Fur: Find unique genomic regions for diagnostic PCR.

MOTIVATION: Unique marker sequences are highly sought after in molecular diagnostics. Nevertheless, there are only few programs available to search for marker sequences, compared to the many programs for similarity search. We therefore wrote the program Fur for Finding Unique genomic Regions. RESULTS: Fur takes as input a sample of target sequences and a sample of closely related neighbors. It returns the regions present in all targets and absent from all neighbors. The recently published program genmap can also be used for this purpose and we compared it to fur. When analyzing a sample of 33 genomes representing the major phylogroups of E.coli, fur was 40 times faster than genmap but used three times more memory. On the other hand, genmap yielded three times more markers, but they were less accurate when tested in silico on a sample of 237 E.coli genomes. We also designed phylogroup-specific PCR primers based on the markers proposed by genmap and fur, and tested them by analyzing their virtual amplicons in GenBank. Finally, we used fur to design primers specific to a Lactobacillus species, and found excellent sensitivity and specificity in vitro. AVAILABILITY AND IMPLEMENTATION: Fur sources and documentation are available from https://github.com/evolbioinf/fur. The compiled software is posted as a docker container at https://hub.docker.com/r/haubold/fox. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DNA chip-based diagnosis of onychomycosis and tinea pedis.

BACKGROUND AND OBJECTIVES: Onychomycosis (OM) and tinea pedis (TP) are common fungal infections. Currently, diagnosis is based on direct microscopy and culture that have a low to moderate sensitivity and/or require up to 3-4 weeks until results are obtained. PCR techniques have emerged for the diagnosis of fungal infections, but little is known about their sensitivity and specificity in diagnosing. Here, we compared the diagnostic value of a DNA-chip technology, that detects 56 fungal pathogens, in a single-center prospective diagnostic study with microscopy and culture in suspected OM/TP. PATIENTS AND METHODS: Microscopy, culture and DNA microarray assays were performed on scraping material from patients with suspected OM (n = 67) or TP (n = 73). To test whether swabs can be used as an alternative for scraping, PCR yields were compared in a further 13 patients with OM and 11 patients with TP. RESULTS: DNA microarrays had the highest sensitivity. Combination of DNA-chip technology with microscopy further increased the sensitivity, and results from this combined laboratory diagnosis can be obtained within 24 hours. Comparison of sampling techniques (scraping, dry or wet swab) for DNA-chip assays showed similar results in suspected OM or TP. CONCLUSIONS: DNA-chip technology shows high sensitivity for OM and TP diagnosis, especially when combined with microscopy.

DNA-Chip-basierte Diagnose der Onychomykose und Tinea pedis.

HINTERGRUND UND ZIELE: Onychomykose (OM) und Tinea pedis (TP) sind häufige Pilzinfektionen der Haut. Aktuell basiert die Diagnose vornehmlich auf mikroskopischem Direktnachweis und/oder Kultur. Beide Methoden haben jedoch eine geringe bis mäßige Sensitivität und benötigen teilweise mehrere Wochen, bis endgültige Laborergebnisse vorliegen. Um die Diagnose kutaner Pilzinfektionen zu verbessern, wurden PCR-basierte Methoden entwickelt. Hier haben wir hier die Sensitivität und Spezifität einer Chip-basierten Multiplex-PCR mit mikroskopischen Direktnachweis und verglichen. PATIENTEN UND METHODIK: In einer monozentrischen, prospektiven Studie wurden bei Patienten mit Verdacht auf OM (n  =  67) oder TP (n  =  73) Schuppenpräparate entnommen und mittels mikroskopischem Direktnachweis, Kultur und DNA-Chip-Technologie der Erregernachweis durchgeführt. In einem weiteren Ansatz wurde überprüft, ob Abstriche als Alternative zur Entnahme eines Schuppenpräparates verwendet werden können. Hierfür wurden 24 weitere OM/TP-Patienten rekrutiert und die Ergebnisse der DNA-Chip-Technologie aus Abstrichen mit denen aus den Schuppenpräparaten verglichen. ERGEBNISSE: Im Vergleich aller Methoden hatte die DNA-Chip-Technologie die höchste Sensitivität, eine Kombination von DNA-Chip-Technologie mit mikroskopischem Direktnachweis erhöhte dies weiter. Ergebnisse dieser kombinierten Labordiagnostik sind innerhalb von 24 Stunden verfügbar. Der Vergleich der Probenentnahmetechniken (Abstrich beziehungsweise Schuppenpräparat) zeigte vergleichbare Ergebnisse. SCHLUSSFOLGERUNGEN: Die molekulare Diagnostik (mittels DNA-Chip-Technologie) hat eine hohe Sensitivität für die OM- und TP-Diagnostik, insbesondere in Kombination mit dem mikroskopischen Direktnachweis.

