly, we found that T cells expressing TCRs containing inactivated (non-signaling) CD3ζ ITAMs (6F-CD3ζ) exhibited reduced ability to discriminate between low- and high-affinity ligands, resulting in enhanced signaling and cytokine responses to low-affinity ligands because of a previously undetected inhibitory function of CD3ζ ITAMs. Also, 6F-CD3ζ TCRs were refractory to antagonism, as predicted by a new in silico adaptive kinetic proofreading model that revises the role of ITAM multiplicity in TCR signaling. Finally, T cells expressing 6F-CD3ζ displayed enhanced cytolytic activity against solid tumors expressing low-affinity ligands, identifying a new counterintuitive approach to TCR-mediated cancer immunotherapy.

Survey on infectious disease telephone hotlines in primary care: General practitioners' satisfaction and compliance with advice

OBJECTIVES

Infectious disease (ID) advice is a major part of antimicrobial stewardship programs. The objective of this study was to assess general practitioners' (GPs)' opinions and compliance with advice given by ID hotlines.

PATIENTS AND METHODS

This multicenter survey was based on the 7-day assessment of initial advice requested by GPs to a hotline set up by volunteer hospital ID teams to record advice for 3 years. The primary endpoint was the GPs' satisfaction with the advice given by ID specialists.

RESULTS

Ten ID teams participated in the study and recorded 4138 requests for advice, of which 1325 requests included a proposal for antibiotic therapy and justified a follow-up call at seven days. Only 398 follow-up calls (30%) were carried out because many GPs were not reachable. GPs were very satisfied with ID hotlines: 58% considered them indispensable and 38% very useful. The recommendations provided by ID specialists were followed by GPs in more than 80% of cases. The two main motivations for GPs to call the hotline were to get quick advice (86%) and to receive help in managing a patient (76%).

CONCLUSIONS

The ID telephone consultations and advice systems for GPs are highly appreciated and are effective in terms of following the recommendations.

Evolution of cell size control is canalized towards adders or sizers by cell cycle structure and selective pressures

Cell size is controlled to be within a specific range to support physiological function. To control their size, cells use diverse mechanisms ranging from 'sizers', in which differences in cell size are compensated for in a single cell division cycle, to 'adders', in which a constant amount of cell growth occurs in each cell cycle. This diversity raises the question why a particular cell would implement one rather than another mechanism? To address this question, we performed a series of simulations evolving cell size control networks. The size control mechanism that evolved was influenced by both cell cycle structure and specific selection pressures. Moreover, evolved networks recapitulated known size control properties of naturally occurring networks. If the mechanism is based on a G1 size control and an S/G2/M timer, as found for budding yeast and some human cells, adders likely evolve. But, if the G1 phase is significantly longer than the S/G2/M phase, as is often the case in mammalian cells in vivo, sizers become more likely. Sizers also evolve when the cell cycle structure is inverted so that G1 is a timer, while S/G2/M performs size control, as is the case for the fission yeast S. pombe. For some size control networks, cell size consistently decreases in each cycle until a burst of cell cycle inhibitor drives an extended G1 phase much like the cell division cycle of the green algae Chlamydomonas. That these size control networks evolved such self-organized criticality shows how the evolution of complex systems can drive the emergence of critical processes.

Arnold tongue entrainment reveals dynamical principles of the embryonic segmentation clock

Living systems exhibit an unmatched complexity, due to countless, entangled interactions across scales. Here, we aim to understand a complex system, that is, segmentation timing in mouse embryos, without a reference to these detailed interactions. To this end, we develop a coarse-grained approach, in which theory guides the experimental identification of the segmentation clock entrainment responses. We demonstrate period- and phase-locking of the segmentation clock across a wide range of entrainment parameters, including higher-order coupling. These quantifications allow to derive the phase response curve (PRC) and Arnold tongues of the segmentation clock, revealing its essential dynamical properties. Our results indicate that the somite segmentation clock has characteristics reminiscent of a highly non-linear oscillator close to an infinite period bifurcation and suggests the presence of long-term feedbacks. Combined, this coarse-grained theoretical-experimental approach reveals how we can derive simple, essential features of a highly complex dynamical system, providing precise experimental control over the pace and rhythm of the somite segmentation clock.

Universal antigen encoding of T cell activation from high-dimensional cytokine dynamics

Systems immunology lacks a framework with which to derive theoretical understanding from high-dimensional datasets. We combined a robotic platform with machine learning to experimentally measure and theoretically model CD8⁺ T cell activation. High-dimensional cytokine dynamics could be compressed onto a low-dimensional latent space in an antigen-specific manner (so-called "antigen encoding"). We used antigen encoding to model and reconstruct patterns of T cell immune activation. The model delineated six classes of antigens eliciting distinct T cell responses. We generalized antigen encoding to multiple immune settings, including drug perturbations and activation of chimeric antigen receptor T cells. Such universal antigen encoding for T cell activation may enable further modeling of immune responses and their rational manipulation to optimize immunotherapies.

