Cyanobacterial ultrastructure in light of genomic sequence data.

Cyanobacteria are physiologically and morphologically diverse photosynthetic microbes that play major roles in the carbon and nitrogen cycles of the biosphere. Recently, they have gained attention as potential platforms for the production of biofuels and other renewable chemicals. Many cyanobacteria were characterized morphologically prior to the advent of genome sequencing. Here, we catalog cyanobacterial ultrastructure within the context of genomic sequence information, including high-magnification transmission electron micrographs that represent the diversity in cyanobacterial morphology. We place the image data in the context of tabulated protein domains-which are the structural, functional, and evolutionary units of proteins-from the 126 cyanobacterial genomes comprising the CyanoGEBA dataset. In particular, we identify the correspondence between ultrastructure and the occurrence of genes encoding protein domains related to the formation of cyanobacterial inclusions. This compilation of images and genome-level domain occurrence will prove useful for a variety of analyses of cyanobacterial sequence data and provides a guidebook to morphological features.

Prognostic role of FGFR1 amplification in early-stage non-small cell lung cancer.

BACKGROUND: Recently, fibroblast growth factor receptor 1 (FGFR1) was discovered in squamous cell carcinomas (SCC) of the lung with FGFR1 amplification described as a promising predictive marker for anti-FGFR inhibitor treatment. Only few data are available regarding prevalence, prognostic significance and clinico-pathological characteristics of FGFR1-amplified and early-stage non-small cell lung carcinomas (NSCLC). We therefore investigated the FGFR1 gene status in a large number of well-characterised early-stage NSCLC. METHODS: FGFR1 gene status was evaluated using a commercially available fluorescent in situ hybridisation (FISH) probe on a tissue microarray (TMA). This TMA harbours 329 resected, formalin-fixed and paraffin-embedded, nodal-negative NSCLC with a UICC stage I-II. The FISH results were correlated with clinico-pathological features and overall survival (OS). RESULTS: The prevalence of an FGFR1 amplification was 12.5% (41/329) and was significantly (P<0.0001) higher in squamous cell carcinoma (SCC) (20.7%) than in adenocarcinoma (2.2%) and large cell carcinoma (13%). Multivariate analysis revealed significantly (P=0.0367) worse 5-year OS in patients with an FGFR1-amplified NSCLC. CONCLUSIONS: FGFR1 amplification is common in early-stage SCC of the lung and is an independent and adverse prognostic marker. Its potential role as a predictive marker for targeted therapies or adjuvant treatment needs further investigation.

MicroRNA-29b is involved in the Src-ID1 signaling pathway and is dysregulated in human lung adenocarcinoma.

The c-Src kinase regulates cancer cell invasion through inhibitor of DNA binding/differentiation 1 (ID1). Src and ID1 are frequently overexpressed in human lung adenocarcinoma. The current study aimed at identifying microRNAs (miRNAs) involved in the Src-ID1 signaling in lung cancer. Incubation of lung cancer cells with the Src inhibitor saracatinib led to the upregulation of several miRNAs including miR-29b, which was the most highly upregulated miRNA with predicted binding to the ID1 3'-untranslated region (UTR). Luciferase reporter assays confirmed direct binding of miR-29b to the ID1 3'-UTR. Expression of miR-29b suppressed ID1 levels and significantly reduced migration and invasion. Expression of antisense-miR-29b (anti-miR-29b), on the other hand, enhanced ID1 mRNA and protein levels, and significantly increased lung cancer cell migration and invasion, a hallmark of the Src-ID1 pathway. The ectopic expression of ID1 in miR-29b-overexpressing cells was able to rescue the migratory potential of these cells. Both, anti-miR-29b and ID1 overexpression diminished the effects of the Src inhibitors saracatinib and dasatinib on migration and invasion. Saracatinib and dasatinib decreased c-Myc transcriptional repression on miR-29b and led to increased ID1 protein levels, whereas forced expression of c-Myc repressed miR-29b and induced ID1. In agreement, we showed direct recruitment of c-Myc to the miR-29b promoter. miR-29b was significantly downregulated in primary lung adenocarcinoma samples compared with matched alveolar lung tissue, and miR-29b expression was a significant prognostic factor for patient outcome. These results suggest that miR-29b is involved in the Src-ID1 signaling pathway, is dysregulated in lung adenocarcinoma and is a potential predictive marker for Src kinase inhibitors.

