Combining avidin with CD63 improves basophil activation test accuracy in classifying peanut allergy

BACKGROUND

Conventional basophil activation tests (BATs) measure basophil activation by the increased expression of CD63. Previously, fluorophore-labeled avidin, a positively-charged molecule, was found to bind to activated basophils, which tend to expose negatively charged granule constituents during degranulation. This study further compares avidin versus CD63 as basophil activation biomarkers in classifying peanut allergy.

METHODS

Seventy subjects with either a peanut allergy (N = 47), a food allergy other than peanut (N = 6), or no food allergy (N = 17) were evaluated. We conducted BATs in response to seven peanut extract (PE) concentrations (0.01-10,000 ng/mL) and four control conditions (no stimulant, anti-IgE, fMLP (N-formylmethionine-leucyl-phenylalanine), and anti-FcεRI). We measured avidin binding and CD63 expression on basophils with flow cytometry. We evaluated logistic regression and XGBoost models for peanut allergy classification and feature identification.

RESULTS

Avidin binding was correlated with CD63 expression. Both markers discriminated between subjects with and without a peanut allergy. Although small by percentage, an avidin+ /CD63- cell subset was found in all allergic subjects tested, indicating that the combination of avidin and CD63 could allow a more comprehensive identification of activated basophils. Indeed, we obtained the best classification accuracy (97.8% sensitivity, 96.7% specificity) by combining avidin and CD63 across seven PE doses. Similar accuracy was obtained by combining PE dose of 10,000 ng/mL for avidin and PE doses of 10 and 100 ng/mL for CD63.

CONCLUSIONS

Avidin and CD63 are reliable BAT activation markers associated with degranulation. Their combination enhances the identification of activated basophils and improves the classification accuracy of peanut allergy.

Untargeted metabolomic profiling in children identifies novel pathways in asthma and atopy

BACKGROUND

Asthma and other atopic disorders can present with varying clinical phenotypes marked by differential metabolomic manifestations and enriched biological pathways.

OBJECTIVE

We sought to identify these unique metabolomic profiles in atopy and asthma.

METHODS

We analyzed baseline nonfasted plasma samples from a large multisite pediatric population of 470 children aged <13 years from 3 different sites in the United States and France. Atopy positivity (At+) was defined as skin prick test result of ≥3 mm and/or specific IgE ≥ 0.35 IU/mL and/or total IgE ≥ 173 IU/mL. Asthma positivity (As+) was based on physician diagnosis. The cohort was divided into 4 groups of varying combinations of asthma and atopy, and 6 pairwise analyses were conducted to best assess the differential metabolomic profiles between groups.

RESULTS

Two hundred ten children were classified as At-As-, 42 as At+As-, 74 as At-As+, and 144 as At+As+. Untargeted global metabolomic profiles were generated through ultra-high-performance liquid chromatography-tandem mass spectroscopy. We applied 2 independent machine learning classifiers and short-listed 362 metabolites as discriminant features. Our analysis showed the most diverse metabolomic profile in the At+As+/At-As- comparison, followed by the At-As+/At-As- comparison, indicating that asthma is the most discriminant condition associated with metabolomic changes. At+As+ metabolomic profiles were characterized by higher levels of bile acids, sphingolipids, and phospholipids, and lower levels of polyamine, tryptophan, and gamma-glutamyl amino acids.

CONCLUSION

The At+As+ phenotype displays a distinct metabolomic profile suggesting underlying mechanisms such as modulation of host-pathogen and gut microbiota interactions, epigenetic changes in T-cell differentiation, and lower antioxidant properties of the airway epithelium.

Cross-reactive MHC class I T cell epitopes may dictate heterologous immune responses between respiratory viruses and food allergens

Respiratory virus infections play a major role in asthma, while there is a close correlation between asthma and food allergy. We hypothesized that T cell-mediated heterologous immunity may induce asthma symptoms among sensitized individuals and used two independent in silico pipelines for the identification of cross-reactive virus- and food allergen- derived T cell epitopes, considering individual peptide sequence similarity, MHC binding affinity and immunogenicity. We assessed the proteomes of human rhinovirus (RV1b), respiratory syncytial virus (RSVA2) and influenza-strains contained in the seasonal quadrivalent influenza vaccine 2019/2020 (QIV 2019/2020), as well as SARS-CoV-2 for human HLA alleles, in addition to more than 200 most common food allergen protein sequences. All resulting allergen-derived peptide candidates were subjected to an elaborate scoring system considering multiple criteria, including clinical relevance. In both bioinformatics approaches, we found that shortlisted peptide pairs that are potentially binding to MHC class II molecules scored up to 10 × lower compared to MHC class I candidate epitopes. For MHC class I food allergen epitopes, several potentially cross-reactive peptides from shrimp, kiwi, apple, soybean and chicken were identified. The shortlisted set of peptide pairs may be implicated in heterologous immune responses and translated to peptide immunization strategies with immunomodulatory properties.

