Thermodynamic behavior of short oligonucleotides in microarray hybridizations can be described using Gibbs free energy in a nearest-neighbor model

While designing oligonucleotide-based microarrays, cross-hybridization between surface-bound oligos and non-intended labeled targets is probably the most difficult parameter to predict. Although literature describes rules-of-thumb concerning oligo length, overall similarity, and continuous stretches, the final behavior is difficult to predict. The aim of this study was to investigate the effect of well-defined mismatches on hybridization specificity using CodeLink Activated Slides, and to study quantitatively the relation between hybridization intensity and Gibbs free energy (Delta G), taking the mismatches into account. Our data clearly showed a correlation between the hybridization intensity and Delta G of the oligos over three orders of magnitude for the hybridization intensity, which could be described by the Langmuir model. As Delta G was calculated according to the nearest-neighbor model, using values related to DNA hybridizations in solution, this study clearly shows that target-probe hybridizations on microarrays with a three-dimensional coating are in quantitative agreement with the corresponding reaction in solution. These results can be interesting for some practical applications. The correlation between intensity and Delta G can be used in quality control of microarray hybridizations by designing probes and corresponding RNA spikes with a range of Delta G values. Furthermore, this correlation might be of use to fine-tune oligonucleotide design algorithms in a way to improve the prediction of the influence of mismatching targets on microarray hybridizations.Comment: 32 pages on a single pdf fil

The effects of mismatches on hybridization in DNA microarrays: determination of nearest neighbor parameters

Quantifying interactions in DNA microarrays is of central importance for a better understanding of their functioning. Hybridization thermodynamics for nucleic acid strands in aqueous solution can be described by the so-called nearest-neighbor model, which estimates the hybridization free energy of a given sequence as a sum of dinucleotide terms. Compared with its solution counterparts, hybridization in DNA microarrays may be hindered due to the presence of a solid surface and of a high density of DNA strands. We present here a study aimed at the determination of hybridization free energies in DNA microarrays. Experiments are performed on custom Agilent slides. The solution contains a single oligonucleotide. The microarray contains spots with a perfect matching complementary sequence and other spots with one or two mismatches: in total 1006 different probe spots, each replicated 15 times per microarray. The free energy parameters are directly fitted from microarray data. The experiments demonstrate a clear correlation between hybridization free energies in the microarray and in solution. The experiments are fully consistent with the Langmuir model at low intensities, but show a clear deviation at intermediate (non-saturating) intensities. These results provide new interesting insights for the quantification of molecular interactions in DNA microarrays.Comment: 31 pages, 5 figure

Comparative Study of the Standard Fluorescent Antibody to Membrane Antigen (FAMA) Assay and a Flow Cytometry-Adapted FAMA Assay To Assess Immunity to Varicella-Zoster Virus

A flow cytometry-adapted fluorescent antibody to membrane antigen (FAMA) assay to detect IgG antibodies against varicella-zoster virus (VZV) was developed and tested in 62 serum samples, showing 90.32% accuracy obtained from a receiver operating characteristic (ROC) curve with a 0.9125 (95% confidence interval [CI], 0.829 to 1.00) area below the curve compared to the result with standard FAMA.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fed Univ São Paulo UNIFESP EPM, Div Pediat Infect Dis, BR-04040000 São Paulo, BrazilColumbia Univ, Dept Pediat, Coll Phys & Surg, New York, NY 10027 USAFed Univ São Paulo UNIFESP EPM, Div Pediat Infect Dis, BR-04040000 São Paulo, BrazilCAPES: 0108-08-1Web of Scienc

Epithelium and stroma from nasal polyp mucosa exhibits inverse expression of TGF- beta(1) as compared with healthy nasal mucosa

