Imaging Protein Fibers at the Nanoscale and In Situ

Protein self-assembly offers a rich repertoire of tools and technologies. However, despite significant progress in this area, a deterministic measure of the phenomenon, which might lead to predictable relationships between protein components, assembly mechanisms, and ultimately function, is lacking. Often the challenge relates to the choice of the most informative and precise measurements that can link the chemistry of the building blocks with the resulting assembly, ideally in situ and in real time. Using the example of protein fibrillogenesis-a self-assembly process fundamental to nearly every aspect of biological organization, from viral assembly to tissue restoration-this chapter demonstrates how protein self-assembly can be visually and precisely measured while providing measurement protocols applicable to other self-assembly systems.

Psychosocial predictors and moderators of weight management programme outcomes in ethnically diverse obese youth

BACKGROUND

An important area of research in childhood obesity is the identification of factors that predict or moderate the responses to obesity intervention programmes, yet few studies have examined the impact of self-esteem and family functioning on obesity treatment outcomes.

OBJECTIVES

We sought to determine whether baseline self-esteem and family functioning predicted or moderated childhood obesity intervention outcomes at 6 months.

METHODS

From 2009 to 2011, seventy-five 10-16 year old, racially/ethnically diverse obese youths with abnormal glucose tolerance were randomized to 6 months of an intensive family-based obesity lifestyle intervention (Bright Bodies) or routine outpatient Clinic Care. We examined youth self-concept, parent-rated family functioning and 6-month outcomes (youths' glucose tolerance, weight, body mass index and percent fat). We set the significance threshold as P ≤ 0.05 for moderator and predictor analyzes.

RESULTS

Having poor family functioning and self-concept scores indicating high anxiety and low self-esteem at baseline predicted poor 6-month outcomes overall (Bright Bodies and Clinic Care groups combined). Additionally, baseline self-esteem and family functioning moderated treatment effects such that Bright Bodies outperformed Clinic Care in youths with low self-esteem and poorly functioning families, whereas youths with high self-esteem and high-functioning families did similarly well with either intervention.

DISCUSSION

Our findings suggest intensive family-based lifestyle programmes are particularly beneficial for youth with low self-esteem and poorly functioning families.

Out-of-Pocket Cost Is a Barrier to Therapeutic Drug Monitoring in Inflammatory Bowel Disease

BACKGROUND

Therapeutic drug monitoring (TDM) is increasingly performed to optimize biologic therapy in inflammatory bowel disease (IBD). However, patients and physicians may be reluctant to perform TDM due to concerns related to potential out-of-pocket costs.

AIMS

The aim of this study was to evaluate patient understanding and attitudes toward TDM in different clinical scenarios with and without potential out-of-pocket costs.

METHODS

Adult IBD patients at a tertiary gastroenterology clinic were anonymously surveyed from March to September 2016 to assess their understanding of and willingness to undergo TDM in a variety of clinical scenarios, both with and without a potential out-of-pocket cost. Responses were analyzed for associations with changes in attitudes if out-of-pocket costs were involved.

RESULTS

Of 118 completed surveys, 68.2% of patients were aware of or had previously undergone TDM. Patient willingness to undergo TDM was high both with and without potential out-of-pocket costs (70 and 98%, respectively); however, patients were significantly less willing with out-of-pocket cost (p < 0.01). Higher disease-related quality of life scores, as measured by the short inflammatory bowel disease questionnaire (SIBDQ), was significantly associated with an increased willingness to assume a potential out-of-pocket cost (p = 0.007).

CONCLUSIONS

Overall, patients understand and are willing to undergo TDM in certain potentially beneficial clinical scenarios, however, are significantly less willing if paying out-of-pocket. A higher SIBDQ score was associated with an increase in willingness to undergo TDM when out-of-pocket cost was involved. Physicians should discuss TDM with their patients in order to make an informed and personalized treatment decision.

CREIM: Coffee Ring Effect Imaging Model for Monitoring Protein Self-Assembly in Situ

Protein self-assembly is fundamental to nanotechnology. Self-assembling structures are produced under static in vitro conditions typically forming over hours. In contrast, hydrodynamic intracellular environments employ far shorter time scales to compartmentalize highly concentrated protein solutions. Herein, we exploit the radial capillary flow within a drying sessile droplet (the coffee ring effect) to emulate dynamic native environments and monitor an archetypal protein assembly in situ using high-speed super-resolution imaging. We demonstrate that the assembly can be empirically driven to completion within minutes to seconds without apparent changes in supramolecular morphology. The model offers a reliable tool for the diagnosis and engineering of self-assembling systems under nonequilibrium conditions.

