Interaction networks for identifying coupled molecular processes in microbial communities

BACKGROUND

Microbial communities adapt to environmental conditions for optimizing metabolic flux. Such adaption may include cooperative mechanisms eventually resulting in phenotypic observables as emergent properties that cannot be attributed to an individual species alone. Understanding the molecular basis of cross-species cooperation adds to utilization of microbial communities in industrial applications including metal bioleaching and bioremediation processes. With significant advancements in metagenomics the composition of microbial communities became amenable for integrative analysis on the level of entangled molecular processes involving more than one species, in turn offering a data matrix for analyzing the molecular basis of cooperative phenomena.

METHODS

We present an analysis framework aligned with a dynamical hierarchies concept for unraveling emergent properties in microbial communities, and exemplify this approach for a co-culture setting of At. ferrooxidans and At. thiooxidans. This minimum microbial community demonstrates a significant increase in bioleaching efficiency compared to the activity of individual species, involving mechanisms of the thiosulfate, the polysulfide and the iron oxidation pathway.

RESULTS

Populating gene-centric data structures holding rich functional annotation and interaction information allows deriving network models at the functional level coupling energy production and transport processes of both microbial species. Applying a network segmentation approach on the interaction network of ortholog genes covering energy production and transport proposes a set of specific molecular processes of relevance in bioleaching. The resulting molecular process model essentially involves functionalities such as iron oxidation, nitrogen metabolism and proton transport, complemented by sulfur oxidation and nitrogen metabolism, as well as a set of ion transporter functionalities. At. ferrooxidans-specific genes embedded in the molecular model representation hold gene functions supportive for ammonia utilization as well as for biofilm formation, resembling key elements for effective chalcopyrite bioleaching as emergent property in the co-culture situation.

CONCLUSIONS

Analyzing the entangled molecular processes of a microbial community on the level of segmented, gene-centric interaction networks allows identification of core molecular processes and functionalities adding to our mechanistic understanding of emergent properties of microbial consortia.

A WD-FYVE protein binds to the kinases Akt and PKCzeta/lambda

WD (tryptophan-aspartic acid dipeptide)-repeat proteins play a central role in signal transduction cascades by co-ordinating the interaction of key signalling molecules. We identified a novel propeller-FYVE [domain identified in Fab1p, YOTB, Vac1p and EEA1 (early endosome antigen 1)] protein, ProF, which is expressed in various cell lines and tissues and consists of seven WD-repeats and a FYVE domain. WD-repeat proteins offer a platform for protein-protein interactions by folding into a seven-bladed propeller-like structure, while the FYVE domain binds to phosphatidylinositol 3-phosphate present mainly on intracellular membranes. The ProF protein partially co-localizes with EEA1 on vesicular structures and binds to the protein kinases Akt and PKCzeta/lambda (protein kinase Czeta/lambda) via its WD-repeat propeller. ProF interacts more strongly with the kinases after hormonal stimulation. Endogenously expressed ProF and the two kinases interact in brain and in the preadipocyte cell line 3T3-L1, suggesting a role in secretory vesicular processes. In summary, we describe a new binding partner for kinases, located on vesicular structures in specialized cells, which may play a role for the spatial organization of signalling cascades.

Magnetresonanztomographie nach Kryoablation langer Röhrenknochen im Tiermodell

PURPOSE

To describe the MR findings following cryoablation of long bones.

MATERIALS AND METHOD

Cryoablation was performed in femoral and tibial bones of 24 sheep under general anesthesia. MRI of the treated and untreated contralateral bones was performed immediately thereafter and at 2, 4 and 6 months after the cryosurgical procedure.

RESULTS

On the MRI performed immediately after cryotherapy, the lesions showed low signal intensities relative to the normal bone marrow on unenhanced T1- and T2-weighted images. At 2, 4 and 6 months after cryoablation, the lesions showed high signal intensities on STIR images, low signal intensities on T1-weighted and heterogeneous enhancement on contrast-enhanced T1-weighted MR images. The femoral lesions decreased in size from 31 +/- 3 mm immediately after the cryotherapy to 13 +/- 4 mm 6 month later and the tibial lesions from 29 +/- 7 mm to 19 +/- 4 mm.