Endocytic proteins with prion-like domains form viscoelastic condensates that enable membrane remodeling

Membrane invagination and vesicle formation are key steps in endocytosis and cellular trafficking. Here, we show that endocytic coat proteins with prion-like domains (PLDs) form hemispherical puncta in the budding yeast, Saccharomyces cerevisiae These puncta have the hallmarks of biomolecular condensates and organize proteins at the membrane for actin-dependent endocytosis. They also enable membrane remodeling to drive actin-independent endocytosis. The puncta, which we refer to as endocytic condensates, form and dissolve reversibly in response to changes in temperature and solution conditions. We find that endocytic condensates are organized around dynamic protein-protein interaction networks, which involve interactions among PLDs with high glutamine contents. The endocytic coat protein Sla1 is at the hub of the protein-protein interaction network. Using active rheology, we inferred the material properties of endocytic condensates. These experiments show that endocytic condensates are akin to viscoelastic materials. We use these characterizations to estimate the interfacial tension between endocytic condensates and their surroundings. We then adapt the physics of contact mechanics, specifically modifications of Hertz theory, to develop a quantitative framework for describing how interfacial tensions among condensates, the membrane, and the cytosol can deform the plasma membrane to enable actin-independent endocytosis.

Pre-existing chromatin accessibility and gene expression differences among naive CD4+ T cells influence effector potential

CD4+ T cells have a remarkable potential to differentiate into diverse effector lineages following activation. Here, we probe the heterogeneity present among naive CD4+ T cells before encountering their cognate antigen to ask whether their effector potential is modulated by pre-existing transcriptional and chromatin landscape differences. Single-cell RNA sequencing shows that key drivers of variability are genes involved in T cell receptor (TCR) signaling. Using CD5 expression as a readout of the strength of tonic TCR interactions with self-peptide MHC, and sorting on the ends of this self-reactivity spectrum, we find that pre-existing transcriptional differences among naive CD4+ T cells impact follicular helper T (TFH) cell versus non-TFH effector lineage choice. Moreover, our data implicate TCR signal strength during thymic development in establishing differences in naive CD4+ T cell chromatin landscapes that ultimately shape their effector potential.

Intracranial primary synovial sarcoma mimicking a spontaneous cerebral hematoma-a case report and review of the literature

BACKGROUND

Synovial sarcoma is a soft tissue sarcoma, of uncertain histological origin, usually located near large joints and concerning mainly young adults. Intracranial presentation in the form of metastasis from a primitive body sarcoma has been rarely reported. However, intracranial primitive synovial sarcoma (IPSS) is extremely rare and only a few cases have been reported in the literature.

CASE DESCRIPTION

We present the case of a 48-year-old man, with no particular medical history, that was referred to our hospital for severe headache with a normal neurological exam and a CT cerebral scan showing a left frontal lobe hematoma. The initial cerebral CT scan didn't show any vascular malformation and the body CT scan was negative for a primitive lesion. A close follow-up with a cerebral MRI three months later, demonstrated a T1 enhanced lesion with an important volume progression. The patient underwent a complete surgical removal of this lesion and the first pathology diagnosis was compatible with a meningioma. After further proofreading by an expert and molecular analysis, the diagnosis of monophasic synovial sarcoma was confirmed. Nine months after the first surgery, the follow-up MRI showed the progressive recurrence of the lesion and in this context the patient underwent a second surgery with total resection of the tumor and frontal thin margin excision. Afterwards, the patient was treated with adjuvant radiotherapy, with a good clinical evolution, and till now the follow-up shows no recurrence.

CONCLUSION

IPSS is an extremely rare sarcoma, with challenging diagnosis and difficult management. Specific molecular analysis is necessary. Complete resection followed by radiotherapy seem to be the most appropriate therapeutic approach. However, the prognosis is still poor. Our case is even rarer because of the initial presentation as a cerebral hematoma.

Security and reliability of CUSTOMBONE cranioplasties: A prospective multicentric study

BACKGROUND

Repairing bone defects generated by craniectomy is a major therapeutic challenge in terms of bone consolidation as well as functional and cognitive recovery. Furthermore, these surgical procedures are often grafted with complications such as infections, breaches, displacements and rejections leading to failure and thus explantation of the prosthesis.

OBJECTIVE

To evaluate cumulative explantation and infection rates following the implantation of a tailored cranioplasty CUSTOMBONE prosthesis made of porous hydroxyapatite. One hundred and ten consecutive patients requiring cranial reconstruction for a bone defect were prospectively included in a multicenter study constituted of 21 centres between December 2012 and July 2014. Follow-up lasted 2 years.

RESULTS

Mean age of patients included in the study was 42±15 years old (y.o), composed mainly by men (57.27%). Explantations of the CUSTOMBONE prosthesis were performed in 13/110 (11.8%) patients, significantly due to infections: 9/13 (69.2%) (p<0.0001), with 2 (15.4%) implant fracture, 1 (7.7%) skin defect and 1 (7.7%) following the mobilization of the implant. Cumulative explantation rates were successively 4.6% (SD 2.0), 7.4% (SD 2.5), 9.4% (SD 2.8) and 11.8% (SD 2.9%) at 2, 6, 12 and 24 months. Infections were identified in 16/110 (14.5%): 8/16 (50%) superficial and 8/16 (50%) deep. None of the following elements, whether demographic characteristics, indications, size, location of the implant, redo surgery, co-morbidities or medical history, were statistically identified as risk factors for prosthesis explantation or infection.