Molecular approaches for monitoring potentially toxic marine and freshwater phytoplankton species.

Harmful phytoplankton species are a growing problem in freshwater and marine ecosystems, because of their ability to synthesize toxins that threaten both animal and human health. The monitoring of these microorganisms has so far been based on conventional methods, mainly involving the microscopic counting and identification of cells, and using analytical and bioanalytical methods to identify and quantify the toxins. However, the increasing number of microbial sequences in the GeneBank database and the development of new tools in the last 15 years nowadays enables the use of molecular methods for detection and quantification of harmful phytoplankton species and their toxins. These methods provide species-level identification of the microorganisms of interest, and their early detection in the environment by PCR techniques. Moreover, real time PCR can be used to quantify the cells of interest, and in some cases to evaluate the proportion of toxin-producing and non-toxin-producing genotypes in a population. Recently, microarray technologies have also been used to achieve simultaneous detection and semi-quantification of harmful species in environmental samples. These methods look very promising, but so far their use remains limited to research. The need for validation for routine use and the cost of these methods still hamper their use in monitoring programs.

Acute respiratory distress syndrome secondary to antisynthetase syndrome is reversible with tacrolimus.

Polymyositis and interstitial lung diseases, predominantly nonspecific interstitial pneumonia (NSIP), are known to be frequent in antisynthetase syndrome, where anti-aminoacyl-tRNA synthetase antibodies are often identified. An unusual case of acute respiratory distress syndrome, secondary to such proven NSIP of cellular type with predominant CD8 lymphocytes, is described herein. The patient described in the present case study initially had a poor recovery with high dose of steroids, but this was followed by a good improvement after the prescription of tacrolimus and a low dose of prednisone. A precise diagnosis in similar circumstances may be life-saving, allowing the successful application of new immunosuppressants.

Origin and prognostic value of circulating KRAS mutations in lung cancer patients.

Because of the current controversy on the origin and clinical value of circulating KRAS codon 12 mutations in lung cancer, we screened 180 patients using a combined restriction fragment-length polymorphism and polymerase chain reaction (RFLP-PCR) assay. We detected KRAS mutations in 9% plasma samples and 0% matched lymphocytes. Plasma KRAS mutations correlated significantly with poor prognosis. We validated the positive results in a second laboratory by DNA sequencing and found matching codon 12 sequences in blood and tumor in 78% evaluable cases. These results support the notion that circulating KRAS mutations originate from tumors and are prognostically relevant in lung cancer.

[Eosinophilia, diarrhea and asthma in a young woman]. / Eosinophilie, Diarrhoe und Asthma bei einer jungen Frau.

We present the case of a young woman that was diagnosed with Churg-Strauss syndrome. The classical as well as the atypical symptoms, signs and findings are discussed in the context of clinically relevant differential diagnoses. The diagnostic criteria and the relevant aspects of pathogenesis, clinical course and treatment are reviewed. In addition, the similarities and differences with respect to the other idiopathic interstitial eosinophilic pneumopathies are described.

Role of cyanobacteria in the biodegradation of crude oil by a tropical cyanobacterial mat.