CONCLUSION

MRI shows bone marrow lesions immediately after cryotherapy and can easily monitor healing lesions. MR imaging is suitable for following cryotherapy.

Cooperation of Ras- and c-Myc-dependent pathways in regulating the growth and invasiveness of synovial fibroblasts in rheumatoid arthritis

OBJECTIVE

To study the specific contribution of MAP kinase activator c-Raf-1 and one of its downstream transcription factors, c-Myc, to the growth and invasive behavior of rheumatoid arthritis synovial fibroblasts (RASFs).

METHODS

RASFs were transduced with retroviral constructs expressing dominant-negative mutants of c-Raf-1 or c-Myc (DN c-Raf-1 or DN c-Myc, respectively) or with the mock vector. The expression of wild-type and mutant proteins was confirmed by Western blotting. Growth curves of RASFs were recorded, and apoptosis was measured by flow cytometry. Invasiveness of RASFs was assessed in the SCID mouse model of RA. Immunohistochemistry was used to study the effects of DN c-Raf-1 on phosphorylated c-Jun and matrix metalloproteinase 1 (MMP-1) in RASFs implanted into SCID mice. The phosphorylation of ERK and JNK in DN c-Raf-1- and mock-transduced RASFs was determined in vitro by Western blotting. The levels of MMPs in these cells were measured by quantitative polymerase chain reaction (PCR).

RESULTS

Neither DN c-Raf-1 alone nor DN c-Myc alone significantly altered proliferation or apoptosis of RASFs, but both mutants together rapidly induced apoptosis. Inhibition of c-Raf-1 or c-Myc significantly reduced the invasiveness of RASFs in the SCID mouse model. DN c-Raf-1 decreased the phosphorylation of ERK and JNK in vitro and reduced the in vivo expression of phosphorylated c-Jun as well as the expression of disease-relevant MMPs. As determined by quantitative PCR, the inhibition was most pronounced for MMP-1 and MMP-3.

CONCLUSION

The data demonstrate that Ras- and c-Myc-dependent signaling events cooperate to regulate the growth and invasiveness of RASFs. Targeting of both c-Raf-1 and c-Myc may constitute an interesting therapeutic approach in RA.

Rate of perioperative complications in thermal ablation of bone: an animal trial

INTRODUCTION

While only few data are available yet for radioablation of bone tissue, the occurrence of bone marrow embolisms during cryoablation has been documented. It was the aim of this study to assess perioperative complication rates of thermoablation in animals using state-of-the-art ablation probes.

MATERIALS AND METHODS

Eight adult sheep were placed under general anaesthesia, and using a radioprobe, thermoablation was performed on the medial side of the head of the right tibia. In addition, freezing was performed with miniature cryoprobes on both femurs and the head of the left tibia. Haemodynamic monitoring and determination of blood gases and electrolytes were done intraoperatively. The animals were killed 1 week after surgery, and the ablation sites and lung tissue examined macroscopically and microscopically.

RESULTS

None of the animals showed pathological changes in any of these parameters. Blood gases remained unremarkable throughout the operation. All eight animals showed an average drop in haemoglobin of 0.97 g/100 ml. Two animals showed fresh embolisms in the pulmonary vessels.

CONCLUSION

Experimental thermoablation of bone tissue in large animals failed to show any significant perioperative complications following surgery. The lung embolisms which did occur were not clinically relevant. The use of mini-cryoprobes or radioprobes as alternative or complementary measures for treating pathologically altered bone tissue seems viable and does not involve any undue risks.