Variability in, and factors associated with, sizing of polyps by endoscopists at a large community practice

BACKGROUND AND AIMS

 Accurate sizing of polyps at time of colonoscopy is critical for determining surveillance intervals. Endoscopists routinely over- or underestimate the size of polyps at colonoscopy. We evaluated the variability in sizing of polyps among multiple endoscopists, and the effect of patient and physician related factors on polyp size estimation in a large community-based practice.

METHODS

 Adult patients who underwent a colonoscopy with polypectomy at five endoscopy centers in Minneapolis/St. Paul by one of 52 endoscopists in 2013 were included in this study. Association of patient, physician, and procedure related factors on polyp sizing was assessed.

RESULTS

 In the study time frame, 38 624 colonoscopies were performed at five ambulatory endoscopy centers. Of these, 16 336 had one or more polyp removed with size information available, and were included in this analysis. There was significant inter-physician variation for estimating polyp sizes larger than 5 mm (intraclass correlation coefficient [ICC] 0.13). Older patient age (OR 1.08, 95 %CI 1.06 - 1.11), and male physician gender (OR 1.92, 95 %CI 1.26 - 2.94) were associated with increased odds of physicians sizing polyps as larger in size. Surveillance procedures had a higher odds of larger polyp sizing compared to screening (OR 0.91, 95 %CI 0.86 - 0.97) and diagnostic procedures (OR 0.86, 95 %CI 0.78 - 0.94).

CONCLUSION

 In a large community setting, variation of polyp sizing estimates exists between physicians. Male physicians were more likely to size polyps as larger in size. Older patients and patients undergoing surveillance procedures were more likely to have polyps that were sized as larger in size.

Foundational and Translational Research Opportunities to Improve Plant Health

Reader Comments | Submit a Comment The white paper reports the deliberations of a workshop focused on biotic challenges to plant health held in Washington, D.C. in September 2016. Ensuring health of food plants is critical to maintaining the quality and productivity of crops and for sustenance of the rapidly growing human population. There is a close linkage between food security and societal stability; however, global food security is threatened by the vulnerability of our agricultural systems to numerous pests, pathogens, weeds, and environmental stresses. These threats are aggravated by climate change, the globalization of agriculture, and an over-reliance on nonsustainable inputs. New analytical and computational technologies are providing unprecedented resolution at a variety of molecular, cellular, organismal, and population scales for crop plants as well as pathogens, pests, beneficial microbes, and weeds. It is now possible to both characterize useful or deleterious variation as well as precisely manipulate it. Data-driven, informed decisions based on knowledge of the variation of biotic challenges and of natural and synthetic variation in crop plants will enable deployment of durable interventions throughout the world. These should be integral, dynamic components of agricultural strategies for sustainable agriculture.

Cognitive impairment in pediatric-onset multiple sclerosis is detected by the Brief International Cognitive Assessment for Multiple Sclerosis and computerized cognitive testing

BACKGROUND

Cognitive impairment is a common and troubling feature of pediatric-onset multiple sclerosis (POMS). Brief cognitive assessment in the outpatient setting can identify and longitudinally monitor cognitive involvement so that early intervention is possible.

OBJECTIVES

The goal of this study was to measure the sensitivity of two cognitive assessment approaches that are brief, repeatable, and suitable for clinical practice and for multicenter investigation.

METHODS

Participants with POMS ( n = 69) were consecutively evaluated as part of outpatient neurologic visits and compared to healthy control participants (HC, n = 66) using the Brief International Cognitive Assessment for MS (BICAMS) approach and timed information processing measures from Cogstate, a computer-based assessment.

RESULTS

There was strong agreement in the detection rate of impairment between both assessments, with 26% for the BICAMS and 27% for Cogstate. Two of the Cogstate tasks were the most sensitive individual measures.

CONCLUSION

Both the BICAMS and Cogstate timed processing measures offer practical, sensitive, and standardized approaches for cognitive screening assessment in POMS.