Cyanobacterial mats are ubiquitous in tropical petroleum-polluted environments. They form a high biodiversity microbial consortium that contains efficient hydrocarbons degraders. A cyanobacterial mat collected from a petroleum-contaminated environment located in Indonesia was studied for its biodegradation potential. In the field, the natural mat was shown to degrade efficiently the crude oil present in the environment. This natural mat demonstrated also a strong activity of degradation on model crude oil under laboratory conditions. In axenic cultures, the monospecific cyanobacterium Phormidium animale that constitute the bulk of the biomass did not exhibit any degradative capacity on hydrocarbons in the range of C13-C35 carbon atom number either in autotrophic or heterotrophic conditions. It was concluded that this cyanobacterial strain living on a heavily contaminated site had no direct effect on biodegradation of crude oil, the degradation activity being exclusively achieved by the other microorganisms present in the microbial consortium of the mat.

Pre-eclampsia with acute heart failure postpartum as primary manifestation of systemic lupus erythematosus.

Pre-eclampsia occurs in 2-5% of pregnancies of healthy women. Here, we present a rare case of pre-eclampsia with overt acute heart failure, which was the primary manifestation of systemic lupus erythematosus with cardiac and renal involvement.

Video thoracoscopic surgery used to manage tuberculosis in thoracic surgery.

BACKGROUND: The aim of this study was to evaluate the indications and results of video-assisted thoracic surgery (VATS) for the management of tuberculosis in 10 patients with unusual clinical and radiologic presentation for the disease. METHODS: From March 2000 to March 2002, 96 diagnostic VATS operations for unclear thoracic lesions were performed at the authors' institution. Their final diagnosis for 10 (10.4%) of these patients was tuberculosis. The suspected preoperative diagnoses were pancoast tumour (n = 1), pericardial effusion (n = 1), pleural mesothelioma (n = 1), pleural empyema (n = 2), mediastinal lymphoma (n = l), and lung cancer (n = 4). RESULTS: For all the patients, the diagnosis of tuberculosis was achieved by VATS. The duration of drainage was 2.5 days. There have been neither morbidity nor mortality since surgery. The hospital stay was 3 to 5 days. CONCLUSION: Thoracoscopy is a safe and effective procedure for the management of tuberculosis. Tuberculosis should be kept in mind during the differential diagnosis of unknown thoracic lesions, and also for patients who live in economically well developed countries and are not immune compromised.

[Acute dyspnea--what should I not forget?]. / Akute Dyspnoe--was darf ich nicht vergessen?

Acute dyspnea represents a diagnostic challenge even for the experienced physician. There are no prospectively evaluated diagnostic algorithms dealing with this frequent clinical problem. First of all, the emergency has to be assessed and life supporting measures have to be considered. In addition to a thorough medical history and clinical examination, chest X-ray, spirometry, ECG, hemoglobin measurement, BNP and D-dimer testing represent valuable diagnostic tools and are available to GP's. Most commonly, acute dyspnoea is pulmonary or cardiac in origin. Up to one third of all cases will have several causes. Functional dyspnea is difficult to diagnose but should be taken into consideration after excluding any somatic cause. Hyperventilation is found in both, organic and non organic diseases, and is therefore an inappropriate criterion to differentiate between the two. The mainstay in the management of any symptom is to primarily treat the underlying disease. A significant hypoxemia (SO2 < 90%, pO2 < 60 mmHg) ought to be corrected by supplemental oxygen. It is inappropriate to withhold oxygen from patients with COPD and severe hypoxemia just to avoid hypercapnia. Besides oxygen, opiates efficiently relief dyspnoea but harbour the risk of respiratory depression, altered mental status or aspiration.

[Rasburicase (Fasturtec)]. / Rasburicase (Fasturtec).

Rasburicase (Fasturtec) is an enzyme that transforms uric acid to the more water soluble allantoin to be excreted by the kidneys. Rasburicase fulfills an unmet clinical need in the treatment of hyperuricemia in that it produces a more rapid action of controlling serum uric acid compared with allopurinol. Tumours with high proliferative rate and sensitive to chemotherapy such as hematological malignancies (mainly) solid tumours (occasionally) may lead to a tumor lysis syndrome. In this situation rasburicase can effectively lower serum uric acid concentrations with a secondary improvement in renal function. Hyperuricemia is the hallmark of severe gout with tophi formation. Rasburicase represents an interesting new option in controlling serum uric acid in patients with severe tophaceous gout.