[Changes in stability after cryosurgical treatment of long tubular bones. An animal experiment study]

The incidence of spontaneous fractures after cryosurgical treatment is described in the literature. The purpose of this study in the sheep model was to analyze the possibility of minimizing the potential risk of bone failure using a new miniature cryoprobe with minimal tissue traumatism and exact control of the ablation. In each of 24 sheep ablations at the right femur and left tibia were performed by drilling. The ablation at the femur was restricted to an area of 2 cm(2) of only one cortical bone, whereas at the proximal tibia the whole tibial plateau was included. The opposite side, which was treated with analog drillings without cryoablation, served as control. The ultimate bending strength of the femur and the ultimate compression strength of the tibia were examined 2, 4, and 6 months after the operation. After 2 months there was a significant difference ( p<0.05) in the ultimate compression strength between the treated and untreated tibiae, whereas the ultimate bending strength of the treated femora tended to be lower. After 4 and 6 months the side treated with cryosurgery was only marginally weaker than the untreated side. Spontaneous fractures were not observed during the whole experimental period. The good controllability of the freezing procedure and the low iatrogenic weakening of the bone using a modern miniature cryoprobe minimizes the risk of pathological postoperative fractures. After ablation of larger bone sections, the treated extremity should be partially unloaded or managed by osteosynthesis for at least 3 months.

Cryosurgery in long bones with new miniature cryoprobe: an experimental in vivo study of the cryosurgical temperature field in sheep

AIM

The aim of this in vivo study was to determine whether new miniature cryoprobes provide adequate tissue cooling in long bones by measuring the field of temperature under various conditions.

METHODS

Freezings were performed in femoral and tibial bones of 10 sheep under general anaesthesia. Applying one cryoprobe, temperatures of -75 degrees C resp. -51 degrees C could be reached within 0.75 cm resp. 1.00 cm of the probe.

RESULTS

Histological examinations revealed compact bone and marrow necroses along the isotherm in all 10 sheep. Using two cryoprobes simultaneously, a mean temperature decrease to -71 degrees C between the two cryoprobes was achieved thanks to the synergistic freezing effect. Looking at consecutive freezes, it was apparent that with similar cryoprobe end temperatures, the temperature dropped faster if the number of freezing cycles was increased.

CONCLUSION

In conclusion, it was seen that despite its small diameter, the new miniature cryoprobe delivers adequate in vivo tissue cooling in long tubular bones. Employing the synergistic freezing effect by using two or more cryoprobes simultaneously, efficient in vivo freezing of larger bone segments is also possible. Thus, cryosurgery with the new miniature probes can provide a valuable complement to conventional resection of long tubular bones, and offers a viable alternative to surgical treatment of neoplastic diseases of the skeletal system.

Linear closed mini DNA generated by the prokaryotic cleaving-joining enzyme TelN is functional in mammalian cells

For application of DNA in gene medicine plasmid or viral DNA is usually used as a vector for the gene of interest. To generate DNA with a minimum of foreign DNA sequences, we used the prokaryotic telomerase, protelomerase TelN, of bacteriophage N15. This is a novel enzyme with cleaving-joining activity, which is required for the formation of linear prophage DNA with closed ends in lysogenic bacteria. Acting on a telomere resolution site telRL, the protelomerase converts circular plasmid DNA into linear covalently closed dumbbell-shaped molecules ("doggybones") in a single-step enzyme reaction. Two such sites were inserted into an expression plasmid flanking a gene of interest. This is cleaved and joined by means of the protelomerase, yielding linear closed mini DNA coding for green fluorescent protein (EGFP) or interleukin-12 (IL-12). Upon transient transfection of human embryonal kidney cells, EGFP was expressed at higher levels from linear closed molecules than from linear open molecules generated by restriction endonucleases for comparison. The level of transcription was comparable to that observed for the parental plasmid DNA. To test whether the linear closed mini DNA molecules are functional in vivo the B16F10/C57BL/6 melanoma metastasis model was applied, where injection of IL-12-expressing DNA inhibits metastasis formation in the lung. The anti-metastatic effect of the IL-12-expressing linear closed DNA was equal or higher than that of the parental plasmid DNA. Therefore, the TelN/ telRL system is well suited to generate linear closed mini DNA with high stability and a minimum of foreign nucleotide sequences.