Granzymes, IL-16, and poly(ADP-ribose) polymerase 1 increase during wildfire smoke exposure

Background

Given the increasing prevalence of wildfires worldwide, understanding the effects of wildfire air pollutants on human health-particularly in specific immunologic pathways-is crucial. Exposure to air pollutants is associated with cardiorespiratory disease; however, immune and epithelial barrier alterations require further investigation.

Objective

We sought to determine the impact of wildfire smoke exposure on the immune system and epithelial barriers by using proteomics and immune cell phenotyping.

Methods

A San Francisco Bay area cohort (n = 15; age 30 ± 10 years) provided blood samples before (October 2019 to March 2020; air quality index = 37) and during (August 2020; air quality index = 80) a major wildfire. Exposure samples were collected 11 days (range, 10-12 days) after continuous exposure to wildfire smoke. We determined alterations in 506 proteins, including zonulin family peptide (ZFP); immune cell phenotypes by cytometry by time of flight (CyTOF); and their interrelationship using a correlation matrix.

Results

Targeted proteomic analyses (n = 15) revealed a decrease of spondin-2 and an increase of granzymes A, B, and H, killer cell immunoglobulin-like receptor 3DL1, IL-16, nibrin, poly(ADP-ribose) polymerase 1, C1q TNF-related protein, fibroblast growth factor 19, and von Willebrand factor after 11 days' average continuous exposure to smoke from a large wildfire (P < .05). We also observed a large correlation cluster between immune regulation pathways (IL-16, granzymes A, B, and H, and killer cell immunoglobulin-like receptor 3DL1), DNA repair [poly(ADP-ribose) 1, nibrin], and natural killer cells. We did not observe changes in ZFP levels suggesting a change in epithelial barriers. However, ZFP was associated with immune cell phenotypes (naive CD4+, TH2 cells).

Conclusion

We observed functional changes in critical immune cells and their proteins during wildfire smoke exposure. Future studies in larger cohorts or in firefighters exposed to wildfire smoke should further assess immune changes and intervention targets.

Proinflammatory polarization of monocytes by particulate air pollutants is mediated by induction of trained immunity in pediatric asthma

BACKGROUND

The impact of exposure to air pollutants, such as fine particulate matter (PM), on the immune system and its consequences on pediatric asthma, are not well understood. We investigated whether ambient levels of fine PM with aerodynamic diameter ≤2.5 microns (PM_2.5 ) are associated with alterations in circulating monocytes in children with or without asthma.

METHODS

Monocyte phenotyping was performed by cytometry time-of-flight (CyTOF). Cytokines were measured using cytometric bead array and Luminex assay. ChIP-Seq was utilized to address histone modifications in monocytes.

RESULTS

Increased exposure to ambient PM_2.5 was linked to specific monocyte subtypes, particularly in children with asthma. Mechanistically, we hypothesized that innate trained immunity is evoked by a primary exposure to fine PM and accounts for an enhanced inflammatory response after secondary stimulation in vitro. We determined that the trained immunity was induced in circulating monocytes by fine particulate pollutants, and it was characterized by the upregulation of proinflammatory mediators, such as TNF, IL-6, and IL-8, upon stimulation with house dust mite or lipopolysaccharide. This phenotype was epigenetically controlled by enhanced H3K27ac marks in circulating monocytes.

CONCLUSION

The specific alterations of monocytes after ambient pollution exposure suggest a possible prognostic immune signature for pediatric asthma, and pollution-induced trained immunity may provide a potential therapeutic target for asthmatic children living in areas with increased air pollution.