CONCLUSION

Our study provides relevant clinical evidence on the performance and safety of CUSTOMBONE prosthesis in cranial procedures. Complications that are difficulty incompressible mainly occur during the first 6 months, but can appear at a later stage (>1 year). Thus assiduous, regular and long-term surveillances are necessary.

Geometric models for robust encoding of dynamical information into embryonic patterns

During development, cells gradually assume specialized fates via changes of transcriptional dynamics, sometimes even within the same developmental stage. For anterior-posterior (AP) patterning in metazoans, it has been suggested that the gradual transition from a dynamic genetic regime to a static one is encoded by different transcriptional modules. In that case, the static regime has an essential role in pattern formation in addition to its maintenance function. In this work, we introduce a geometric approach to study such transition. We exhibit two types of genetic regime transitions arising through local or global bifurcations, respectively. We find that the global bifurcation type is more generic, more robust, and better preserves dynamical information. This could parsimoniously explain common features of metazoan segmentation, such as changes of periods leading to waves of gene expressions, ‘speed/frequency-gradient’ dynamics, and changes of wave patterns. Geometric approaches appear as possible alternatives to gene regulatory networks to understand development.

A High-Throughput Image Correlation Method for Rapid Analysis of Fluorophore Photoblinking and Photobleaching Rates

Super-resolution fluorescence imaging based on localization microscopy requires tuning the photoblinking properties of fluorescent dyes employed. Missing is a rapid way to analyze the blinking rates of the fluorophore probes. Herein we present an ensemble autocorrelation technique for rapidly and simultaneously measuring photoblinking and bleaching rate constants from a microscopy image time series of fluorescent probes that is significantly faster than individual single-molecule trajectory analysis approaches. Our method is accurate for probe densities typically encountered in single-molecule studies as well as for higher density systems which cannot be analyzed by standard single-molecule techniques. We also show that we can resolve characteristic blinking times that are faster than camera detector exposure times, which cannot be accessed by threshold-based single-molecule approaches due to aliasing. We confirm this through computer simulation and single-molecule imaging data of DNA-Cy5 complexes. Finally, we demonstrate that with sufficient sampling our technique can accurately recover rates from stochastic optical reconstruction microscopy super-resolution data.

Long term surgical results of 154 petroclival meningiomas: A retrospective multicenter study

BACKGROUND

Outcomes of petroclival meningiomas (PCM) (morbidity, permanent cranial nerves deficit, tumor removal and recurrence) are inconsistent in the literature, making it a challenge to predict surgical morbidity.

METHODS

A multicenter study of patients with PCMs larger than 2.5cm between 1984 and 2017 was conducted. The authors retrospectively reviewed the patients' medical records, imaging studies and pathology reports to analyze presentation, surgical approach, neurological outcomes, complications, recurrence rates and predictive factors.

RESULTS

There were 154 patients. The follow-up was 76.8 months on average (range 8-380 months). Gross total resection (GTR) was achieved in 40 (26.0%) patients, subtotal resection (STR) in 101 (65.6%), and partial resection in 13 (8.3%). Six (2.6%) perioperative deaths occurred. The 5-year, 10-year and 15-year progression-free survival (PFS) of GTR and STR with radiation therapy (RT) was similar (100%, 90% and 75%). PFS of STR without adjuvant radiation was associated with progression in 71%, 51% and 31%, respectively. Anterior petrosectomy and combined petrosectomy were associated with higher postoperative CN V and CN VI deficits compared to the retrosigmoid approach. The latter had a significantly higher risk of CN VII, CN VIII and LCN deficit. Temporal lobe dysfunction (seizure and aphasia) were significantly associated with the anterior petrosectomy approach.

CONCLUSIONS

Our study shows that optimal subtotal resection of PCMs associated with postoperative RT or stereotactic radiosurgery results in long-term tumor control to equivalent radical surgery. Case selection and appropriate intraoperative judgement are required to reduce the morbidity.

In Silico Evolution of Biochemical Log-Response

Numerous biological systems are known to harbor a form of logarithmic behavior, from Weber's law to bacterial chemotaxis. Such a log-response allows for sensitivity to small relative variations of biochemical inputs over a large range of concentration values. Here we use a genetic algorithm to evolve biochemical networks displaying a logarithmic response. A quasi-perfect log-response implemented by the same core network evolves in a convergent way across our different in silico replications. The best network is able to fit a logarithm over 4 orders of magnitude with an accuracy of the order of 1%. At the heart of this network, we show that a logarithmic approximation may be implemented with one single nonlinear interaction, that can be interpreted either as multisite phosphorylations or as a ligand induced multimerization. We provide an analytical explanation for the effect and exhibit constraints on parameters. Biological log-response might thus be easier to implement than usually assumed.

