ALBERT

Description: Background: Influenza virus pandemics vary dramatically in their severity and mortality. Thus, it is very important to identify populations with high risks of developing severe illness to reduce mortality in future pandemics. The purpose was to determine the mortality-associated risk factors in hospitalized Mexican patients infected with influenza A/H1N1. Results: The risk factors associated with mortality were: male sex [odds ratio (OR) = 5.25, confidence interval (CI) = 1.22–28.95], medical attention delayed 〉3 days (OR = 9.9, CI = 1.51–64.52), anti-flu therapy delayed 〉3 days (OR = 10.0, CI = 1.07–93.43), admission to intensive care unit (ICU) (OR = 9.9, CI = 1.51–64.52) and creatinine levels 〉1.0 mg/dL when admitted to hospital (OR = 11.2, CI = 1.05–120.32). After adjusting for the effects of potentially confounding variables in a logistic regression model, delayed medical attention (OR = 13.91, CI = 1.09–41.42, p = 0.044) and ICU hospitalization (OR = 11.02, CI = 1.59–76.25, p = 0.015) were the only predictors of mortality. Conclusion: Early medical attention is essential for reducing the mortality risk in patients with influenza A/H1N1, while a requirement for ICU management increases the risk.

Description: Background: Crescentic glomerulonephritis is a rare condition in children and is typically associated with renal insufficiency. Dysfunction of the alternative complement pathway is an unusual aetiology with an unknown mechanism.Case presentationWe report a case of a previously healthy 12-year-old Caucasian girl who was examined on emergency owing to an asymptomatic gross haematuria. An active urinary sediment and nephrotic-range proteinuria were identified, and serologic examination showed a decreased serum C3 concentration not associated with any immunologic or infectious cause. Oedema, hypertension, and renal insufficiency were not observed. A renal biopsy was performed, and crescentic glomerulonephritis associated with C3 glomerulonephritis was diagnosed. Prompt treatment with intravenous steroids resulted in complete resolution of the gross haematuria. Further examination did not detect any underlying acquired cause. A combination of oral steroids and cyclophosphamide, followed by mycophenolate mofetil, was maintained and resulted in clinical remission during an 8-month follow-up. Conclusion: The presence of severe injury such as crescentic glomerulonephritis secondary to C3 glomerulonephritis is extremely unusual in children. This is the first known case of paediatric crescentic glomerulonephritis secondary to C3 glomerulonephritis that presented with gross haematuria and was treated early and effectively with immunosuppressive therapy based on its severe histologic features.

Description: Background: The rearrangements in the 22q11.2 chromosomal region, responsible for the 22q11.2 deletion and microduplication syndromes, are frequently associated with congenital heart disease (CHD). The present work aimed to identify the genetic basis of CHD in 87 patients from the S?o Miguel Island, Azores, through the detection of copy number variants (CNVs) in the 22q11.2 region. These structural variants were searched using multiplex ligation-dependent probe amplification (MLPA). In patients with CNVs, we additionally performed fluorescent in situ hybridization (FISH) for the assessment of the exact number of 22q11.2 copies among each chromosome, and array comparative genomic hybridization (array-CGH) for the determination of the exact length of CNVs. Results: We found that four patients (4.6%; A to D) carried CNVs. Patients A and D, both affected with a ventricular septal defect, carried a de novo 2.5?Mb deletion of the 22q11.2 region, which was probably originated by inter-chromosomal (inter-chromatid) non-allelic homologous recombination (NAHR) events in the regions containing low-copy repeats (LCRs). Patient C, with an atrial septal defect, carried a de novo 2.5?Mb duplication of 22q11.2 region, which could have been probably generated during gametogenesis by NAHR or by unequal crossing-over; additionally, this patient presented a benign 288 Kb duplication, which included the TOP3B gene inherited from her healthy mother. Finally, patient B showed a 3?Mb triplication associated with dysmorphic facial features, cognitive deficit and heart defects, a clinical feature not reported in the only case described so far in the literature. The evaluation of patient B?s parents revealed a 2.5?Mb duplication in her father, suggesting a paternal inheritance with an extra copy. Conclusions: This report allowed the identification of rare deletion and microduplication syndromes in Azorean CHD patients. Moreover, we report the second patient with a 22q11.2 triplication, and we suggest that patients with triplications of chromosome 22q11.2, although they share some characteristic features with the deletion and microduplication syndromes, present a more severe phenotype probably due to the major dosage of implicated genes.

Description: Background: Innate immune system is the first line of research when studying immune response to diverse infections and autoimmune/inflammatory diseases. This immune response has been reported to be genetically diverse, due to polymorphisms coded by different genes. For this reason, our purpose was to develop a multiplex assay that allows the genotyping of candidate single nucleotide polymorphisms (SNPs) in innate immune genes.FindingsWe developed three multiplex PCR panels coupled with the minisequencing (SNaPshot) technique (multiplex PCR, multiplex primer extension, and capillary electrophoresis). The panels were tested in a sample set composed of 100 anonymous DNAs from healthy blood donors living in Sao Miguel Island (Azores, Portugal). Sixteen relevant SNPs among nine genes of the innate immune system -- IL1alpha, IL1beta, IL6, IL10, IL12RB1, TLR2, TLR4, TLR9 and CD14 -- were genotyped and validated by direct sequencing, with the exception of one that was undetected by minisequencing. We suggest that these panels can be used in future studies for detection of risk gene variants in several populations and/or diseases. Conclusions: In summary, we propose a multiplex assay that is able to identify the most frequent candidate SNPs in innate immune genes, using a medium scale genotyping platform. The assays can be used to evaluate the risk gene variants in populations of various geographic origins.