Is surgical plume developing during routine LEEPs contaminated with high-risk HPV? A pilot series of experiments.

INTRODUCTION: Growing evidence shows a causal role of high-risk humane papillomavirus (HPV) infections in the development of head and neck cancer. A recent case report shows two patients suffering from tonsillar cancer without any risk factors apart from their work as gynecologists doing laser ablations and loop electrosurgical excision procedures (LEEP). The aim of the present investigation is to evaluate whether surgical plume resulting from routine LEEPs of HSIL of the cervix uteri might be contaminated with the DNA of high-risk HPV. MATERIALS AND METHODS: The prospective pilot study is done at the Department of Gynecology and Obstetrics of the University of Lübeck, Germany. The primary outcome was defined as HPV subtype in resected cone and in surgical plume resulting from LEEPs of HSIL of the cervix uteri. Plume resulting from LEEPs was analyzed using a Whatman FTA Elute Indicating Card which was placed in the tube of an exhaust suction device used to remove the resulting aerosols. For detection of HPV and analysis of its subtype, the novel EUROArray HPV test was performed. Resected cones of LEEPs were evaluated separately for HPV subtypes. RESULTS: Four samples of surgical plume resulting from routine LEEPs indicated contamination with high-risk HPV and showed the same HPV subtype as identified in the resected cones. CONCLUSION: Surgical plume resulting from routine LEEPs for HSIL of the cervix uteri has the risk of contamination with high-risk HPV. Further investigations of infectiousness of surgical plume are necessary for evaluation of potential hazards to involved healthcare professionals.

Prevalence of sexually transmitted infections and human papillomavirus in cervical samples from incarcerated women in São Paulo, Brazil: a retrospective single-center study.

Introduction: Sexually transmitted infections (STIs) cause considerable morbidity worldwide and, depending on the specific pathogen, may lead to serious complications in the female reproductive tract. Incarcerated women are particularly vulnerable to health problems with a disproportionate high rate of STIs, including infections with human papillomavirus (HPV). Methods: Here, cervical swab samples collected from 299 women (18 to 64 years) living in one of the women's prisons of São Paulo, Brazil were submitted for liquid-based cytology to determine the prevalence of precancerous lesions. Furthermore, direct detection of 30 genital HPV genotypes (18 high-risk and 12 low-risk types) and 11 additional STIs (Chlamydia trachomatis, Neisseria gonorrhoeae, Herpes simplex virus 1 and 2, Haemophilus ducreyi, Mycoplasma genitalium and hominis, Treponema pallidum, Trichomonas vaginalis, Ureaplasma parvum and urealyticum) were performed by molecular typing using two PCR-based DNA microarray systems, i.e., EUROArray HPV and EUROArray STI (EUROIMMUN), respectively. Results: The overall prevalence of cytological abnormalities was 5.8%, including five women with low-grade and five women with high-grade squamous intraepithelial lesions. The overall prevalence of HPV was 62.2, and 87.1% of the HPV-positive women were infected with oncogenic high-risk (HR) HPV types. HPV types 16 (24.1%), 33 and 52 (both 10.4%) were the most frequently detected. The prevalence of the other STIs was 72.8%. Up to four different pathogens were found in the infected women, the most frequent being Ureaplasma parvum (45.3%), Mycoplasma hominis (36.2%) and Trichomonas vaginalis (24.8%). Conclusion: The high number of HR-HPV infections and other STIs described here highlights the fact that the Brazilian female prison population requires more attention in the country's health policies. The implementation of screening programs and treatment measures might contribute to a decrease in the incidence of STIs and cervical cancer in this vulnerable population. However, for such measures to be effective, further studies are needed to investigate the best practice to get more women to engage in in-prison prevention programs, e.g., through offering further sexual health education and self-sampling.