Remotely Supervised Transcranial Direct Current Stimulation Increases the Benefit of At-Home Cognitive Training in Multiple Sclerosis

OBJECTIVE

To explore the efficacy of remotely-supervised transcranial direct current stimulation (RS-tDCS) paired with cognitive training (CT) exercise in participants with multiple sclerosis (MS).

METHODS

In a feasibility study of RS-tDCS in MS, participants completed ten sessions of tDCS paired with CT (1.5 mA × 20 min, dorsolateral prefrontal cortex montage). RS-tDCS participants were compared to a control group of adults with MS who underwent ten 20-min CT sessions through the same remotely supervised procedures. Cognitive outcomes were tested by composite scores measuring change in performance on standard tests (Brief International Cognitive Assessment in MS or BICAMS), basic attention (ANT-I Orienting and Attention Networks, Cogstate Detection), complex attention (ANT-I Executive Network, Cogstate Identification and One-Back), and intra-individual response variability (ANT-I and Cogstate identification; sensitive markers of disease status).

RESULTS

After ten sessions, the tDCS group (n = 25) compared to the CT only group (n = 20) had significantly greater improvement in complex attention (p = 0.01) and response variability (p = 0.01) composites. The groups did not differ in measures of basic attention (p = 0.95) or standard cognitive measures (p = 0.99).

CONCLUSIONS

These initial findings indicate benefit for RS-tDCS paired with CT in MS. Exploratory analyses indicate that the earliest tDCS cognitive benefit is seen in complex attention and response variability. Telerehabilitation using RS-tDCS combined with CT may lead to improved outcomes in MS.

Influenza virus exploits tunneling nanotubes for cell-to-cell spread

Tunneling nanotubes (TNTs) represent a novel route of intercellular communication. While previous work has shown that TNTs facilitate the exchange of viral or prion proteins from infected to naïve cells, it is not clear whether the viral genome is also transferred via this mechanism and further, whether transfer via this route can result in productive replication of the infectious agents in the recipient cell. Here we present evidence that lung epithelial cells are connected by TNTs, and in spite of the presence of neutralizing antibodies and an antiviral agent, Oseltamivir, influenza virus can exploit these networks to transfer viral proteins and genome from the infected to naïve cell, resulting in productive viral replication in the naïve cells. These observations indicate that influenza viruses can spread using these intercellular networks that connect epithelial cells, evading immune and antiviral defenses and provide an explanation for the incidence of influenza infections even in influenza-immune individuals and vaccine failures.

Nano-mechanical single-cell sensing of cell-matrix contacts

Extracellular protein matrices provide a rigidity interface exhibiting nano-mechanical cues that guide cell growth and proliferation. Cells sense such cues using actin-rich filopodia extensions which encourage favourable cell-matrix contacts to recruit more actin-mediated local forces into forming stable focal adhesions. A challenge remains in identifying and measuring these local cellular forces and in establishing empirical relationships between them, cell adhesion and filopodia formation. Here we investigate such relationships using a micromanipulation system designed to operate at the time scale of focal contact dynamics, with the sample frequency of a force probe being 0.1 ms, and to apply and measure forces at nano-to-micro Newton ranges for individual mammalian cells. We explore correlations between cell biomechanics, cell-matrix attachment forces and the spread areas of adhered cells as well as their relative dependence on filopodia formation using synthetic protein matrices with a proven ability to induce enhanced filopodia numbers in adherent cells. This study offers a basis for engineering exploitable cell-matrix contacts in situ at the nanoscale and single-cell levels.

Erratum to: 36th International Symposium on Intensive Care and Emergency Medicine: Brussels, Belgium. 15-18 March 2016

[This corrects the article DOI: 10.1186/s13054-016-1208-6.].