Objective: To evaluate TGF-beta(1) expression in polypoid mucosa (epithelium and stroma) of patients with chronic rhinosinusitis with nasal polyposis (CRSwNP).Methods: Cross-sectional study with two groups: 17 patients with nasal polyposis and 11 controls. Polyps and normal nasal mucosa were processed by immunohistochemical methods for TGF-beta 1 visualization. Then, the percentage of TGF-beta 1 expression in stroma and epithelium was objectively quantified using UT Morph software.Results: A lower percentage of positive expression was found in the epithelium of CRSwNP patients (32.44%) versus normal controls (55.91%) (p < 0.05), and a higher percentage of positive expression in the stroma of CRSwNP patients (23.24%) versus controls (5.88%) (p < 0.05).Conclusion: the lower percentage of TGF-beta(1) expression in the nasal epithelium of CRSwNP patients may have an impact on epithelium-directed topical treatments employed in this patient population.Universidade Federal de São Paulo, Dept Otolaryngol Head & Neck Surg, São Paulo, BrazilUniv Ghent, Ghent Univ Hosp, Dept Otorhinolaryngol, Upper Airway Res Lab, B-9000 Ghent, BelgiumUniversidade Federal de São Paulo, Dept Pathol, São Paulo, BrazilUniversidade Federal de São Paulo, Dept Otolaryngol Head & Neck Surg, São Paulo, BrazilUniversidade Federal de São Paulo, Dept Pathol, São Paulo, BrazilWeb of Scienc

Squamous cell carcinoma of the lip: assessment of prognostic factors

Among lip cancers, 90% to 95% of them affect the lower lip and squamous cell carcinoma is the most frequent type. The TNM classification synthesizes the clinical characteristics of the tumor that allows prognosis and makes possible the comparisons of the results. Three parameters have to be considered: size of the tumor (T), propagation to regional lymphatic ganglion (N) and metastasis (M); however, patterns starting from 2cm are established by the TNM classification. In the case of squamous cell carcinoma of the lips, 2cm lesions are considered extremely large. AIM: The objective of this study was to verify the correlation among epidemiologic, clinical, evolutionary and histopathological characteristics of squamous cell carcinoma of the lips, having as parameter lesions as small as 0.5cm. MATERIAL AND METHODS: In the period 1993-2000 in São Paulo, Brazil, a transversal retrospective study was performed with patients exhibiting squamous cell carcinoma of the lips. The characteristics of the tumor were investigated through the analysis of patients' medical charts, original reports of the histopathological exams and tumors' samples. The tumors were classified from 0.5 to 2.5cm. In addition, type, grade of histologic differentiation, the presence of desmoplasia, muscular, neural and vascular infiltration, and type of inflammatory infiltrate were investigated. RESULTS: The statistical analyses indicated that metastasis and recurrences do not depend on patients' gender and race. The independence of the tumor's localization, either in the upper or lower lip, and the incidence of metastasis and recurrence were demonstrated. A correlation between lesions as large as 0.5cm and the occurrence of metastasis and recurrence was verified. Furthermore, it was observed that the size of lesion determines the infiltration in other tissues. Lymphoplasmocytarian is the type of inflammatory infiltrate that was found in each and every lesion. On the other hand, in some of the lesions, the inflammatory infiltrate was associated with eosinophils without correlation to size of tumor. CONCLUSION: Smaller tumors than 2cm, from a histopathological and clinical point of view, may present a distinct evolution behavior. Most of the lesions are ulcerative, though the ulcerative-vegetative is the one that presents the most metastasis and recurrence. The ulcerative-vegetative and vegetative types are associated with the largest lesions. The size of the tumor is related, in a similar way, to grades II and III, in which higher rates of metastasis and recurrence were observed. In decreasing order of frequency, the tumor invades muscles, nerves and blood vessels, which can be related to the size of the lesion. Thus, in order to have metastasis, it is necessary to have infiltration of muscles. Yet, blood vessels can only be involved when there is concomitant infiltration of nerves. As a result, desmoplasia is directly related to size of the lesion as well as to occurrence of metastasis.Dentre os cânceres do lábio de 90% a 95% dos casos afetam o lábio inferior, sendo o carcinoma espinocelular o mais freqüente. A classificação TNM sintetiza as características clínicas do tumor, permitindo realizar um prognóstico e possibilitando comparações dos resultados. Relaciona três parâmetros: tamanho do tumor (T), propagação aos gânglios linfáticos regionais (N) e metástases à distância (M), mas estabelece padrões a partir de 2cm. Para o carcinoma espinocelular do lábio lesões com 2cm são extremamente grandes. OBJETIVO: O objetivo deste estudo é verificar a relação entre as características epidemiológicas, clínicas, evolutivas e histopatológicas do carcinoma espinocelular do lábio tendo como parâmetro lesões de tamanhos a partir de 0,5cm. CASUÍSTICA E MÉTODO: Foi elaborado um estudo retrospectivo transversal em pacientes com carcinoma espinocelular do lábio, no período 1993-2000, em São Paulo, Brasil. Estudou-se prontuários, laudos originais dos exames histopatológicos e lâminas de tumores de pacientes com carcinoma espinocelular do lábio. Os tumores foram classificados de 0.5 em 0.5cm, sendo verificado o tipo, o grau de diferenciação histológica, a presença de desmoplasia, as invasões muscular, neural e vascular, e o tipo de infiltrado inflamatório. RESULTADOS: A análise estatística mostrou que metástases e recidivas não dependem da cor de pele ou do sexo dos pacientes e que há independência entre a localização do tumor, no lábio superior ou inferior, e a incidência de metástases e recidiva. Houve correlação entre o tamanho da lesão a partir de 0,5cm e a ocorrência de metástases e recidiva. Verificou-se que o tamanho da lesão determina a invasão em outros tecidos. O infiltrado inflamatório verificado em todas as lesões era linfoplasmocitário e, em algumas, associado com eosinófilos sem relação com o tamanho do tumor. CONCLUSÃO: Tumores menores que 2cm podem apresentar comportamentos evolutivos distintos, sob o ponto de vista clínico e histopatológico. O tipo mais prevalente de lesão é o ulcerativo e o que mais metastatiza e recidiva é o úlcero-vegetante. Os tipos úlcero-vegetante e vegetante estão ligados a lesões de maior tamanho. O tamanho do tumor se relaciona, de forma semelhante, com os graus II e III, nos quais ocorrem os maiores índices de metástases e recidivas. O tumor invade em ordem decrescente de freqüência músculos, nervos e vasos sanguíneos, e esta pode ser prevista pelo tamanho da lesão. É necessária a invasão dos músculos para a ocorrência de metástases, sendo que os vasos sanguíneos somente podem estar implicados quando há invasão concomitante dos nervos. A desmoplasia está diretamente relacionada ao tamanho da lesão e à ocorrência de metástases.UNIFESP-EPMUNIFESP-EPM setor de EstomalogiaUNIFESP-EPM Departamento de DermatologiaUNIFESP, EPM, setor de EstomalogiaUNIFESP, EPM Depto. de DermatologiaSciEL