φ-evo: A program to evolve phenotypic models of biological networks

Molecular networks are at the core of most cellular decisions, but are often difficult to comprehend. Reverse engineering of network architecture from their functions has proved fruitful to classify and predict the structure and function of molecular networks, suggesting new experimental tests and biological predictions. We present φ-evo, an open-source program to evolve in silico phenotypic networks performing a given biological function. We include implementations for evolution of biochemical adaptation, adaptive sorting for immune recognition, metazoan development (somitogenesis, hox patterning), as well as Pareto evolution. We detail the program architecture based on C, Python 3, and a Jupyter interface for project configuration and network analysis. We illustrate the predictive power of φ-evo by first recovering the asymmetrical structure of the lac operon regulation from an objective function with symmetrical constraints. Second, we use the problem of hox-like embryonic patterning to show how a single effective fitness can emerge from multi-objective (Pareto) evolution. φ-evo provides an efficient approach and user-friendly interface for the phenotypic prediction of networks and the numerical study of evolution itself.

Preventable deaths in a French regional trauma system: A six-year analysis of severe trauma mortality

BACKGROUND

Analyzing mortality in a mature trauma system is useful to improve quality of care of severe trauma patients. Standardization of error reporting can be done using the classification of the Joint Commission on the Accreditation of Healthcare Organizations (JCAHO). The aim of our study was to describe preventable deaths in our trauma system and to classify errors according to the JCAHO taxonomy.

METHODS

We performed a six-year retrospective study using the registry of the Northern French Alps trauma network (TRENAU). Consecutive patients who died in the prehospital field or within their stay at hospital were included. An adjudication committee analyzed deaths to identify preventable or potentially preventable deaths from 2009 to 2014. All errors were classified using the JCAHO taxonomy.

RESULTS

Within the study period, 503 deaths were reported among 7484 consecutive severe trauma patients (overall mortality equal to 6.7%). Seventy-two (14%) deaths were judged as potentially preventable and 36 (7%) deaths as preventable. Using the JACHO taxonomy, 170 errors were reported. These errors were detected both in the prehospital setting and in the hospital phase. Most were related to clinical performance of physicians and consisted of rule-based or knowledge based failures. Prevention or mitigation of errors required an improvement of communication among caregivers.

CONCLUSIONS

Standardization of error reporting is the first step to improve the efficiency of trauma systems. Preventable deaths are frequently related to clinical performance in the early phase of trauma management. Universal strategies are necessary to prevent or mitigate these errors.

Modelling Time-Dependent Acquisition of Positional Information

Theoretical and computational modelling are crucial to understand dynamics of embryonic development. In this tutorial chapter, we describe two models of gene networks performing time-dependent acquisition of positional information under control of a dynamic morphogen: a toy-model of a bistable gene under control of a morphogen, allowing for the numerical computation of a simple Waddington's epigenetic landscape, and a recently published model of gap genes in Tribolium under control of multiple enhancers. We present detailed commented implementations of the models using python and jupyter notebooks.

Untangling the Hairball: Fitness-Based Asymptotic Reduction of Biological Networks

Complex mathematical models of interaction networks are routinely used for prediction in systems biology. However, it is difficult to reconcile network complexities with a formal understanding of their behavior. Here, we propose a simple procedure (called ϕ¯) to reduce biological models to functional submodules, using statistical mechanics of complex systems combined with a fitness-based approach inspired by in silico evolution. The ϕ¯ algorithm works by putting parameters or combination of parameters to some asymptotic limit, while keeping (or slightly improving) the model performance, and requires parameter symmetry breaking for more complex models. We illustrate ϕ¯ on biochemical adaptation and on different models of immune recognition by T cells. An intractable model of immune recognition with close to a hundred individual transition rates is reduced to a simple two-parameter model. The ϕ¯ algorithm extracts three different mechanisms for early immune recognition, and automatically discovers similar functional modules in different models of the same process, allowing for model classification and comparison. Our procedure can be applied to biological networks based on rate equations using a fitness function that quantifies phenotypic performance.

[Treatment of wrinkles of the upper lip by emulsified fat or "Nanofat": Biological and clinical study about 4 cases]

OBJECTIVE

Emulsified fat injection showed its interest in aesthetic facial surgery. The adipose tissue harvested is mechanically emulsified and filtered. The suspension obtained is injected into the dermis through small diameter needles (27 to 30 gauges). The objective of our study was to evaluate the biological composition of emulsified fat and its clinical effectiveness in the treatment of peri-oral wrinkles in 4 patients aged 50 to 59 years.

MATERIAL AND METHOD

Each patient received an intradermal injection of emulsified fat in the peri-oral wrinkles prepared from abdominal fat under local anesthesia. The cell viability, stromal vascular fraction (FVS) composition in emulsified fat and the adipocyte differentiation capacity of mesenchymal stem cells (MSC) were studied. The clinical results were evaluated by standardized photographs, 3D microphotography, confocal microscopy, and self-evaluation of patient satisfaction over a period of 4 months.

