Module-detection approaches for the integration of multilevel omics data highlight the comprehensive response of Aspergillus fumigatus to caspofungin.

BACKGROUND: Omics data provide deep insights into overall biological processes of organisms. However, integration of data from different molecular levels such as transcriptomics and proteomics, still remains challenging. Analyzing lists of differentially abundant molecules from diverse molecular levels often results in a small overlap mainly due to different regulatory mechanisms, temporal scales, and/or inherent properties of measurement methods. Module-detecting algorithms identifying sets of closely related proteins from protein-protein interaction networks (PPINs) are promising approaches for a better data integration. RESULTS: Here, we made use of transcriptome, proteome and secretome data from the human pathogenic fungus Aspergillus fumigatus challenged with the antifungal drug caspofungin. Caspofungin targets the fungal cell wall which leads to a compensatory stress response. We analyzed the omics data using two different approaches: First, we applied a simple, classical approach by comparing lists of differentially expressed genes (DEGs), differentially synthesized proteins (DSyPs) and differentially secreted proteins (DSePs); second, we used a recently published module-detecting approach, ModuleDiscoverer, to identify regulatory modules from PPINs in conjunction with the experimental data. Our results demonstrate that regulatory modules show a notably higher overlap between the different molecular levels and time points than the classical approach. The additional structural information provided by regulatory modules allows for topological analyses. As a result, we detected a significant association of omics data with distinct biological processes such as regulation of kinase activity, transport mechanisms or amino acid metabolism. We also found a previously unreported increased production of the secondary metabolite fumagillin by A. fumigatus upon exposure to caspofungin. Furthermore, a topology-based analysis of potential key factors contributing to drug-caused side effects identified the highly conserved protein polyubiquitin as a central regulator. Interestingly, polyubiquitin UbiD neither belonged to the groups of DEGs, DSyPs nor DSePs but most likely strongly influenced their levels. CONCLUSION: Module-detecting approaches support the effective integration of multilevel omics data and provide a deep insight into complex biological relationships connecting these levels. They facilitate the identification of potential key players in the organism's stress response which cannot be detected by commonly used approaches comparing lists of differentially abundant molecules.

Novel method for the measurement of liquid film thickness during fuel spray impingement on surfaces.

This paper describes the development and application of a novel optical technique for the measurement of liquid film thickness formed on surfaces during the impingement of automotive fuel sprays. The technique makes use of the change of the light scattering characteristics of a metal surface with known roughness, when liquid is deposited. Important advantages of the technique over previously established methods are the ability to measure the time-dependent spatial distribution of the liquid film without a need to add a fluorescent tracer to the liquid, while the measurement principle is not influenced by changes of the pressure and temperature of the liquid or the surrounding gas phase. Also, there is no need for non-fluorescing surrogate fuels. However, an in situ calibration of the dependence of signal intensity on liquid film thickness is required. The developed method can be applied to measure the time-dependent and two-dimensional distribution of the liquid fuel film thickness on the piston or the liner of gasoline direct injection (GDI) engines. The applicability of this technique was evaluated with impinging sprays of several linear alkanes and alcohols with different thermo-physical properties. The surface temperature of the impingement plate was controlled to simulate the range of piston surface temperatures inside a GDI engine. Two sets of liquid film thickness measurements were obtained. During the first set, the surface temperature of the plate was kept constant, while the spray of different fuels interacted with the surface. In the second set, the plate temperature was adjusted to match the boiling temperature of each fuel. In this way, the influence of the surface temperature on the liquid film created by the spray of different fuels and their evaporation characteristics could be demonstrated.

An inorganic geochemical argument for coupled anaerobic oxidation of methane and iron reduction in marine sediments.