Proposal for a unified nomenclature for target-site mutations associated with resistance to fungicides

Evolved resistance to fungicides is a major problem limiting our ability to control agricultural, medical and veterinary pathogens and is frequently associated with substitutions in the amino acid sequence of the target protein. The convention for describing amino acid substitutions is to cite the wild-type amino acid, the codon number and the new amino acid, using the one-letter amino acid code. It has frequently been observed that orthologous amino acid mutations have been selected in different species by fungicides from the same mode of action class, but the amino acids have different numbers. These differences in numbering arise from the different lengths of the proteins in each species. The purpose of the present paper is to propose a system for unifying the labelling of amino acids in fungicide target proteins. To do this we have produced alignments between fungicide target proteins of relevant species fitted to a well-studied 'archetype' species. Orthologous amino acids in all species are then assigned numerical 'labels' based on the position of the amino acid in the archetype protein. © 2016 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Investigation of mechanosensation in C. elegans using light field calcium imaging

We describe a new experimental approach to investigate touch sensation in the model organism C. elegans using light field deconvolution microscopy. By combining fast volumetric image acquisition with controlled indentation of the organism using a high sensitivity force transducer, we are able to simultaneously measure activity in multiple touch receptor neurons expressing the calcium ion indicator GCaMP6s. By varying the applied mechanical stimulus we show how this method can be used to quantify touch sensitivity in C. elegans. We describe some of the challenges of performing light field calcium imaging in moving samples and demonstrate that they can be overcome by simple data processing.

Super-resolution microscopy as a potential approach to diagnosis of platelet granule disorders

BACKGROUND

Many platelet functions are dependent on bioactive molecules released from their granules. Deficiencies of these granules in number, shape or content are associated with bleeding. The small size of these granules is such that imaging them for diagnosis has traditionally required electron microscopy. However, recently developed super-resolution microscopes provide sufficient spatial resolution to effectively image platelet granules. When combined with automated image analysis, these methods provide a quantitative, unbiased, rapidly acquired dataset that can readily and reliably reveal differences in platelet granules between individuals.

OBJECTIVE

To demonstrate the ability of structured illumination microscopy (SIM) to efficiently differentiate between healthy volunteers and three patients with Hermansky-Pudlak syndrome.

METHODS

Blood samples were taken from three patients with Hermansky-Pudlak syndrome and seven controls. Patients 1-3 have gene defects in HPS1, HPS6 and HPS5, respectively; all controls were healthy volunteers. Platelet-rich plasma was isolated from blood and the platelets fixed, stained for CD63 and processed for analysis by immunofluorescence microscopy, using a custom-built SIM microscope.

RESULTS

SIM can successfully resolve CD63-positive structures in fixed platelets. A determination of the number of CD63-positive structures per platelet allowed us to conclude that each patient was significantly different from all of the controls with 99% confidence.

CONCLUSIONS

A super-resolution imaging approach is effective and rapid in objectively differentiating between patients with a platelet bleeding disorder and healthy volunteers. CD63 is a useful marker for predicting Hermansky-Pudlak syndrome and could be used in the diagnosis of patients suspected of other platelet granule disorders.

Determination of Predominance of Influenza Virus Strains in the Americas

During 2001–2014, predominant influenza A(H1N1) and A(H3N2) strains in South America predominated in all or most subsequent influenza seasons in Central and North America. Predominant A(H1N1) and A(H3N2) strains in North America predominated in most subsequent seasons in Central and South America. Sharing data between these subregions may improve influenza season preparedness.

X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes

X-linked intellectual disability (XLID) is a clinically and genetically heterogeneous disorder. During the past two decades in excess of 100 X-chromosome ID genes have been identified. Yet, a large number of families mapping to the X-chromosome remained unresolved suggesting that more XLID genes or loci are yet to be identified. Here, we have investigated 405 unresolved families with XLID. We employed massively parallel sequencing of all X-chromosome exons in the index males. The majority of these males were previously tested negative for copy number variations and for mutations in a subset of known XLID genes by Sanger sequencing. In total, 745 X-chromosomal genes were screened. After stringent filtering, a total of 1297 non-recurrent exonic variants remained for prioritization. Co-segregation analysis of potential clinically relevant changes revealed that 80 families (20%) carried pathogenic variants in established XLID genes. In 19 families, we detected likely causative protein truncating and missense variants in 7 novel and validated XLID genes (CLCN4, CNKSR2, FRMPD4, KLHL15, LAS1L, RLIM and USP27X) and potentially deleterious variants in 2 novel candidate XLID genes (CDK16 and TAF1). We show that the CLCN4 and CNKSR2 variants impair protein functions as indicated by electrophysiological studies and altered differentiation of cultured primary neurons from Clcn4(-/-) mice or after mRNA knock-down. The newly identified and candidate XLID proteins belong to pathways and networks with established roles in cognitive function and intellectual disability in particular. We suggest that systematic sequencing of all X-chromosomal genes in a cohort of patients with genetic evidence for X-chromosome locus involvement may resolve up to 58% of Fragile X-negative cases.