RESULTS

The biological study of the emulsified fat found a lysis of all the adipocytes. The mean number of FVS cells was 126,330±2758 cells by cc of emulsified fat with preserved cell viability (85.1±6.84 %) and a good proportion of regeneratives cells (18.77±6.2 %). The clinical study found a tendency to decrease the volume of wrinkles on standardized photography and 3D microphotography no significative. Patients were satisfied with treatment with an average score of 7±1.15/10 to 4 months.

CONCLUSION

Intradermal injection of emulsified fat seems to be an interesting treatment of face wrinkles. Our study has shown its safety, but additional studies seems necessary to confirm its clinical efficacy.

Analysis of the prophages carried by human infecting isolates provides new insight into the evolution of Group B Streptococcus species

OBJECTIVES

Group B Streptococcus (GBS) emerged in the 1970s as a major cause of neonatal infections, and has been increasingly associated with infections in adults since the 1990s. Prophages have been suspected to have driven these epidemiological trends. We have characterized the prophages harboured by 275 human GBS isolates belonging to the major lineages.

METHODS

We applied whole genome sequencing (WGS) to 14 isolates representative of the diversity within GBS species, located and identified their prophages. Using prediction tools, we searched for prophage elements potentially involved with the ability of GBS to infect humans. Using the data obtained by WGS, we designed a PCR-based tool and studied the prophage content of 275 isolates.

RESULTS

WGS of the 14 isolates revealed 22 prophages (i) distributed into six groups (A-F), (ii) similar to phages and prophages from GBS and non-GBS streptococci recovered from livestock, and (iii) carrying genes encoding factors previously associated with host adaptation and virulence. PCR-based detection of prophages revealed the presence of at least one prophage in 72.4% of the 275 isolates and a significant association between neonatal infecting isolates and prophages C, and between adult infecting isolates and prophages A.

CONCLUSIONS

Our results suggest that prophages (possibly animal-associated) have conditioned bacterial adaptation and ability to cause infections in neonates and adults, and support a role of lysogeny with the emergence of GBS as a pathogen in human.

Sorting at embryonic boundaries requires high heterotypic interfacial tension

The establishment of sharp boundaries is essential for segregation of embryonic tissues during development, but the underlying mechanism of cell sorting has remained unclear. Opposing hypotheses have been proposed, either based on global tissue adhesive or contractile properties or on local signalling through cell contact cues. Here we use ectoderm-mesoderm separation in Xenopus to directly evaluate the role of these various parameters. We find that ephrin-Eph-based repulsion is very effective at inducing and maintaining separation, whereas differences in adhesion or contractility have surprisingly little impact. Computer simulations support and generalise our experimental results, showing that a high heterotypic interfacial tension between tissues is key to their segregation. We propose a unifying model, in which conditions of sorting previously considered as driven by differential adhesion/tension should be viewed as suboptimal cases of heterotypic interfacial tension.The mechanisms that cause different cells to segregate into distinct tissues are unclear. Here the authors show in Xenopus that formation of a boundary between two tissues is driven by local tension along the interface rather than by global differences in adhesion or cortical contractility.

Looking at hospitalized persons throughout the prism of the handicap

OBJECTIVE

To describe the disability status of non-selected hospitalized persons.

METHODS AND FINDINGS

We conducted a cross-sectional survey to assess activity limitations of every person older than 18 years hospitalized in a regional university hospital covering all medical fields. Evaluators rated, on a scale from 0 to 4, 22 selected items of the International Classification of Functioning (ICF), covering the 6 following domains: learning and applying knowledge, general tasks and demands, communication, mobility, self-care, and interpersonal interactions and relationships. Univariate and multivariate analyses were performed to analyze the prevalence, severity and profile of the handicap in terms of sociodemographic characteristics and care pathways.

RESULTS

Among 1572 eligible persons, 1267 (81%) were surveyed (mean age 62.7±20.4years; 655 males [51.7%]). Overall, 82% showed at least one activity limitation. For 52%, disability was severe or total for at least one ICF item. Prevalence of disabilities was higher for mobility (75%) and self-care domains (63%). Disability was strongly related to age: age older than 80years versus 18 to 44years (OR=12.8 95% CI 6.4-27.9]; P<0.01). Disability was associated with hospitalization in rehabilitation units (96%; OR=4.3 [95% CI 2.2-5.3]; P<0.01). Severe disability was associated with hospitalization in critical care units (OR=6.7 [CI 3.2-15.1]; P<0.001) and psychiatry units (OR=5.3 [CI 2.7-11.4]; P<0.001).

CONCLUSION

Handicap was common in hospitalized persons, involving all 6 tested ICF activity domains, particularly mobility and self-care. This study alerts care givers, hospital administrators, and in general, people influencing health policies about the need to plan actions to reduce activity limitations of hospitalized persons, whatever the cause of the hospitalization.

