Improving Mutation Screening in Familial Hematuric Nephropathies through Next Generation Sequencing

Alport syndrome is an inherited nephropathy associated with mutations in genes encoding type IV collagen chains present in the glomerular basement membrane. COL4A5 mutations are associated with the major X-linked form of the disease, and COL4A3 and COL4A4 mutations are associated with autosomal recessive and dominant forms (thought to be involved in 15% and 1%–5% of the families, respectively) and benign familial hematuria. Mutation screening of these three large genes is time-consuming and expensive. Here, we carried out a combination of multiplex PCR, amplicon quantification, and next generation sequencing (NGS) analysis of three genes in 101 unrelated patients. We identified 88 mutations and 6 variations of unknown significance on 116 alleles in 83 patients. Two additional indel mutations were found only by secondary Sanger sequencing, but they were easily identified retrospectively with the web-based sequence visualization tool Integrative Genomics Viewer. Altogether, 75 mutations were novel. Sequencing the three genes simultaneously was particularly advantageous as the mode of inheritance could not be determined with certainty in many instances. The proportion of mutations in COL4A3 and COL4A4 was notably high, and the autosomal dominant forms of Alport syndrome appear more frequently than reported previously. Finally, this approach allowed the identification of large COL4A3 and COL4A4 rearrangements not described previously. We conclude that NGS is efficient, reduces screening time and cost, and facilitates the provision of appropriate genetic counseling in Alport syndrome.     

How much energy is locked in the USA? Alternative metrics for characterising the magnitude of overweight and obesity derived from BRFSS 2010 data

Objectives

Four metrics to characterise population overweight are described.

Methods

Behavioural Risk Factors Surveillance System data were used to estimate the weight the US population needed to lose to achieve a BMI < 25. The metrics for population level overweight were total weight, total volume, total energy, and energy value.

Results

About 144 million people in the US need to lose 2.4 million metric tonnes. The volume of fat is 2.6 billion litres—1,038 Olympic size swimming pools. The energy in the fat would power 90,000 households for a year and is worth around 162 million dollars.

Conclusions

Four confronting ways of talking about a national overweight and obesity are described. The value of the metrics remains to be tested.     

Anticaries activity of egg ovalbumin in an experimental caries biofilm model on enamel and dentin

Objectives

Limited evidence suggests a putative inhibitory effect of dietary proteins on demineralization during the carious process. The aim was to explore a potential anticaries activity of the egg protein ovalbumin on a relevant in vitro approach.

Materials and methods

Biofilms of Streptococcus mutans UA159 were formed on saliva-coated enamel and dentin bovine slabs. Biofilms were challenged with 10% sucrose followed by either a 200 μg/mL solution of ovalbumin or 1:10, 1:100, and 1:1000 (v/v) serial dilutions of that ovalbumin solution, for the entire length of the experiment. Biofilms exposed to 10% sucrose followed only by 0.9% NaCl served as caries-positive control. Once completed the experimental phase, biofilms were analyzed for biomass, viable bacteria, and polysaccharide formation. Final surface hardness (SH) was obtained to calculate %SH loss (demineralization). Two independent experiments were conducted, in triplicate. Data were analyzed by ANOVA and a post hoc test at the 95% confidence level.

Results

A reduction (p < 0.05) in biomass and extracellular polysaccharide formation, but not in the number of viable cells, was observed for both dental substrates. All ovalbumin concentrations tested showed lower demineralization than the positive control (p < 0.05), in a dose-dependent manner. The highest concentration showed a reduction in the %SH loss of about 30% for both enamel and dentin.

Conclusion

Egg ovalbumin presented to sucrose-challenged biofilms of Streptococcus mutans seems to reduce cariogenicity of a biofilm-caries model.

Clinical relevance

Ovalbumin may counteract the cariogenic effect of sugars. If these findings are clinically confirmed, novel preventive approaches for caries are warranted.