Pangenome Analysis of the Soilborne Fungal Phytopathogen Rhizoctonia solani and Development of a Comprehensive Web Resource: RsolaniDB

Rhizoctonia solani is a collective group of genetically and pathologically diverse basidiomycetous fungi that damage economically important crops. Its isolates are classified into 13 Anastomosis Groups (AGs) and subgroups having distinctive morphology and host ranges. The genetic factors driving the unique features of R. solani pathology are not well characterized due to the limited availability of its annotated genomes. Therefore, we performed genome sequencing, assembly, annotation and functional analysis of 12 R. solani isolates covering 7 AGs and select subgroups (AG1-IA; AG1-IB; AG1-IC; AG2-2IIIB; AG3-PT, isolates Rhs 1AP and the hypovirulent Rhs1A1; AG3-TB; AG4-HG-I, isolates Rs23 and R118-11; AG5; AG6; and AG8), in which six genomes are reported for the first time. Using a pangenome comparative analysis of 12 R. solani isolates and 15 other Basidiomycetes, we defined the unique and shared secretomes, CAZymes, and effectors across the AGs. We have also elucidated the R. solani-derived factors potentially involved in determining AG-specific host preference, and the attributes distinguishing them from other Basidiomycetes. Finally, we present the largest repertoire of R. solani genomes and their annotated components as a comprehensive database, viz. RsolaniDB, with tools for large-scale data mining, functional enrichment and sequence analysis not available with other state-of-the-art platforms.

The genome of the zoonotic malaria parasite Plasmodium simium reveals adaptations to host switching

BACKGROUND

Plasmodium simium, a malaria parasite of non-human primates (NHP), was recently shown to cause zoonotic infections in humans in Brazil. We sequenced the P. simium genome to investigate its evolutionary history and to identify any genetic adaptions that may underlie the ability of this parasite to switch between host species.

RESULTS

Phylogenetic analyses based on whole genome sequences of P. simium from humans and NHPs reveals that P. simium is monophyletic within the broader diversity of South American Plasmodium vivax, suggesting P. simium first infected NHPs as a result of a host switch of P. vivax from humans. The P. simium isolates show the closest relationship to Mexican P. vivax isolates. Analysis of erythrocyte invasion genes reveals differences between P. vivax and P. simium, including large deletions in the Duffy-binding protein 1 (DBP1) and reticulocyte-binding protein 2a genes of P. simium. Analysis of P. simium isolated from NHPs and humans revealed a deletion of 38 amino acids in DBP1 present in all human-derived isolates, whereas NHP isolates were multi-allelic.

CONCLUSIONS

Analysis of the P. simium genome confirmed a close phylogenetic relationship between P. simium and P. vivax, and suggests a very recent American origin for P. simium. The presence of the DBP1 deletion in all human-derived isolates tested suggests that this deletion, in combination with other genetic changes in P. simium, may facilitate the invasion of human red blood cells and may explain, at least in part, the basis of the recent zoonotic infections.

Global survey-based assessment of lifestyle changes during the COVID-19 pandemic

Along with the major impact on public health, the COVID-19 outbreak has caused unprecedented concerns ranging from sudden loss of employment to mental stress and anxiety. We implemented a survey-based data collection platform to characterize how the COVID-19 pandemic has affected the socio-economic, physical and mental health conditions of individuals. We focused on three broad areas, namely, changes in social interaction during home confinement, economic impact and their health status. We identified a substantial increase in virtual interaction among individuals, which might be a way to alleviate the sudden unprecedented mental health burden, exacerbated by general awareness about viral infections or other manifestations associated with them. The majority of participants (85%) lived with one or more companions and unemployment issues did not affect 91% of the total survey takers, which was one of the crucial consequences of the pandemic. Nevertheless, measures such as an increased frequency of technology-aided distant social interaction, focus on physical fitness and leisure activities were adopted as coping mechanisms during this period of home isolation. Collectively, these metrics provide a succinct and informative summary of the socio-economic and health impact of the COVID-19 pandemic on the individuals. Findings from our study reflect that continuous surveillance of the psychological consequences for outbreaks should become routine as part of preparedness efforts worldwide. Given the limitations of analyzing the large number of variables, we have made the raw data publicly available on the OMF ME/CFS Data Center server to facilitate further analyses (https://igenomed.stanford.edu/dataset/survey-study-on-lifestyle-changes-during-covid-19-pandemic).