A Protocol for the Use of Remotely-Supervised Transcranial Direct Current Stimulation (tDCS) in Multiple Sclerosis (MS)

Transcranial direct current stimulation (tDCS) is a noninvasive brain stimulation technique that uses low amplitude direct currents to alter cortical excitability. With well-established safety and tolerability, tDCS has been found to have the potential to ameliorate symptoms such as depression and pain in a range of conditions as well as to enhance outcomes of cognitive and physical training. However, effects are cumulative, requiring treatments that can span weeks or months and frequent, repeated visits to the clinic. The cost in terms of time and travel is often prohibitive for many participants, and ultimately limits real-world access. Following guidelines for remote tDCS application, we propose a protocol that would allow remote (in-home) participation that uses specially-designed devices for supervised use with materials modified for patient use, and real-time monitoring through a telemedicine video conferencing platform. We have developed structured training procedures and clear, detailed instructional materials to allow for self- or proxy-administration while supervised remotely in real-time. The protocol is designed to have a series of checkpoints, addressing attendance and tolerability of the session, to be met in order to continue to the next step. The feasibility of this protocol was then piloted for clinical use in an open label study of remotely-supervised tDCS in multiple sclerosis (MS). This protocol can be widely used for clinical study of tDCS.

Differences in influenza seasonality by latitude, northern India

The seasonality of influenza in the tropics complicates vaccination timing. We investigated influenza seasonality in northern India and found influenza positivity peaked in Srinagar (34.09°N) in January–March but peaked in New Delhi (28.66°N) in July–September. Srinagar should consider influenza vaccination in October–November, but New Delhi should vaccinate in May–June.

Clonidine withdrawal induced sympathetic surge

A 30-year-old man with a history of epilepsy and substance misuse presented to the hospital with status epilepticus. Difficult seizure control necessitated anaesthetising the patient followed by intubation and ventilation. A clonidine infusion was started as the patient developed withdrawal syndrome and was difficult to wean off mechanical ventilation. Once the withdrawal syndrome was controlled, the clonidine was abruptly stopped. Two hours after stopping the infusion, the patient developed high-grade fever, severe hypertension, tachycardia, profound sweating and lacrimation. The patient then developed respiratory distress syndrome secondary to acute pulmonary oedema. Clonidine withdrawal as a cause of such response was proposed. Reversal of symptoms and successful reweaning was achieved by restarting a low-dose clonidine infusion followed by slow downward titration and use of oral clonidine as a step-down measure. The patient was subsequently discharged from the intensive care unit.

Investigation of an Outbreak of Variant Influenza A(H3N2) Virus Infection Associated With an Agricultural Fair-Ohio, August 2012

BACKGROUND

In 2012, one third of cases in a multistate outbreak of variant influenza A(H3N2) virus ([H3N2]v) infection occurred in Ohio. We conducted an investigation of (H3N2)v cases associated with agricultural Fair A in Ohio.

METHODS

We surveyed Fair A swine exhibitors and their household members. Confirmed cases had influenza-like illness (ILI) and a positive laboratory test for (H3N2)v, and probable cases had ILI. We calculated attack rates. We determined risk factors for infection, using multivariable log-binomial regression.

RESULTS

We identified 20 confirmed and 94 probable cases associated with Fair A. Among 114 cases, the median age was 10 years, there were no hospitalizations or deaths, and 82% had swine exposure. In the exhibitor household cohort of 359 persons (83 households), we identified 6 confirmed cases (2%) and 40 probable cases (11%). An age of <10 years was a significant risk factor (P < .01) for illness. One instance of likely human-to-human transmission was identified.

CONCLUSIONS

In this (H3N2)v outbreak, no evidence of sustained human-to-human (H3N2)v transmission was found. Our risk factor analysis contributed to the development of the recommendation that people at increased risk of influenza-associated complications, including children aged <5 years, avoid swine barns at fairs during the 2012 fair season.