     

Idiopathic CD4 Lymphocytopenia: Clinical and Immunologic Characteristics and Follow-Up of 40 Patients

Idiopathic CD4 T lymphocytopenia (ICL) is a rare and severe condition with limited available data. We conducted a French multicenter study to analyze the clinical and immunologic characteristics of a cohort of patients with ICL according to the Centers for Disease Control criteria.We recruited 40 patients (24 female) of mean age 44.2 ± 12.2 (19–70) years. Patients underwent T-lymphocyte phenotyping and lymphoproliferation assay at diagnosis, and experiments related to thymic function and interferon (IFN)-γ release by natural killer (NK) cell were performed. Mean follow-up was 6.9 ± 6.7 (0.14–24.3) years. Infectious, autoimmune, and neoplastic events were recorded, as were outcomes of interleukin 2 therapy.In all, 25 patients had opportunistic infections (12 with human papillomavirus infection), 14 had autoimmune symptoms, 5 had malignancies, and 8 had mild or no symptoms. At the time of diagnosis, the mean cell counts were as follows: mean CD4 cell count: 127/mm³ (range, 4–294); mean CD8: 236/mm³ (range, 1–1293); mean CD19: 113/mm³ (range, 3–547); and mean NK cell count: 122/mm³ (range, 5–416). Most patients had deficiency in CD8, CD19, and/or NK cells. Cytotoxic function of NK cells was normal, and patients with infections had a significantly lower NK cell count than those without (p = 0.01). Patients with autoimmune manifestations had increased CD8 T-cell count. Proliferation of thymic precursors, as assessed by T-cell rearrangement excision circles, was increased. Six patients died (15%). CD4 T-cell count <150/mm³ and NK cell count <100/mm³ were predictors of death.In conclusion, ICL is a heterogeneous disorder often associated with deficiencies in CD8, CD19, and/or NK cells. Long-term prognosis may be related to initial CD4 and NK cell deficiency.Abbreviations: AIHA = autoimmune hemolytic anemia, CDC = Centers for Disease Control, CMV = cytomegalovirus, cpm = count per minute, CVID = common variable immunodeficiency, CXCR4 = C-X-C chemokine receptor type 4, HIV = human immunodeficiency virus, HLA = human leukocyte antigen, HPV = human papillomavirus, HTLV-1/2 = human T-cell lymphotropic 1/2, ICL = idiopathic CD4 T lymphocytopenia, IFN-γ = interferon-γ, IL = interleukin, JC virus = John Cunningham virus, LPA = lymphocyte proliferation assay, NK = natural killer, P = patient, PBMC = peripheral blood mononuclear cell, Pwd = pokeweed, SI = stimulation index, sj = signal joint, TREC = T-cell rearrangement excision circle     

System factors to explain H1N1 state vaccination rates for adults in US emergency response to pandemic

Introduction

During the 2009–2010 H1N1 pandemic, vaccine in short supply was allocated to states pro rata by population, yet the vaccination rates of adults differed by state. States also differed in their campaign processes and decisions. Analyzing the campaign provides an opportunity to identify specific approaches that may result in higher vaccine uptake in a future event of this nature.

Objective

To determine supply chain and system factors associated with higher state H1N1 vaccination coverage for adults in a system where vaccine was in short supply.

Methods

Regression analysis of factors predicting state-specific H1N1 vaccination coverage in adults. Independent variables included state campaign information, demographics, preventive or health-seeking behavior, preparedness funding, providers, state characteristics, and H1N1-specific state data.

Results

The best model explained the variation in state-specific adult vaccination coverage with an adjusted R-squared of 0.76. We found that higher H1N1 coverage of adults is associated with program aspects including shorter lead-times (i.e., the number of days between when doses were allocated to a state and were shipped, including the time for states to order the doses) and less vaccine directed to specialist locations. Higher vaccination coverage is also positively associated with the maximum number of ship-to locations, past seasonal influenza vaccination coverage, the percentage of women with a Pap smear, the percentage of the population that is Hispanic, and negatively associated with a long duration of the epidemic peak.

Conclusion

Long lead-times may be a function of system structure or of efficiency and may suggest monitoring or redesign of distribution processes. Sending vaccine to sites with broad access could be useful when covering a general population. Existing infrastructure may be reflected in the maximum number of ship-to locations, so strengthening routine influenza vaccination programs may help during emergency vaccinations also. Future research could continue to inform program decisions.     