CyAnno: A semi-automated approach for cell type annotation of mass cytometry datasets

MOTIVATION

For immune system monitoring in large-scale studies at the single-cell resolution using CyTOF, (semi-)automated computational methods are applied for annotating live cells of mixed cell types. Here, we show that the live cell pool can be highly enriched with undefined heterogeneous cells, i.e., 'ungated' cells, and that current semi-automated approaches ignore their modeling resulting in misclassified annotations.

RESULT

We introduce 'CyAnno', a novel semi-automated approach for deconvoluting the unlabeled cytometry dataset based on a machine learning framework utilizing manually gated training data that allows the integrative modeling of 'gated' cell types and the 'ungated' cells. By applying this framework on several CyTOF datasets, we demonstrated that including the 'ungated' cells can lead to a significant increase in the precision of the 'gated' cell types prediction. CyAnno can be used to identify even a single cell type, including rare cells, with higher efficacy than current state-of-the-art semi-automated approaches.

AVAILABILITY

The CyAnno is available as a python script with a user-manual and sample dataset at https://github.com/abbioinfo/CyAnno.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Homologies between SARS-CoV-2 and allergen proteins may direct T cell-mediated heterologous immune responses

The outbreak of the new Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is a public health emergency. Asthma does not represent a risk factor for COVID-19 in several published cohorts. We hypothesized that the SARS-CoV-2 proteome contains T cell epitopes, which are potentially cross-reactive to allergen epitopes. We aimed at identifying homologous peptide sequences by means of two distinct complementary bioinformatics approaches. Pipeline 1 included prediction of MHC Class I and Class II epitopes contained in the SARS-CoV-2 proteome and allergens along with alignment and elaborate ranking approaches. Pipeline 2 involved alignment of SARS-CoV-2 overlapping peptides with known allergen-derived T cell epitopes. Our results indicate a large number of MHC Class I epitope pairs including known as well as de novo predicted allergen T cell epitopes with high probability for cross-reactivity. Allergen sources, such as Aspergillus fumigatus , Phleum pratense and Dermatophagoides species are of particular interest due to their association with multiple cross-reactive candidate peptides, independently of the applied bioinformatic approach. In contrast, peptides derived from food allergens, as well as MHC class II epitopes did not achieve high in silico ranking and were therefore not further investigated. Our findings warrant further experimental confirmation along with examination of the functional importance of such cross-reactive responses.

Novel tumour suppressor roles for GZMA and RASGRP1 in Theileria annulata-transformed macrophages and human B lymphoma cells

Theileria annulata is a tick-transmitted apicomplexan parasite that infects and transforms bovine leukocytes into disseminating tumours that cause a disease called tropical theileriosis. Using comparative transcriptomics we identified genes transcriptionally perturbed during Theileria-induced leukocyte transformation. Dataset comparisons highlighted a small set of genes associated with Theileria-transformed leukocyte dissemination. The roles of Granzyme A (GZMA) and RAS guanyl-releasing protein 1 (RASGRP1) were verified by CRISPR/Cas9-mediated knockdown. Knocking down expression of GZMA and RASGRP1 in attenuated macrophages led to a regain in their dissemination in Rag2/γC mice confirming their role as dissemination suppressors in vivo. We further evaluated the roles of GZMA and RASGRP1 in human B lymphomas by comparing the transcriptome of 934 human cancer cell lines to that of Theileria-transformed bovine host cells. We confirmed dampened dissemination potential of human B lymphomas that overexpress GZMA and RASGRP1. Our results provide evidence that GZMA and RASGRP1 have a novel tumour suppressor function in both T. annulata-infected bovine host leukocytes and in human B lymphomas.

Metal removal and recovery using bioelectrochemical technology: The major determinants and opportunities for synchronic wastewater treatment and energy production

Microbial fuel cell (MFC) technology has emerged as a new and attractive bioelectrochemical approach in the last one and a half decade that offers an alternative to conventional treatment methods to remove and recover heavy metals and organics from wastewaters with simultaneous energy production. This technique has advantage over the conventional wastewater treatment techniques, which are energy intensive, sludge producing and with little effectivity at high concentrations. Significant work has been done in the recent years on MFC principle, electrode configuration, biofilm composition, application of MFC in wastewater treatment, metal removal or recovery and energy production. Basically, metal in the cathode chamber acts as acceptor of the electrons released from the oxidation of organic matter in the anode chamber by electrogenic microbes. Literature shows that efficacy of MFCs in removal and recovery of metals and power production is significantly influenced by redox potential of the metal, initial concentration, mix metal systems, carbon source in substrate, pH, biocathode, biofilm composition, gaseous environment in cathode, electrode modification and external resistance, which have been critically reviewed for the first time in the present paper to understand the role of the determinant factors that may be explored for improvement of the MFC performance. The paper provides further insights into the techno-economic aspects of MFC technology and suggests research needs for enhanced performance and reduced costs to increase its feasibility for application at commercial level.