S100A2 is strongly expressed in airway basal cells, preneoplastic bronchial lesions and primary non-small cell lung carcinomas.

S100A2 gene products were shown to be frequently and dramatically over-represented in non-small cell lung cancer (NSCLC) lesions over normal tissue by microarray analysis. We have now analysed an independent series of NSCLC tumours and multiple matched normal bronchial epithelial sites by RT-PCR and immunohistochemistry to investigate: whether this expression pattern can be confirmed and whether elevated expression is associated with tumour histology, clinical outcome or preneoplasia. In this second series, S100A2 was strongly expressed in 76% (35 out of 46) of tumours, more frequently in squamous cell than adenocarcinomas (P<0.002). This strong expression was not related to high-level gene amplification, but was associated in one of five informative cases with an allele-specific imbalance in transcript levels. Most tumours strongly expressed the DeltaNp63 transcript, the product of which is a putative regulator of S100A2 transcription and while all but one of the tumours positive for DeltaNp63 expressed S100A2, others negative for this regulator also expressed the gene. Contrary to the hypothesis that S100A2 is a tumour suppressor, no somatic mutations were identified in the coding sequence in 44 tumours. Furthermore, an examination of multiple tumour-free epithelial sites from 20 patients showed that strong expression was often associated with increasing levels of disorder in preinvasive bronchial lesions (P<0.0001).

Cellular detection of sst2A receptors in human gastrointestinal tissue.

BACKGROUND AND AIMS: Many neuroendocrine gastrointestinal tumours express receptors for the regulatory peptide somatostatin. Among the five existing somatostatin receptor (sst) subtypes, sst2A is the most frequently expressed in these tumours. However, little information is available about the cellular location of sst2A in corresponding non-neoplastic epithelial tissues. METHODS: We searched for sst2A immunoreactive cells in non-neoplastic gastrointestinal tissues, and evaluated their number and immunohistochemical characteristics with neuroendocrine markers. RESULTS: The gastric antrum showed numerous sst2A cells, situated in the epithelium, corresponding to gastrin containing neuroendocrine cells, while the gastric corpus was largely devoid of sst2A cells, including enterochromaffin-like cells. The remaining foregut, namely the duodenum and proximal jejunum, also contained a large number of sst2A cells, all being neuroendocrine cells and many of them characterised as gastrin cells. Sst2A cells were also detected in the midgut, in low numbers in the epithelium of the distal jejunum and ileum, but not in the appendix vermiformis, the caecum, or the hindgut, despite the large number of neuroendocrine cells present in this area. In addition, sst2A cells were found in the whole gastrointestinal tract in the myenteric and submucosal plexus. CONCLUSIONS: While sst2A receptors on antral gastrin cells presumably mediate somatostatin inhibition of gastrin secretion, the effects of somatostatin on motility and ion transport in the lower gastrointestinal tract may be mediated by sst2A receptors in the neural plexus. These data provide a molecular basis for the physiological actions of somatostatin in human gastrointestinal tissue.

Immunohistochemical localization of somatostatin receptor sst2A in human gut and lung tissue: possible implications for physiology and carcinogenesis.

Many neuroendocrine gastrointestinal and lung tumors express sst2A somatostatin receptors. Because the cellular location of sst2A in the corresponding non-neoplastic tissue is unknown, we searched for sst2A immuno-reactive cells and characterized their type in these tissues using a highly specific sst2A antibody (R2-88). Epithelial sst2A cells, identified as neuroendocrine, gastrin-producing cells, were found in large numbers in the antrum and the duodenum, but not in the gastric corpus. They were also present in the proximal jejunum, rarely noted in the distal jejunum and ileum, and absent in the large intestine and the appendix vermiformis. Moreover, sst2A cells were found abundantly in the neural plexus. sst2A receptors on antral gastrin cells could mediate somatostatin inhibition on gastrin secretion, whereas those in the neural plexus could mediate somatostatin effects on motility and ion transport in the lower gastrointestinal tract. Rare sst2A cells in bronchi and bronchioles located basally and parabasally in the gastrointestinal epithelium were detected that could represent stem/progenitor cells. It is currently not clear whether and which of the identified sst2A cells are at the origin of sst2A-positive neuroendocrine gut or lung tumors.