Here, we present results from sediments collected in the Argentine Basin, a non-steady state depositional marine system characterized by abundant oxidized iron within methane-rich layers due to sediment reworking followed by rapid deposition. Our comprehensive inorganic data set shows that iron reduction in these sulfate and sulfide-depleted sediments is best explained by a microbially mediated process-implicating anaerobic oxidation of methane coupled to iron reduction (Fe-AOM) as the most likely major mechanism. Although important in many modern marine environments, iron-driven AOM may not consume similar amounts of methane compared with sulfate-dependent AOM. Nevertheless, it may have broad impact on the deep biosphere and dominate both iron and methane cycling in sulfate-lean marine settings. Fe-AOM might have been particularly relevant in the Archean ocean, >2.5 billion years ago, known for its production and accumulation of iron oxides (in iron formations) in a biosphere likely replete with methane but low in sulfate. Methane at that time was a critical greenhouse gas capable of sustaining a habitable climate under relatively low solar luminosity, and relationships to iron cycling may have impacted if not dominated methane loss from the biosphere.

[Pelvic osseous infections: clinical outcome and surgical treatment]. / Die bakterielle und abakterielle Osteitis des Beckens: Manifestations- und Therapieformen.

BACKGROUND: Pelvic osteomyelitis is a bacterial infection of the pelvine skeleton. Apart from rare haematogen diffusion, it can occur after pelvic trauma or operation. Furthermore, it exists a sterile osteitis pubis after repetitive periostial microtrauma. Chronic progressions are possible. Further problems are fistulas and abscesses. With involvement of symphysis or iliosacral joint, the development of septic pelvine instability is possible. Due to the anatomic complexity of the pelvis, this affection can be neglected or underdiagnosed. METHODS: We have analysed septic pelvic operations performed during 1997 to 2006. We excluded septic affections of the hip joint after joint replacement. In 15 cases we found both radiological and microbiological signs of osseous inclusion in terms of pelvic osteomyelitis. RESULTS AND CONCLUSION: 15 patients were operated after preoperatively performed bacterial asservation and conventional X-ray, fistula scanning and pelvic CT scans. In 3 cases we placed drainages into abscess formations under CT-guidance. In 14 cases osseous infected areas existed in the pelvic skeleton and we performed a local bony resection. In 3 patients we performed removal of bacterially contaminated metal implants. In 3 cases an additional pelvic instability due to involvement of the symphysis was present. Here we resected the infected joint and performed an arthrodesis to reestablish the pelvic ring stability. Due to the localisation of the infected pelvic bone, different regimes of therapy are necessary. Iliac osteomyelitis can be treated by resection or sequestrectomy, pubic osteomyelitis or sterile osteitis can be treated similarly. Septic iliosacral joint infections as well as septic symphysis joint infections can be treated by resection and can lead to a pelvic ring instability. Simple revision surgery of fistula without removement of the fistula's origin will fail, as 9 of our patients had already had several fistula revisions without any signs of healing.

Survival of Campylobacter jejuni in water: effect of grazing by the freshwater crustacean Daphnia carinata (Cladocera).

Environmental studies of the human-pathogenic bacterium Campylobacter jejuni have focused on linking distributions with potential sources. However, in aquatic ecosystems, the abundance of C. jejuni may also be regulated by predation. We examine the potential for grazing by the freshwater planktonic crustacean Daphnia carinata to reduce the survival of C. jejuni. We use a system for measuring grazing and clearance rates of D. carinata on bacteria and demonstrate that D. carinata can graze C. jejuni cells at a rate of 7% individual(-1) h(-1) under simulated natural conditions in the presence of an algal food source. We show that passage of C. jejuni through the Daphnia gut and incorporation into fecal material effectively reduces survival of C. jejuni. This is the first evidence to suggest that grazing by planktonic organisms can reduce the abundance of C. jejuni in natural waters. Biomanipulation of planktonic food webs to enhance Daphnia densities offers potential for reducing microbial pathogen densities in drinking water reservoirs and recreational water bodies, thereby reducing the risk of contracting water-borne disease.

Neutral sterols of rat epididymis. High concentrations of dehydrocholesterols in rat caput epididymidis.