Emission characteristics of ultrafine particles from bare and Al2O3 coated graphite for high temperature applications

Owing to its exceptional properties at high temperature, graphite is used in several applications such as structural material and fuel block in high temperature nuclear reactors. Air ingress is one of the serious safety concerns in these reactors. Oxidation of graphite leading to increased porosity affects its mechanical strength and may lead to core collapse resulting in a severe accident. During such a scenario, generation of graphite particles could be the main hazard. Once generated, these particles often in fine and ultrafine sizes, may carry radioactivity to large distances and/or for long times. These particles owing to their higher surface to volume ratio possess an additional inhalation hazard. Ultrafine particles have the potential to enter into respiratory tract and cause damage to body organs. Coating of graphite components is preferred to reduce the oxidation induced damages at high temperatures. In the present work, effect of alumina (Al2O3) coating on the emission characteristics of particles from graphite under high temperature conditions has been investigated. Bare and Al2O3 coated graphite specimens were heated within a closed chamber at varying temperatures during these experiments. Temporal evolution of concentrations of gases (CO and CO2) and particles were measured. The results reveal that Al2O3 coating on the graphite delayed the oxidation behavior and the structure of graphite remained largely intact at high temperatures. A significant reduction in aerosol formation and CO emission was also noticed for the coated specimens.

Nano-enabled biosensing systems for intelligent healthcare: towards COVID-19 management

Biosensors are emerging as efficient (sensitive and selective) and affordable analytical diagnostic tools for early-stage disease detection, as required for personalized health wellness management. Low-level detection of a targeted disease biomarker (pM level) has emerged extremely useful to evaluate the progression of disease under therapy. Such collected bioinformatics and its multi-aspects-oriented analytics is in demand to explore the effectiveness of a prescribed treatment, optimize therapy, and correlate biomarker level with disease pathogenesis. Owing to nanotechnology-enabled advancements in sensing unit fabrication, device integration, interfacing, packaging, and sensing performance at point-of-care (POC) has rendered diagnostics according to the requirements of disease management and patient disease profile i.e. in a personalized manner. Efforts are continuously being made to promote the state of art biosensing technology as a next-generation non-invasive disease diagnostics methodology. Keeping this in view, this progressive opinion article describes personalized health care management related analytical tools which can provide access to better health for everyone, with overreaching aim to manage healthy tomorrow timely. Considering accomplishments and predictions, such affordable intelligent diagnostics tools are urgently required to manage COVID-19 pandemic, a life-threatening respiratory infectious disease, where a rapid, selective and sensitive detection of human beta severe acute respiratory system coronavirus (SARS-COoV-2) protein is the key factor.

Paediatric morphoea: a holistic review. Part 1: epidemiology, aetiopathogenesis and clinical classification

Morphoea, also known as localized scleroderma, is a debilitating fibrosing disorder of uncertain aetiology, affecting the skin and subcutaneous tissues. Paediatric-onset disease is not uncommon and is associated with frequent relapses. The disease has complex pathogenetic mechanisms and multiple clinical subtypes, and affects children of all ages. Recent research has focused on elucidating the disease pathophysiology and identifying measures of disease activity. We performed a literature search on PubMed, MEDLINE and Google Scholar, using keywords such as 'pediatric morphea', 'juvenile localised scleroderma' and 'juvenile systemic sclerosis'. Relevant studies, including randomized trials, reviews of standard current guidelines and original research articles, were selected, and results were analysed before being summarized. In the first of this two-part review, we provide a bird's-eye view of the current literature concerning the epidemiology, aetiopathogenesis and clinical classification of paediatric morphoea; in Part 2, we review the diagnosis, markers of disease activity, management and natural history.