Correlation in chicken between the marker LEI0258 alleles and Major Histocompatibility Complex sequences

<p>Abstract</p> <p>Background</p> <p>The LEI0258 marker is located within the B region of the chicken Major Histocompatibility Complex (MHC), and is surprisingly well associated with serology. Therefore, the correlation between the LEI0258 alleles and the MHC class I and the class II alleles at the level of sequences is worth investigating in chickens. Here we describe to which extent the LEI0258 alleles are associated with alleles of classical class I genes and non-classical class II genes, in reference animals as well as local breeds with unknown MHC haplotypes.</p> <p>Methods</p> <p>For the class I region, in an exploratory project, we studied 10 animals from 3 breeds: Rhode Island Red, White Leghorn and Fayoumi chickens, by cloning and sequencing <it>B-F1</it> and <it>B-F2</it> cDNA from exon 1 to 3’UTR. For the class II region, we reconstructed haplotypes of the 8.8 kb genomic region encompassing three non-classical class II genes: <it>B-DMA</it>, <it>B-DMB1</it> and <it>B-DMB2</it>, for 146 animals from more than 50 breeds including wild species of jungle fowls.</p> <p>Results</p> <p>Overall we found that the LEI0258 marker genotypes gave good indications of the MHC haplotypes, and a very good predictions (>0.95) of the heterozygosity of an animal at the MHC locus.</p> <p>Conclusions</p> <p>Our results show that the LEI0258 alleles are strongly associated with haplotypes of classical class I genes and non-classical class II genes, unravelling the reasons why this marker is becoming the reference marker for MHC genotyping in chickens.</p

Genes for hereditary sensory and autonomic neuropathies: a genotype–phenotype correlation