Evaluation of 16S rRNA Gene PCR Sensitivity and Specificity for Diagnosis of Prosthetic Joint Infection: a Prospective Multicenter Cross-Sectional Study

There is no standard method for the diagnosis of prosthetic joint infection (PJI). The contribution of 16S rRNA gene PCR sequencing on a routine basis remains to be defined. We performed a prospective multicenter study to assess the contributions of 16S rRNA gene assays in PJI diagnosis. Over a 2-year period, all patients suspected to have PJIs and a few uninfected patients undergoing primary arthroplasty (control group) were included. Five perioperative samples per patient were collected for culture and 16S rRNA gene PCR sequencing and one for histological examination. Three multicenter quality control assays were performed with both DNA extracts and crushed samples. The diagnosis of PJI was based on clinical, bacteriological, and histological criteria, according to Infectious Diseases Society of America guidelines. A molecular diagnosis was modeled on the bacteriological criterion (≥1 positive sample for strict pathogens and ≥2 for commensal skin flora). Molecular data were analyzed according to the diagnosis of PJI. Between December 2010 and March 2012, 264 suspected cases of PJI and 35 control cases were included. PJI was confirmed in 215/264 suspected cases, 192 (89%) with a bacteriological criterion. The PJIs were monomicrobial (163 cases [85%]; staphylococci, n = 108; streptococci, n = 22; Gram-negative bacilli, n = 16; anaerobes, n = 13; others, n = 4) or polymicrobial (29 cases [15%]). The molecular diagnosis was positive in 151/215 confirmed cases of PJI (143 cases with bacteriological PJI documentation and 8 treated cases without bacteriological documentation) and in 2/49 cases without confirmed PJI (sensitivity, 73.3%; specificity, 95.5%). The 16S rRNA gene PCR assay showed a lack of sensitivity in the diagnosis of PJI on a multicenter routine basis.     

Prospective Evaluation of Diagnostic Accuracy of Dried Blood Spots from Finger Prick Samples for Determination of HIV-1 Load with the NucliSENS Easy-Q HIV-1 Version 2.0 Assay in Malawi

HIV-1 viral load (VL) testing is not widely available in resource-limited settings. The use of finger prick dried blood spot (FP-DBS) samples could remove barriers related to sample collection and transport. Measurement of VL using DBS from EDTA venous blood (VB-DBS) in place of plasma has previously been validated using the NucliSENS Easy-Q HIV-1 v2.0 assay, but information on the accuracy of FP-DBS samples for measuring VL is limited. This prospective study, conducted at Thyolo District Hospital in southern Malawi, compared VL levels measured on FP-DBS samples and plasma using the NucliSENS Easy-Q HIV-1 v2.0 assay. Comparability was assessed by means of agreement and correlation (131 patients with VLs of ≥100 copies/ml), sensitivity, and specificity (612 patients on antiretroviral treatment [ART]). Samples of EDTA venous blood and FP-DBS from 1,009 HIV-infected individuals were collected and prepared in the laboratory. Bland-Altman analysis found good agreement between plasma and FP-DBS VL levels, with a mean difference of −0.35 log₁₀, and 95% limits of agreement from −1.26 to 0.55 log₁₀. FP-DBS had a sensitivity of 88.7% (95% confidence interval [CI], 81.1 to 94.4%) and a specificity of 97.8% (95% CI, 96.1 to 98.9%) using a 1,000-copies/ml cut point and a sensitivity of 83.0% (95% CI, 73.4 to 90.1%) and a specificity of 100% (95% CI, 99.3 to 100%) using a 5,000-copies/ml cut point. This study shows that FP-DBS is an acceptable alternative to plasma for measuring VL using the NucliSENS Easy-Q HIV-1 v2.0. We are conducting a second study to assess the proficiency of health workers at preparing FP-DBS in primary health care clinics.     

The Lepidopteran endoribonuclease-U domain protein P102 displays dramatically reduced enzymatic activity and forms functional amyloids

Hemocytes of Heliothis virescens (F.) (Lepidoptera, Noctuidae) larvae produce a protein, P102, with a putative endoribonuclease-U domain. In previous works we have shown that P102 is involved in Lepidopteran immune response by forming amyloid fibrils, which catalyze and localize melanin deposition around non-self intruders during encapsulation, preventing harmful systemic spreading. Here we demonstrate that P102 belongs to a new class of proteins that, at least in Lepidoptera, has a diminished endoribonuclease-U activity probably due to the lack of two out of five catalytically essential residues. We show that the P102 homolog from Trichoplusia ni (Lepidoptera, Noctuidae) displays catalytic site residues identical to P102, a residual endoribonuclease-U activity and the ability to form functional amyloids. On the basis of these results as well as sequence and structural analyses, we hypothesize that all the Lepidoptera endoribonuclease-U orthologs with catalytic site residues identical to P102 form a subfamily with similar function.