Phospholipids and sterols are known to have multiple functions in reproductive tissue of mammals. High concentrations of the cholesterol precursor desmosterol have been described in testis, epididymis, and spermatozoa of various species. These findings and the recent discovery of some cholesterol precursors as meiosis-activating sterols suggest important functions of cholesterol precursors in fertility. Many sterol intermediates appear from the 19-step conversion of lanosterol, the first sterol synthesized in the cascade of cholesterol synthesis, to cholesterol. The biochemical basis of the genetically inherited Smith-Lemli-Opitz syndrome has been described as a defective conversion of 7-dehydrocholesterol to cholesterol. Since this discovery, interest has focused on this special cholesterol precursor. Here, we report high concentrations of 7- and 8-dehydrocholesterol in caput epididymidis and spermatozoa derived from caput epididymidis of Sprague-Dawley and Wistar rats, which comprised up to 30% of total sterols. In contrast to caput epididymidis, 7- and 8-dehydrocholesterol were barely detected in cauda epididymidis or testis. Desmosterol increased several times from caput to cauda epididymidis. This is the first report of the natural appearance of high concentrations of dehydrocholesterols in mammalian tissue, and it underlines the putative importance of cholesterol precursors in reproductive tissue.

Concentration of alpha 1-acid glycoprotein in dogs with malignant neoplasia.

Serum alpha 1-acid glycoprotein (alpha 1AG) concentrations were determined in 55 dogs with previously untreated, histologically confirmed, high-grade lymphoblastic lymphoma, and in 34 dogs with histologically confirmed nonhematopoietic malignancies (13 dogs with carcinomas and 21 dogs with sarcomas). Serum concentrations were again determined in 32 dogs with lymphoma that were in complete remission 3 weeks after 1 dose of doxorubicin (30 mg/m2 of body surface, i.v.) and in 22 dogs that were still in complete remission 3 weeks after a fourth dose of doxorubicin. For comparison, serum alpha 1AG concentrations were measured in 19 clinically normal (control) dogs of similar weight and age. Eight of the control dogs were given 1 dose of doxorubicin (30 mg/m2, i.v.), and serum alpha 1AG concentrations were measured 3 weeks later. In control dogs, mean serum alpha 1AG concentration after treatment with doxorubicin was not significantly different from mean concentration before treatment. Mean alpha 1AG concentrations in untreated dogs with lymphoma, in dogs with sarcomas, and in dogs with carcinomas were all significantly higher than mean concentration for untreated control dogs. In addition, the mean concentration for dogs with osteosarcomas was significantly higher than mean concentration for untreated control dogs. There were no significant differences in mean serum alpha 1AG concentrations among dogs with different clinical stages of lymphoma (stage IIIa, stage IVa, stage Va). However, mean serum alpha 1AG concentrations were significantly increased for dogs with stages IIIa, IVa, and Va lymphoma, compared with mean concentration for untreated control dogs.(ABSTRACT TRUNCATED AT 250 WORDS)

Prevalence of nephrotoxicosis associated with a four-hour saline solution diuresis protocol for the administration of cisplatin to dogs with naturally developing neoplasms.