Hereditary sensory and autonomic neuropathies (HSAN) are clinically and genetically heterogeneous disorders characterized by axonal atrophy and degeneration, exclusively or predominantly affecting the sensory and autonomic neurons. So far, disease-associated mutations have been identified in seven genes: two genes for autosomal dominant (SPTLC1 and RAB7) and five genes for autosomal recessive forms of HSAN (WNK1/HSN2, NTRK1, NGFB, CCT5 and IKBKAP). We performed a systematic mutation screening of the coding sequences of six of these genes on a cohort of 100 familial and isolated patients diagnosed with HSAN. In addition, we screened the functional candidate gene NGFR (p75/NTR) encoding the nerve growth factor receptor. We identified disease-causing mutations in SPTLC1, RAB7, WNK1/HSN2 and NTRK1 in 19 patients, of which three mutations have not previously been reported. The phenotypes associated with mutations in NTRK1 and WNK1/HSN2 typically consisted of congenital insensitivity to pain and anhidrosis, and early-onset ulcero-mutilating sensory neuropathy, respectively. RAB7 mutations were only found in patients with a Charcot-Marie-Tooth type 2B (CMT2B) phenotype, an axonal sensory-motor neuropathy with pronounced ulcero-mutilations. In SPTLC1, we detected a novel mutation (S331F) corresponding to a previously unknown severe and early-onset HSAN phenotype. No mutations were found in NGFB, CCT5 and NGFR. Overall disease-associated mutations were found in 19% of the studied patient group, suggesting that additional genes are associated with HSAN. Our genotype–phenotype correlation study broadens the spectrum of HSAN and provides additional insights for molecular and clinical diagnosis

Linkage and association studies identify a novel locus for Alzheimer disease at 7q36 in a Dutch population-based sample

We obtained conclusive linkage of Alzheimer disease (AD) with a candidate region of 19.7 cM at 7q36 in an extended multiplex family, family 1270, ascertained in a population-based study of early-onset AD in the northern Netherlands. Single-nucleotide polymorphism and haplotype association analyses of a Dutch patient-control sample further supported the linkage at 7q36. In addition, we identified a shared haplotype at 7q36 between family 1270 and three of six multiplex AD-affected families from the same geographical region, which is indicative of a founder effect and defines a priority region of 9.3 cM. Mutation analysis of coding exons of 29 candidate genes identified one linked synonymous mutation, g.38030G-->C in exon 10, that affected codon 626 of the PAX transactivation domain interacting protein gene (PAXIP1). It remains to be determined whether PAXIP1 has a functional role in the expression of AD in family 1270 or whether another mutation at this locus explains the observed linkage and sharing. Together, our linkage data from the informative family 1270 and the association data in the population-based early-onset AD patient-control sample strongly support the identification of a novel AD locus at 7q36 and re-emphasize the genetic heterogeneity of AD

Novel computational methods for increasing PCR primer design effectiveness in directed sequencing

<p>Abstract</p> <p>Background</p> <p>Polymerase chain reaction (PCR) is used in directed sequencing for the discovery of novel polymorphisms. As the first step in PCR directed sequencing, effective PCR primer design is crucial for obtaining high-quality sequence data for target regions. Since current computational primer design tools are not fully tuned with stable underlying laboratory protocols, researchers may still be forced to iteratively optimize protocols for failed amplifications after the primers have been ordered. Furthermore, potentially identifiable factors which contribute to PCR failures have yet to be elucidated. This inefficient approach to primer design is further intensified in a high-throughput laboratory, where hundreds of genes may be targeted in one experiment.</p> <p>Results</p> <p>We have developed a fully integrated computational PCR primer design pipeline that plays a key role in our high-throughput directed sequencing pipeline. Investigators may specify target regions defined through a rich set of descriptors, such as Ensembl accessions and arbitrary genomic coordinates. Primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the specified target regions. As part of the tiling process, primer pairs are computationally screened to meet the criteria for success with one of two PCR amplification protocols. In the process of improving our sequencing success rate, which currently exceeds 95% for exons, we have discovered novel and accurate computational methods capable of identifying primers that may lead to PCR failures. We reveal the laboratory protocols and their associated, empirically determined computational parameters, as well as describe the novel computational methods which may benefit others in future primer design research.</p> <p>Conclusion</p> <p>The high-throughput PCR primer design pipeline has been very successful in providing the basis for high-quality directed sequencing results and for minimizing costs associated with labor and reprocessing. The modular architecture of the primer design software has made it possible to readily integrate additional primer critique tests based on iterative feedback from the laboratory. As a result, the primer design software, coupled with the laboratory protocols, serves as a powerful tool for low and high-throughput primer design to enable successful directed sequencing.</p