Paediatric morphoea: a holistic review. Part 2: diagnosis, measures of disease activity, management and natural history

Paediatric morphoea is a debilitating fibrosing disorder of uncertain aetiology, affecting the skin and subcutaneous tissues. Defining optimum management strategies in paediatric morphoea remains an ongoing challenge, owing to the varied presentations and a relative paucity of paediatric-specific studies. We performed a literature search on PubMed, MEDLINE and Google Scholar, using keywords such as 'pediatric morphea', 'juvenile localised scleroderma' and 'juvenile systemic sclerosis'. Relevant studies, including randomized trials, reviews of standard current guidelines and original research articles, were selected and results analysed before summarizing them. In Part 1 of this review, we described the epidemiology, aetiopathogenesis and clinical classification; in this part, we discuss the diagnosis, markers of disease activity, management and natural history in paediatric morphoea.

Changes in strand 6B and helix B during neuroserpin inhibition: Implication in severity of clinical phenotype

Neuroserpin (NS) is predominantly expressed in brain and inhibits tissue-type plasminogen activator (tPA) with implications in brain development and memory. Nature of conformational change in pathological variants in strand 6B and helix B of NS that cause a relatively mild to severe epilepsy (and/or dementia) remains largely elusive. MD simulation with wild type (WT) NS, strand 6B and helix B variants indicated that substitution in this region affects the conformation of the strands 5B, 5A and reactive centre loop. Therefore, we designed variants of NS in strand 6B (I46D and F48S) and helix B (A54F, L55A and L55P) to investigate their role in tPA inhibition mechanism and propensity to aggregate. An interaction analysis showed disturbance of a hydrophobic patch centered at strands 5B, 6B and helix B in I46D and F48S but not in A54F, L55A, L55P and WT NS. Purified I46D, F48S and L55P variants showed decrease in fluorescence emission intensity but have similar α-helical content, however results of A54F and L55A were comparable to WT NS. Analysis of tPA inhibition showed marginal effect on A54F and L55A variant with tPA-NS complex formation. In contrast, I46D, F48S and L55P variants showed massive decrease in tPA inhibition, with no tPA-NS complex formation. Analysis of native PAGE under under polymerization condition showed prompt conversion of I46D, F48S and L55P to latent conformation but not A54F and L55A variants. Identification of these novel conformational changes will aid in the understanding of variable clinical phenotype of shutter region NS variants and other serpins.

Measuring stigma in children receiving mental health treatment: Validation of the Paediatric Self-Stigmatization Scale (PaedS)

Background:

Research on the impact of stigma associated with mental illness in children is scarce. Considering the known negative effects of stigma associated with mental illness in adults, it is crucial to explore the stigma experienced by children who access mental health treatment. However, no scale measuring self-stigmatization in younger children is available to date. This study aimed to develop and validate such a scale, the Paediatric Self-Stigmatization Scale (PaedS).

Methods:

A total of 156 children (119 receiving outpatient and 37 receiving inpatient treatment), aged 8–12 years, completed the PaedS, the Self-Perception Profile for Children and the Pediatric Quality of Life Inventory (PedsQL – Child Report, ages 8–12). In addition, parents completed the PedsQL (Parent Report for Children, ages 8–12), the Strengths and Difficulties Questionnaire (SDQ) and a modified subscale of the PaedS measuring the children's rejection by others due to their mental health difficulties.

Results:

A confirmatory factor analysis showed that a four-factor structure, comprising Societal Devaluation, Personal Rejection, Self-Stigma and Secrecy scales, had excellent fit to the data (CFI = 0.95; TLI = 0.95; RMSEA = 0.05). Child-reported PaedS scores were positively correlated with parental-reported PaedS scores and negatively with PedsQL, the SDQ, and 5 out of 6 subscales of the Self-Perception Profile for Children, suggesting adequate convergent validity (all P-values < 0.05).

Conclusions:

The PaedS is a valid instrument, which is hoped to advance the understanding of self-stigmatization in children with mental health difficulties and contribute to its prevention.

P1496Use of strain, strain rate, tissue velocity imaging and endothelial function for early detection of cardiovascular involvement in young diabetics

Background

Subtle structural and functional changes may precede the onset of overt global left ventricular dysfunction and obvious reduction of ejection fraction (EF), especially in young diabetics. Data pertaining to tissue velocity indices (TVI) and strain imaging to assess regional myocardial function and flow mediated vasodilatation is limited in young patients with diabetes.