Antimicrobial activity of ceftaroline against methicillin-resistant Staphylococcus aureus (MRSA) isolates collected in 2013-2014 at the Geneva University Hospitals

Ceftaroline is a broad-spectrum antibiotic with activity against methicillin-resistant Staphylococcus aureus (MRSA) strains. Ceftaroline susceptibility of an MRSA set archived between 1994 and 2003 in the Geneva University Hospitals detected a high percentage (66 %) of ceftaroline resistance in clonotypes ST228 and ST247 and correlated with mutations in PBP2a. The ceftaroline mechanism of action is based on the inhibition of PBP2a; thus, the identification of PBP2a mutations of recently circulating clonotypes in our institution was investigated. We analyzed ceftaroline susceptibility in MRSA isolates (2013 and 2014) and established that resistant strains correlated with PBP2a mutations and specific clonotypes. Ninety-six MRSA strains were analyzed from independent patients and were isolated from blood cultures (23 %), deep infections (38.5 %), and superficial (skin or wound) infections (38.5 %). This sample showed a ceftaroline minimum inhibitory concentration (MIC) range between 0.25 and 2 μg/ml and disk diameters ranging from 10 to 30 mm, with a majority of strains showing diameters ≥20 mm. Based on the European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints, 76 % (73/96) of isolates showed susceptibility to ceftaroline. Nevertheless, we still observed 24 % (23/96) of resistant isolates (MIC = 2 μg/ml). All resistant isolates were assigned to clonotype ST228 and carried the N146K mutation in PBP2a. Only two ST228 isolates showed ceftaroline susceptibility. The decreasing percentage of ceftaroline-resistant isolates in our hospital can be explained by the decline of ST228 clonotype circulating in our hospital since 2008. We present evidence that ceftaroline is active against recent MRSA strains from our hospital; however, the presence of PBP2a variants in particular clonotypes may affect ceftaroline efficacy.

Multiscale quantification of tissue behavior during amniote embryo axis elongation

Embryonic axis elongation is a complex multi-tissue morphogenetic process responsible for the formation of the posterior part of the amniote body. How movements and growth are coordinated between the different posterior tissues (e.g. neural tube, axial and paraxial mesoderm, lateral plate, ectoderm, endoderm) to drive axis morphogenesis remain largely unknown. Here, we use quail embryos to quantify cell behavior and tissue movements during elongation. We quantify the tissue-specific contribution to axis elongation by using 3D volumetric techniques, then quantify tissue-specific parameters such as cell density and proliferation. To study cell behavior at a multi-tissue scale, we used high-resolution 4D imaging of transgenic quail embryos expressing fluorescent proteins. We developed specific tracking and image analysis techniques to analyze cell motion and compute tissue deformations in 4D. This analysis reveals extensive sliding between tissues during axis extension. Further quantification of tissue tectonics showed patterns of rotations, contractions and expansions, which are coherent with the multi-tissue behavior observed previously. Our approach defines a quantitative and multiscale method to analyze the coordination between tissue behaviors during early vertebrate embryo morphogenetic events.

Phenotypic spandrel: absolute discrimination and ligand antagonism

We consider the general problem of sensitive and specific discrimination between biochemical species. An important instance is immune discrimination between self and not-self, where it is also observed experimentally that ligands just below the discrimination threshold negatively impact response, a phenomenon called antagonism. We characterize mathematically the generic properties of such discrimination, first relating it to biochemical adaptation. Then, based on basic biochemical rules, we establish that, surprisingly, antagonism is a generic consequence of any strictly specific discrimination made independently from ligand concentration. Thus antagonism constitutes a 'phenotypic spandrel': a phenotype existing as a necessary by-product of another phenotype. We exhibit a simple analytic model of discrimination displaying antagonism, where antagonism strength is linear in distance from the detection threshold. This contrasts with traditional proofreading based models where antagonism vanishes far from threshold and thus displays an inverted hierarchy of antagonism compared to simpler models. The phenotypic spandrel studied here is expected to structure many decision pathways such as immune detection mediated by TCRs and FCϵRIs, as well as endocrine signalling/disruption.

Oxidants at the Surface of Mars: A Review in Light of Recent Exploration Results

In 1976, the Viking landers carried out the most comprehensive search for organics and microbial life in the martian regolith. Their results indicate that Mars' surface is lifeless and, surprisingly, depleted in organics at part-per-billion levels. Several biology experiments on the Viking landers gave controversial results that have since been explained by the presence of oxidizing agents on the surface of Mars. These oxidants may degrade abiotic or biological organics, resulting in their nondetection in the regolith. As several exploration missions currently focus on the detection of organics on Mars (or will do so in the near future), knowledge of the oxidative state of the surface is fundamental. It will allow for determination of the capability of organics to survive on a geological timescale, the most favorable places to seek them, and the best methods to process the samples collected at the surface. With this aim, we review the main oxidants assumed to be present on Mars, their possible formation pathways, and those laboratory studies in which their reactivity with organics under Mars-like conditions has been evaluated. Among the oxidants assumed to be present on Mars, only four have been detected so far: perchlorate ions (ClO₄^-) in salts, hydrogen peroxide (H₂O₂) in the atmosphere, and clays and metal oxides composing surface minerals. Clays have been suggested as catalysts for the oxidation of organics but are treated as oxidants in the following to keep the structure of this article straightforward. This work provides an insight into the oxidizing potential of the surface of Mars and an estimate of the stability of organic matter in an oxidizing environment. Key Words: Mars surface-Astrobiology-Oxidant-Chemical reactions. Astrobiology 16, 977-996.