[Detection of air embolism by a re-usable Doppler probe integrated in a central venous line--application in-vivo]

PROBLEM

Air embolism frequently occurs under neurosurgical operations performed in the sitting position. Recently we reported the idea of inserting a re-usable doppler probe into a blind-ending lumen of a central venous catheter (Schregel-Volk-Catheter, SVC). In vitro testing in a circulation model showed a high sensitivity: air bubbles as small as 0.5 microliter were reliably detected at a distance up to 4 cm from the tip of the SVC.

METHOD

After approval by the local ethics committee pigs were anaesthetised and a cardiopulmonary bypass was connected. During the bypass period a 12 F SVC (Medex Medical, Germany) with one blind-ending lumen was positioned into the proximal vena cava cranialis or vena cava caudalis. An 8 MHz doppler probe (MTB Basler, Suisse) was introduced into the SVC and connected with the doppler device Multi-Dop T (DWL, Germany). Well defined air bubbles (3-6 microliter) were generated by a bubble generator and injected into the right femoral vein or the left vena jugularis interna.

RESULTS

All bubbles were reliably detected by the re-usable doppler probe. Embolic events can be documented, counted and quantified by the Multi-Dop T.

CONCLUSION

Using SVC's with a blind-ending lumen could improve and simplify the detection of air embolism. We see several advantages (e.g. sensitivity, costs) compared with established methods (precordial doppler, TEE) for detection of air embolism.

Regulation of Raf-Akt Cross-talk

We have recently shown that the Ras-Raf-MEK-ERK and phosphatidylinositol 3-kinase (PI3K)-Akt signaling pathways can cross-talk in the human breast cancer cell line MCF-7. High Raf activity induces growth arrest and differentiation in these cells, whereas high PI3K/Akt activity correlates with cell survival and proliferation. Here we show that the Raf-Akt cross-talk is regulated in a concentration- and ligand-dependent manner. High doses of insulin-like growth factor I (IGF-I) activate Akt quickly and strongly enough to suppress Raf kinase activity via phosphorylation of Ser-259, whereas low doses of IGF-I do not trigger this cross-talk but are still mitogenic. Phorbol 12-myristate 13-acetate, a differentiation-inducing stimulus, potently activates the Ras-Raf-MEK-ERK pathway but only weakly activates PI3K/Akt and does not trigger the cross-talk. Thus, the herein analyzed parameters such as ligand type, concentration, and time course may contribute to the cellular response of either proliferation or differentiation. This is highly relevant to understanding cellular transformation and may be of use in areas like tissue engineering.

Induction of putative tumor-suppressing genes in Rat-1 fibroblasts by oncogenic Raf-1 as evidenced by robot-assisted complex hybridization

The growth factor receptor-dependent protein kinase Raf-1 is activated by GTP-bound Ras, thereby activating the mitogen-activated protein kinase pathway. To study the role of Raf in transformation we transduced Rat-1 cells with a tetracycline-regulatable retroviral vector encoding the constitutively active oncogenic C-terminal fragment of the human Raf-1 protein. Using subtractive hybridization of mRNAs from induced and noninduced cells and robot-assisted screening by complex hybridization, Raf-induced genes with various different characteristics of induction were investigated. Among the strongly induced genes were those involved in carcinogenesis such as metalloproteinases 3, 10 and 13, cathepsin L, ornithine decarboxylase, and putative tumor-suppressing genes such as monocyte chemoattracting protein 1, interferon-induced protein 10, a recently identified 2'-5' oligoadenylate synthetase-like protein, and plasminogen activator inhibitor type 2. Other components of the plasminogen activator system were not induced. Plasminogen activator inhibitor type 2 is a down-regulator of the proteolytic cascade consisting of various metalloproteinases, some of which are induced by a carboxy-terminal Raf mutant (RafCT). In conclusion, RafCT induces factors which act in a conflicting manner in respect of carcinogenesis, especially within the proteolytic system of the extracellular matrix.

[Surgery of the external auditory canal in familial bilateral auditory canal atresia]

BACKGROUND

Inherited isolated bilateral atresia of the external auditory canal is rare. Ear canal surgery procedure is difficult.

METHODS

Basing on a case report of a family with inherited isolated bilateral atresia of the external auditory canal in 4 cases the way of preoperative diagnostics including human genetics and our surgical concept is described.