A drastic reduction in DOF1 transcript levels does not affect C4-specific gene expression in maize.

The transcription factor DOF1 has been suggested to regulate photosynthetic gene expression in maize. By screening a RescueMu transposon-tagged mutant library, we identified a maize mutant with a transposon integration in the Dof1 gene 16 bp upstream of the transcription initiation site (TIS). Sequencing of the Dof1 promoter region revealed an unusual promoter structure missing any typical elements. Homozygous (ho) mutant lines were generated by selfing and subsequent PCR and DNA gel blot analyses. The transposon integration reduced Dof1 transcript levels to less than 20% compared to the wild-type and overlapping RT-PCR systems revealed that these transcripts were not initiated from the native transcription start site. Dof1 transcripts transiently accumulate in wild-type plants after illumination of darkened seedlings, but this accumulation cannot be observed in mutant lines. However, the time-course of transcript accumulation from the C(4)-specific phosphoenolpyruvate carboxylase (PEPC) gene, a possible target of DOF1, is not altered. Moreover, no impact on the steady-state levels of five additional transcripts involved in C(4)-metabolism can be observed. The contents of amino acids, glucose, and malate as well as the carbon to nitrogen ratio in the leaves remained unchanged when comparing wild-type and mutant plants. Our data question the importance of DOF1 in the control of photosynthetic gene expression in maize.

Rapid microarray processing using a disposable hybridization chamber with an integrated micropump.

We present a disposable microarray hybridization chamber with an integrated micropump to speed up diffusion based reaction kinetics by generating convective flow. The time-to-result for the hybridization reaction was reduced from 60 min (standard protocol) down to 15 min for a commercially available microarray. The integrated displacement micropump is pneumatically actuated. It includes two active microvalves and is designed for low-cost, high volume manufacturing. The setup is made out of two microstructured polymer parts realized in polycarbonate (PC) separated by a 25 µm thermoplastic elastomer (TPE) membrane. Pump rate can be controlled between 0.3 µl s(-1) and 5.7 µl s(-1) at actuation frequencies between 0.2 Hz and 8.0 Hz, respectively.

Restriction accessibility in isolated nuclei reveals light-induced chromatin reorganization at the PEPC promoter in maize.

Expression of genes necessary to perform C4 photosynthesis in maize is activated by light. It is not known how this activation is regulated on the chromatin level in vivo. We analysed alterations in the chromatin structure of the promoter of the C4-specific isoform of phosphoenolpyruvate carboxylase (PEPC) after illumination of seedlings. A protocol was established that facilitates the preparation of nuclei from maize leaves with intact chromatin structure and resistance to DNA degradation during prolonged incubation at high temperatures. The presence of non-spliced transcripts from the C4-PEPC gene in the nuclei was demonstrated by RT-PCR. The chromatin was partially digested with restriction endonucleases. Quantitative PCR analyses revealed a clear increase in the accessibility of the promoter chromatin to restriction dependent on illumination of the seedlings. The data indicate chromatin reorganization at the C4-PEPC promoter during activation.

The interaction of DOF transcription factors with nucleosomes depends on the positioning of the binding site and is facilitated by maize HMGB5.

The expression of genes involved in C(4) photosynthesis in maize is under tight tissue-specific and light-dependent control. There is strong evidence that this control is at least in part brought about by DOF transcription factors binding to the respective promoters. We analyzed the interaction of DOF1 and DOF2 proteins with a functional and a cryptic endogenous binding site derived from the maize phosphoenolpyruvate carboxylase promoter (-300 bp region) in the nucleosomal context. Various DNA fragments comprising this promoter region were reconstituted into mononucleosomes from purified components, resulting in different positions of the DOF binding sites on the nucleosome surface. Binding of recombinant transcription factors to the different types of nucleosomes was examined using electrophoretic mobility shift assays. Changing the translational position of the binding site on the nucleosome surface strongly affected the efficiency of the interaction with the DOF factors. Deletion of individual recognition motifs revealed a positive impact of DOF protein binding to the main binding site on interactions with the cryptic binding site. The addition of the chromosomal high-mobility group (HMG) protein HMGB5 to the binding reaction mixture facilitated nucleosome binding of the transcription factor independent from the position of the recognition sites. The relevance of the data for the activation of the promoter in vivo is discussed.