Imipenem heteroresistance in nontypeable Haemophilus influenzae is linked to a combination of altered PBP3, slow drug influx and direct efflux regulation

OBJECTIVE

To investigate the potential roles of PBPs, efflux pumps and slow drug influx for imipenem heteroresistance in nontypeable Haemophilus influenzae (NTHi).

METHODS

Fifty-nine NTHi clinical isolates examined in this study were collected at Geneva University Hospitals between 2009 and 2014. Alterations in PBPs were investigated by gene sequencing. To evaluate the affinities of the PBPs to imipenem, steady-state concentration-response experiments were carried out using imipenem in a competition assay with Bocillin-FL. The effect of the carbonyl cyanide m-chlorophenylhydrazone (CCCP) on imipenem susceptibility was assessed using broth dilution and viable cell counting. Using whole-genome sequencing, we explored the potential roles of outer membrane protein P2 (OmpP2), LytM proteins and the dcw gene cluster in imipenem heteroresistance.

RESULTS

All 46 imipenem-heteroresistant isolates (IMI^hR) harboured amino acid substitutions in the ftsI gene, which encodes PBP3, corresponding to 25 different mutation patterns that varied from the ftsI gene mutation patterns found in imipenem-susceptible isolates. Among all PBPs, the highest affinity to imipenem was documented for PBP3 (IC₅₀, 0.004 μg/mL). Different amino acid substitutions and insertions were noted in OmpP2, suggesting a relationship with imipenem heteroresistance. The IMI^hR isolates were affected by CCCP differently and displayed a higher percentage of killing by imipenem in CCCP-treated cells at concentrations ranging between 0.5 and 8 μg/mL.

CONCLUSIONS

The present study provides robust evidence indicating that in combination with the altered PBP3, the slowed drug influx and its enhanced efflux due to the loss of regulation led to the development of imipenem heteroresistance in NTHi.

Critical Timing without a Timer for Embryonic Development

Timing of embryonic development is precisely controlled, but the mechanisms underlying biological timers are still unclear. Here, a validated model for timing under control of Sonic Hedgehog is revisited and generalized to an arbitrary number of genes. The developmental dynamics where a temporal sequence of gene expression recapitulates a steady-state spatial pattern can be realized through a simple network close to criticality, controlled by the duration of exposure to a morphogen. Criticality simultaneously accounts for many observed biological properties, such as timing, multistability, and canalization of genetic expression. This process can be parsimoniously generalized in many dimensions with a minimum number of genes, all repressing each other with asymmetrical strengths, which also explains sequential activation of different fates. Separation of timescales allows for a simple analytical interpretation. Finally, it is shown that even in the presence of noise, coupling between cells preserves criticality and robust patterning. The model offers a simple theoretical framework for the study of emergent developmental timers.

Positional information from oscillatory phase shifts : insights from in silico evolution

Complex cellular decisions are based on temporal dynamics of pathways, including genetic oscillators. In development, recent works on vertebrae formation have suggested that relative phase of genetic oscillators encode positional information, including differentiation front defining vertebrae positions. Precise mechanisms for this are still unknown. Here, we use computational evolution to find gene network topologies that can compute the phase difference between oscillators and convert it into a decoder morphogen concentration. Two types of networks are discovered, based on symmetry properties of the decoder gene. So called asymmetric networks are studied, and two submodules are identified converting phase information into an amplitude variable. Those networks naturally display a 'shock' for a well defined phase difference, that can be used to define a wavefront of differentiation. We show how implementation of these ideas reproduce experimental features of vertebrate segmentation.

Predicting Ancestral Segmentation Phenotypes from Drosophila to Anopheles Using In Silico Evolution

Molecular evolution is an established technique for inferring gene homology but regulatory DNA turns over so rapidly that inference of ancestral networks is often impossible. In silico evolution is used to compute the most parsimonious path in regulatory space for anterior-posterior patterning linking two Dipterian species. The expression pattern of gap genes has evolved between Drosophila (fly) and Anopheles (mosquito), yet one of their targets, eve, has remained invariant. Our model predicts that stripe 5 in fly disappears and a new posterior stripe is created in mosquito, thus eve stripe modules 3+7 and 4+6 in fly are homologous to 3+6 and 4+5 in mosquito. We can place Clogmia on this evolutionary pathway and it shares the mosquito homologies. To account for the evolution of the other pair-rule genes in the posterior we have to assume that the ancestral Dipterian utilized a dynamic method to phase those genes in relation to eve.