We evaluated the development of nephrotoxicosis in 64 dogs with malignant neoplasia given cisplatin during 4-hour saline solution diuresis. Cisplatin (70 mg/m2 of body surface area, IV, q 21 d) was given to 8 dogs once, 22 dogs twice, 9 dogs 3 times, and 25 dogs 4 times. For each treatment, cisplatin was given over a 20-minute period after saline (0.9% NaCl) solution was administered IV for 3 hours at a rate of 25 ml/kg/h. After cisplatin infusion, saline solution diuresis was continued at the same rate for 1 hour. Before each treatment with cisplatin, the dogs were evaluated by conducting a physical examination, CBC; and analysis of serum urea nitrogen and creatinine concentrations, and in most cases, serum phosphorus concentration and urine specific gravity were determined. Exogenous creatinine clearance also was evaluated in 8 dogs prior to 1 (n = 8), 2 (n = 8), 3 (n = 6), and 4 (n = 4) treatments. Five (7.8%) of 64 dogs developed clinically evident renal disease after two (n = 3) and three (n = 2) doses of cisplatin. Two of the 5 dogs had preexisting diseases of the urinary tract prior to the start of treatment. Survival time in dogs that developed renal disease (median, 114 days; range, 26 to 273 days) was similar to that of all dogs in this study (median, 145 days; range, 5 to 586 days), with 30 dogs still alive at the conclusion of the study. Three of the 5 dogs that developed renal disease were alive at the conclusion of the study, 1 died of tumor-related causes, and another died as a direct result of nephrotoxicosis. There was a significant (P < 0.05) decrease in median neutrophil counts and a significant (P < 0.05) increase in median creatinine concentrations prior to the third and fourth treatments, compared with pretreatment values.(ABSTRACT TRUNCATED AT 250 WORDS)

[Salmonella enteritidis in chicken eggs]. / Salmonella enteritidis in Hühnereiern.

After an outbreak caused by salmonella enteritidis (SE) of which home-made mayonnaise and remoulade sauce were found to be the cause, SE was detected in ten of the remaining eggs. Subsequently 409 eggs of the next shipment from the same outlet were examined bacteriologically. Of 70 of the eggs examined, SE was found in 5 egg yolk samples and in 3 egg white samples as well as in 2 of 7 pooled shell samples. Five out of 35 pooled whole egg samples comprising a total of 349 eggs were likewise positive for SE. The isolates belonged to the phage types 4 and 7 carried the virulence plasmid pRQ29.

Teachers' conceptualization of pupil control in elementary school physical education.

Management of conduct has been considered the most important problem facing schools in America during 16 of the last 20 years (Gallup, 1988). Yet little is known about specific techniques teachers use to achieve pupil control in physical education. One purpose of this work is to describe the development of a conceptual framework for pupil control techniques. The framework was derived from 64 live observations and audiotapes of elementary school physical education lessons. A second purpose is to describe how teachers may potentially foster pupil self-control. Data were reduced through analytic induction, constant comparison, and topological analysis. The investigator placed 23 categories into three classifications as perceived by teachers: anticipatory, tutorial, and punitive. Teachers confirmed frequency of using techniques during interviews and on surveys. Intraobserver agreement tests yielded 88% for distinguishing among categories. Interobserver scores ranged from 83 to 86% agreement. Categories may serve to increase teachers' repertoire of control techniques in accordance with their ideological beliefs. For teachers in this study, facilitating self-control involves (a) selecting tutorial control techniques, (b) using indirect forms of techniques, and (c) conveying reasons for using techniques.

[Glass ionomer cements as orthodontic bracket adhesives. An in vitro study with 4 glass ionomer cements (GIC) and 2 conventional orthodontic bracket adhesives as the comparative group]. / Glasionomer-Zemente als kieferorthopädische Bracketkleber. Eine In-vitro-Studie mit vier Glasionomer-Zementen (GIZ) und zwei konventionellen kieferorthopädischen Bracketklebern als Vergleichgruppe.

240 orthodontic brackets were bonded to buccal surfaces of bovine teeth. As bonding material we used four glass ionomer cements without etching and two normal orthodontic bracket bonding materials with etching of enamel. Brackets of group 1 were tested with a material testing machine for shear and tensile strength after ten minutes. Brackets of group 2, 3 and 4 were tested after one day, 28 days and 98 days, respectively. In the average the bonding strength of glass ionomer cements was 50% less than the bonding strength of the comparison group with etching. The fracture of the bonding took place to 80% between the mesh base and the glass ionomer cements. Defects of the enamel surface were never observed. The bonding between mesh-base and glass ionomer cements has to be improved before the use of this bonding material can be recommended for the use in a busy practice.