Description: Background: Restriction site-associated DNA sequencing (RAD-Seq) is a genome complexity reduction technique that facilitates large-scale marker discovery and genotyping by sequencing. Recent applications of RAD-Seq have included linkage and QTL mapping with a particular focus on non-model species. In the current study, we have applied RAD-Seq to two Atlantic salmon families from a commercial breeding program. The offspring from these families were classified into resistant or susceptible based on survival/mortality in an Infectious Pancreatic Necrosis (IPN) challenge experiment, and putative homozygous resistant or susceptible genotype at a major IPN-resistance QTL. From each family, the genomic DNA of the two heterozygous parents and seven offspring of each IPN phenotype and genotype was digested with the SbfI enzyme and sequenced in multiplexed pools. Results: Sequence was obtained from approximately 70,000 RAD loci in both families and a filtered set of 6,712 segregating SNPs were identified. Analyses of genome-wide RAD marker segregation patterns in the two families suggested SNP discovery on all 29 Atlantic salmon chromosome pairs, and highlighted the dearth of male recombination. The use of pedigreed samples allowed us to distinguish segregating SNPs from putative paralogous sequence variants resulting from the relatively recent genome duplication of salmonid species. Of the segregating SNPs, 50 were linked to the QTL. A subset of these QTL-linked SNPs were converted to a high-throughput assay and genotyped across large commercial populations of IPNV-challenged salmon fry. Several SNPs showed highly significant linkage and association with resistance to IPN, and population linkage-disequilibrium-based SNP tests for resistance were identified. Conclusions: We used RAD-Seq to successfully identify and characterise high-density genetic markers in pedigreed aquaculture Atlantic salmon. These results underline the effectiveness of RAD-Seq as a tool for rapid and efficient generation of QTL-targeted and genome-wide marker data in a large complex genome, and its possible utility in farmed animal selection programs.

Description: Background: Keeping up-to-date with bioscience literature is becoming increasingly challenging. Several recent methods help meet this challenge by allowing literature search to be launched based on lists of abstracts that the user judges to be 'interesting'. Some methods go further by allowing the user to provide a second input set of 'uninteresting' abstracts; these two input sets are then used to search and rank literature by relevance. In this work we present the service 'Caipirini' (http://caipirini.org) that also allows two input sets, but takes the novel approach of allowing ranking of literature based on one or more sets of genes. Results: To evaluate the usefulness of Caipirini, we used two test cases, one related to the human cell cycle, and a second related to disease defense mechanisms in Arabidopsis thaliana. In both cases, the new method achieved high precision in finding literature related to the biological mechanisms underlying the input data sets. Conclusions: To our knowledge Caipirini is the first service enabling literature search directly based on biological relevance to gene sets; thus, Caipirini gives the research community a new way to unlock hidden knowledge from gene sets derived via high-throughput experiments.

Description: Background: Crescentic glomerulonephritis is a rare condition in children and is typically associated with renal insufficiency. Dysfunction of the alternative complement pathway is an unusual aetiology with an unknown mechanism.Case presentationWe report a case of a previously healthy 12-year-old Caucasian girl who was examined on emergency owing to an asymptomatic gross haematuria. An active urinary sediment and nephrotic-range proteinuria were identified, and serologic examination showed a decreased serum C3 concentration not associated with any immunologic or infectious cause. Oedema, hypertension, and renal insufficiency were not observed. A renal biopsy was performed, and crescentic glomerulonephritis associated with C3 glomerulonephritis was diagnosed. Prompt treatment with intravenous steroids resulted in complete resolution of the gross haematuria. Further examination did not detect any underlying acquired cause. A combination of oral steroids and cyclophosphamide, followed by mycophenolate mofetil, was maintained and resulted in clinical remission during an 8-month follow-up. Conclusion: The presence of severe injury such as crescentic glomerulonephritis secondary to C3 glomerulonephritis is extremely unusual in children. This is the first known case of paediatric crescentic glomerulonephritis secondary to C3 glomerulonephritis that presented with gross haematuria and was treated early and effectively with immunosuppressive therapy based on its severe histologic features.

Description: Pine wilt disease (PWD) is a worldwide threat to pine forests, and is caused by the pine wood nematode (PWN) Bursaphelenchus xylophilus. Bacteria are known to be associated with PWN and may have an important role...

Description: Ligation of the mesovarium in female dogs may be cumbersome with risk of complications and is associated with intense noxious stimuli. A resorbable implant, a self-locking loop designed for surgery, was develo...

Description: Infectious Pancreatic Necrosis (IPN) is a highly contagious birnavirus disease of farmed salmonid fish, which often causes high levels of morbidity and mortality. A large host genetic component to resistance h...