The last common ancestor of the fruit fly (Drosophila) and mosquito (Anopheles) lived more than 200 Million years ago. Can we use available data on insects alive today to infer what their ancestor looked like? In this manuscript, we focus on early embryonic development, when stripes of genetic expression appear and define the location of insect segments (“segmentation”). We use an evolutionary algorithm to reconstruct and predict dynamics of genes controlling stripes in the last common ancestor of fly and mosquito. We predict a new and different combinatorial logic of stripe formation in mosquito compared to fly, which is fully consistent with development of intermediate species such as moth-fly (Clogmia). Our simulations further suggest that the dynamics of gene expression in this last common ancestor were similar to other insects, such as wasps (Nasonia). Our method illustrates how computational methods inspired by machine learning and non-linear physics can be used to infer gene dynamics in species that disappeared millions of years ago.

An empirical model for calculation of the collimator contamination dose in therapeutic proton beams

Collimators are used as lateral beam shaping devices in proton therapy with passive scattering beam lines. The dose contamination due to collimator scattering can be as high as 10% of the maximum dose and influences calculation of the output factor or monitor units (MU). To date, commercial treatment planning systems generally use a zero-thickness collimator approximation ignoring edge scattering in the aperture collimator and few analytical models have been proposed to take scattering effects into account, mainly limited to the inner collimator face component. The aim of this study was to characterize and model aperture contamination by means of a fast and accurate analytical model. The entrance face collimator scatter distribution was modeled as a 3D secondary dose source. Predicted dose contaminations were compared to measurements and Monte Carlo simulations. Measurements were performed on two different proton beam lines (a fixed horizontal beam line and a gantry beam line) with divergent apertures and for several field sizes and energies. Discrepancies between analytical algorithm dose prediction and measurements were decreased from 10% to 2% using the proposed model. Gamma-index (2%/1 mm) was respected for more than 90% of pixels. The proposed analytical algorithm increases the accuracy of analytical dose calculations with reasonable computation times.

Randomized, placebo-controlled, double-blind clinical trial to evaluate the efficacy of polyhexanide for topical decolonization of MRSA carriers

OBJECTIVES

The objective of this study was to evaluate the efficacy of polyhexanide (Prontoderm(®)) in eliminating MRSA carriage.

METHODS

In a 1900 bed teaching hospital, MRSA-colonized patients were randomized into a double-blind, placebo-controlled superiority trial between January 2011 and July 2014. Patients were treated with either polyhexanide or placebo applied to the anterior nares (thrice daily) and skin (once daily) for 10 days. The primary outcome was MRSA decolonization at day 28 (D28) after the end of treatment assessed by ITT responder and PP analyses (microbiological follow-up ± 7 days and topical treatment ≥ 5 days). Secondary outcomes included safety, emergence of resistance and MRSA genotype changes. Registered trial number ISRCTN02288276.

RESULTS

Of 2590 patients screened, 146 (polyhexanide group, 71; placebo group, 75) were included. ITT analysis showed that 24/71 (33.8%) patients in the polyhexanide group versus 22/75 (29.3%) in the placebo group were MRSA-free at D28 (risk difference, 4.5%; 95% CI, -10.6% to 19.5%; P = 0.56). PP analysis confirmed the results with 19/53 (35.8%) decolonized polyhexanide-treated patients versus 17/56 (30.4%) in the placebo arm (risk difference, 5.5%; 95% CI, -12.2% to 23%; P = 0.54). Nine serious adverse events occurred in the polyhexanide group versus 12 in the placebo group; none was attributable to study medication. Emergence of polyhexanide resistance or cross-resistance between polyhexanide and chlorhexidine was not observed. No case of exogenous recolonization by a genotypically different MRSA strain was documented.

CONCLUSIONS

This study suggests that under real-life conditions, a single polyhexanide decolonization course is not effective in eradicating MRSA carriage.

Dynamics of the slowing segmentation clock reveal alternating two-segment periodicity

The formation of reiterated somites along the vertebrate body axis is controlled by the segmentation clock, a molecular oscillator expressed within presomitic mesoderm (PSM) cells. Although PSM cells oscillate autonomously, they coordinate with neighboring cells to generate a sweeping wave of cyclic gene expression through the PSM that has a periodicity equal to that of somite formation. The velocity of each wave slows as it moves anteriorly through the PSM, although the dynamics of clock slowing have not been well characterized. Here, we investigate segmentation clock dynamics in the anterior PSM in developing zebrafish embryos using an in vivo clock reporter, her1:her1-venus. The her1:her1-venus reporter has single-cell resolution, allowing us to follow segmentation clock oscillations in individual cells in real-time. By retrospectively tracking oscillations of future somite boundary cells, we find that clock reporter signal increases in anterior PSM cells and that the periodicity of reporter oscillations slows to about ∼1.5 times the periodicity in posterior PSM cells. This gradual slowing of the clock in the anterior PSM creates peaks of clock expression that are separated at a two-segment periodicity both spatially and temporally, a phenomenon we observe in single cells and in tissue-wide analyses. These results differ from previous predictions that clock oscillations stop or are stabilized in the anterior PSM. Instead, PSM cells oscillate until they incorporate into somites. Our findings suggest that the segmentation clock may signal somite formation using a phase gradient with a two-somite periodicity.