Cyclin D1 overexpression in bronchial epithelia of patients with lung cancer is associated with smoking and predicts survival.

PURPOSE: Cyclin D1 is overexpressed in almost 60% of resectable non-small-cell lung cancer (NSCLC). In the absence of cyclin D1 gene amplification, overexpression is characterized by allelic imbalanced transcript levels. METHODS: The aims were to study cyclin D1 expression by immunohistochemistry and allelic balance of transcripts in tumor-free bronchial epithelia from patients with resectable NSCLC by using monoclonal antibodies (48 patients and 288 sites), microdissection/reverse transcriptase polymerase chain reaction/restriction fragment length polymorphism analyses (24 patients and 144 sites). Derived data were related to patient characteristics-in particular, smoking habits. RESULTS: In 167 (58%) of 288 sites, cyclin D1 was overexpressed, with cytoplasmic and nuclear sublocalization in 53% and 7% of all sites, respectively. Nuclear overexpression was more frequent in premalignant versus normal or hyperplastic epithelia (55% v 3%; P <.0001). Allele-specific expression imbalances were found in 69 (48%) of 144 sites; in particular, those in which cyclin D1 was overexpressed (P =.004). In 14 (58%) of 24 patients, balanced or imbalanced transcript ratios and degree of expression were consistent at all sites for the same patient, whereas in another 10 patients, transcript balances and cyclin D1 expression patterns varied across the sites. Nuclear cyclin D1 expression in at least one site (14 of 48 patients) was linked to heavy smoking (> 40 pack-years; P =.02) and shorter overall survival (P =.01). CONCLUSION: Allele-specific, probably damage-driven, deregulation of the cyclin D1 gene may precede and perhaps facilitate the spread of preneoplastic clones across the bronchial epithelial surface in a significant number of patients. Cyclin D1 expression at multiple bronchial sites may identify a subgroup of heavy-smoking patients with poor outcome.

[Virtual endoscopy of the upper, central and peripheral airways with multirow detector CT]. / Virtuelle Endoskopie der oberen, zentralen und peripheren Atemwege mit Mehrzeilen-Spiral-CT.

Virtual endoscopy of the upper, central and peripheral airways (virtual laryngoscopy or virtual bronchoscopy) produces endoluminal images similar to those of fiberoptic endoscopy. In particular, virtual endoscopy is useful for the assessment of endoluminal tumor extent and tracheobronchial stenosis. Especially since the introduction of multirow detector CT, high-resolution virtual-endoscopic images of the airways can be reconstructed. Either surface rendering or volume rendering can be used for realistic depiction of the airways. Semitransparent color-coded volume rendering is advantageous, because adjacent structures can be displayed in addition to endoluminal views. A major advantage of virtual endoscopy over fiberoptic endoscopy is its non-invasiveness. With virtual endoscopy, even a high-grade stenosis is passable, enabling evaluation of the distal airways. Disadvantages are its inability to depict mucosal color and to perform therapeutic maneuvers. In comparison to other CT display modes, virtual endoscopy allows a more realistic assessment of tracheobronchial stenosis than axial CT slices and multiplanar reformats. Virtual endoscopy of the airways can be used complementary to fiberoptic endoscopy before tracheotomy, stent implantation or lung resection and for post-operative follow-up. In the future, virtual airway endoscopy will be increasingly applied for interactive virtual reality guidance of airway procedures such as bronchoscopy and surgery.