Purpose

To evaluate conventional echocardiography parameters, tissue doppler indices, global and regional strain, carotid intimal medial thickness (CIMT), endothelial dependent (FMD) and independent function (NMD) of brachial artery in young patients (age <18 years) with type 1 diabetes and compare them with matched controls.

Methods

Conventional echocardiography parameters, tissue velocity indices (TVI) parameters along with strain (S), and strain rate (SR) in basal and mid left ventricular (LV) lateral wall, right ventricular (RV) lateral wall and septum were measured in 50 young diabetics (age 15.16±2.95 years, mean HBA1c 8.15±1.37 gm %) and 25 controls (age 15.60±2.51 years). Flow-mediated dilatation (FMD), nitrate mediated dilatation and carotid intimal media thickness (CIMT) were also estimated.

Results

Conventional echocardiography parameters were similar in patients and controls however deceleration time of the mitral inflow velocity (EDT) was significantly shorter in patients when compared with controls (149.06±31.66 vs. 184.56±19.27 ms, p<0.05). Lateral early diastolic myocardial velocity (LV-Em) was significantly lower (10.30±0.99 vs. 11.67±3.21, p<0.05) whereas lateral late diastolic myocardial velocity (LV-Am) was significantly higher than controls (11.73±1.44 vs. 8.82±1.69, p<0.05), thus a significantly lower ratio of early/late diastolic velocity at the basal segment of lateral LV (LV-Em/Am). Lower strain values at the basal lateral LV (21.39±4.12 vs. 23.78±2.02; p<0.05), mid lateral LV (21.43±4.27 vs. 23.17±1.92; p<0.05), basal septum (20.59±5.28 vs. 22.91±2.00; p<0.05), and mid septum (22.06±4.75 vs. 24.10±1.99; p<0.05) as compared to controls. SR at the basal and mid segments of the lateral LV wall and at the basal septum were also significantly lower in diabetic subjects. Strain rate (SR) in mid septal, basal and mid RV were lower than controls although not statistically significant. Patients also had significantly lower flow mediated dilatation (FMD) (8.36±4.27 vs. 10.57±4.12, p<0.05) implying endothelial dysfunction.

Strain rate in diabetic patient

Conclusion

Left ventricular strain indices are impaired in asymptomatic children and adolescents with type 1 DM despite absence of overt heart failure and normal ejection fraction. Early detection of subclinical regional myocardial dysfunction by deformation analysis including strain and strain rate may be useful in the asymptomatic diabetic population. In addition, evidence of endothelial dysfunction in the form of impaired flow mediated vasodilatation was observed in the diabetic children.

Acknowledgement/Funding

None

ApicoTFdb: the comprehensive web repository of apicomplexan transcription factors and transcription-associated co-factors

Despite significant progress in apicomplexan genome sequencing and genomics, the current list of experimentally validated transcription factors (TFs) in these genomes is incomplete and mainly consists of AP2 family of proteins, with only a limited number of non-AP2 family TFs and transcription-associated co-factors (TcoFs). We have performed a systematic bioinformatics-aided prediction of TFs and TcoFs in apicomplexan genomes and developed the ApicoTFdb database which consists of experimentally validated as well as computationally predicted TFs and TcoFs in 14 apicomplexan species. The predicted TFs are manually curated to complement the existing annotations. The current version of the database includes 1292 TFs which includes experimentally validated and computationally predicted TFs, representing 20 distinct families across 14 apicomplexan species. The predictions include TFs of TUB, NAC, BSD, HTH, Cupin/Jumonji, winged helix and FHA family proteins, not reported earlier as TFs in the genomes. Apart from TFs, ApicoTFdb also classifies TcoFs into three main subclasses: TRs, CRRs and RNARs, representing 2491 TcoFs in 14 apicomplexan species, are analyzed in this study. The database is designed to integrate different tools for comparative analysis. All entries in the database are dynamically linked with other databases, literature reference, protein–protein interactions, pathways and annotations associated with each protein. ApicoTFdb will be useful to the researchers interested in less-studied gene regulatory mechanisms mediating the complex life cycle of the apicomplexan parasites. The database will aid in the discovery of novel drug targets to much needed combat the growing drug resistance in the parasites.