Evaluation of Salivary Transcriptome Markers for the Early Detection of Oral Squamous Cell Cancer in a Prospective Blinded Trial

BACKGROUND

Oral squamous cell cancer (OSCC) is often diagnosed in late stages. Informative biomarkers could play a key role in early diagnosis. Prior case-control studies identified discriminatory salivary mRNA markers for OSCC. The National Cancer Institute (NCI) recommends prospective-specimencollection, retrospective-blinded-evaluation (PRoBE) design study for rigorous biomarker identification and validation.

METHODS

A PRoBE design study enrolled 170 patients with lesions suspicious for OSCC. Saliva was collected before performing oral biopsy. Six pre-specified oral-cancer-associated mRNAs (IL1β, IL8, OAZ1, SAT, S100P, and DUSP1) and five housekeeping mRNAs (MT-ATP6, RPL30, RPL37A, RPL0, and RPS17) were measured by quantitative polymerase chain reaction (PCR) without knowledge of tissue diagnosis. A pre-specified multi-marker panel from prior NCI - Early Detection Research Network (EDRN) studies was evaluated in this new PRoBE dataset. Individual marker cycle thresholds (Ct) from PCR were also compared in cancer versus control, and new discriminatory models were generated.

RESULTS

The EDRN model was validated based on pre-specified statistical analysis plan. Ct values of individual mRNAs reflect an approximately twofold to nearly fourfold increase in concentration in invasive OSCC (P less than 0.01 for all). A new model from this intended-use population with incorporation of housekeeping genes demonstrates a maximal sum of sensitivity and specificity of 150.7% with an area under the receiver operating characteristic (ROC) curve of over 0.85.

CONCLUSION

The validation of six pre-specified individual salivary transcriptome markers of OSCC and a pre-specified multi-marker model in a new prospective population supports the robustness of these markers and the multi-marker methodology. New models generated in this intended-use population have the potential to further enhance the decision process for early biopsy. Lesions at very low risk for cancer could be identified noninvasively as could those at significantly increased risk. Further study is necessary to assure effective implementation of this technology into routine clinical practice.

New insights into Brunner syndrome and potential for targeted therapy

We report two families with Brunner syndrome living in one state of Australia. The first family had a predicted protein-truncating variant of monoamine oxidase A (MAOA) (p.S251KfsX2). Affected males had mild intellectual disability (ID), obsessive behaviour, limited friendships and were introverted and placid during clinical interview. The family disclosed episodic explosive aggression after a diagnosis was made. The second family had a missense variant in MAOA (p.R45W). Affected males had borderline-mild ID, attention deficit disorder and limited friendships. One had a history of explosive aggression in childhood and episodic symptoms of flushing, headaches and diarrhoea. Their carrier mother had normal intelligence but similar episodic symptoms. Characteristic biochemical abnormalities included high serum serotonin and urinary metanephrines and low urinary 5-hydroxyindoleacetic acid (5-HIAA) and vanillylmandelic acid (VMA). Symptomatic individuals in the second family had particularly high serotonin levels, and treatment with a serotonin reuptake inhibitor and dietary modification resulted in reversal of biochemical abnormalities, reduction of 'serotonergic' symptoms and behavioural improvement. Brunner syndrome should be considered as a cause of mild ID with paroxysmal behavioural symptoms. It can be screened for with serum/urine metanephrine and serotonin measurement. Cautious treatment with a serotonin reuptake inhibitor, dietary modifications and avoidance of medications contraindicated in patients on monoamine oxidase inhibitors can improve symptoms.

Complex clinical reasoning in the critical care unit - difficulties, pitfalls and adaptive strategies

Diagnostic error has implications for both clinical outcome and resource utilisation, and may often be traced to impaired data gathering, processing or synthesis because of the influence of cognitive bias. Factors inherent to the intensive/acute care environment afford multiple additional opportunities for such errors to occur. This article illustrates many of these with reference to a case encountered on our intensive care unit. Strategies to improve completeness of data gathering, processing and synthesis in the acute care environment are critically appraised in the context of early detection and amelioration of cognitive bias. These include reflection, targeted simulation training and the integration of social media and IT based aids in complex diagnostic processes. A framework which can be quickly and easily employed in a variety of clinical environments is then presented.