RESULTS

Resulting clinical findings showed complete epithelialization of the ear canal and ear drum with slight conductive hearing loss.

CONCLUSIONS

Canaloplasty in atresia can be easily and successfully accomplished by our modified technique.

Blood eosinophil leukotriene C4 production in asthma of different severities

In asthma, activation and recruitment of eosinophils to the bronchial mucosa amplifies many cellular functions. The blood eosinophil count and the number of hypodense eosinophils increase with asthma severity. Eosinophils produce numerous proinflammatory mediators in response to a variety of agonists, notably the peptido-leukotriene (LT) C4, a potent bronchoconstrictor. In this study, we have evaluated blood eosinophil LTC4 release and its modulation by cytokines in normal individuals and in subjects with asthma of various severities: mild (beta 2-agonist on demand); moderate (inhaled steroids on a regular basis); and severe (inhaled and oral steroids on a regular basis). Eosinophils were isolated using a modified Percoll gradient technique, which recovers both hypodense and normodense eosinophils in a global cell population. Eosinophils released detectable amounts of LTC4 only in the presence of the stimulus (calcium ionophore A23187, 2 microM). The ionophore-induced LTC4 release was greater in moderate asthmatics (mean +/- SEM 5.7 +/- 1.3 pg x 10(3)/250,000 eosinophils) than in normal individuals (1.6 +/- 0.4 pg x 10(3)/250,000 eosinophils), mild asthmatics (1.8 +/- 0.3 pg x 10(3)/250,000 eosinophils) and severe asthmatics (2.0 +/- 0.3 pg x 10(3)/250,000 eosinophils). Granulocyte/macrophage colony-stimulating factor (GM-CSF) and interleukin-5 (IL-5) amplified the ionophore-induced LTC4 release in the four groups from 1.9 to 2.6 and 1.9 to 2.8 fold, respectively. Interleukin-3 (IL-3) did not increase LTC4 production except by the eosinophils of the severe asthmatics whose ionophore-induced LTC4 production was enhanced by 1.9 fold. These data demonstrate that the asthmatic bronchial inflammatory process may modify blood eosinophil LTC4 release and its modulation by cytokines according to asthma severity and treatment.

Seroprevalence of human immunodeficiency virus, hepatitis B virus, hepatitis C virus, and rapid plasma reagin in a trauma population

We evaluated the presence of human immunodeficiency virus (HIV), hepatitis B virus (HBV), hepatitis C virus (HCV), and rapid plasma reagin (RPR) among patients admitted to our trauma unit from April 15 to June 30, 1993. Of 984 patients tested, we found 255 (26%) had evidence of exposure to one or more of these agents: HIV, 4%; HBV, 20%; HCV, 14%; and RPR, 1%. Thirty-eight percent of patients had more than one positive serology, 75% of the HIV patients, 49% of the HBV patients, and 66% of the HCV patients. There was no difference between penetrating and nonpenetrating trauma with respect to any of the viruses. The risk factors for HIV-positive patients were non-White race, positive drug screen, positive alcohol screen, and city resident. Risk factors for HBV patients were non-White race, positive drug screen, and city resident. Risk factors for HBC patients were male sex, non-White race, positive alcohol screen, positive drug screen, and city resident. The risk of blood-borne infections in this group of patients is substantial.

Dysbaric osteonecrosis of the femoral diametaphysis

A 28-year-old submarine officer was involved in a dysbaric exposure at 155 feet for 21 hours. Subsequent to rescue, he developed a painful osteonecrosis involving over two-thirds of the femoral shaft and distal metaphysis. Pain is totally atypical for a bony injury of this distribution but because of failure to improve after 12 months, he underwent a series of three operations: (1) core biopsy, (2) intramedullary reaming and intramedullary rod fixation of the femur, and (3) bone grafting to a metaphyseal defect in the distal femur. Serial MRI scans were used to follow the progression of his osteonecrosis. This case report documents the first reported dysbaric diaphyseal osteonecrosis requiring surgery and intramedullary fixation to obtain a satisfactory clinical result.

Structural stiffness of the Hoffmann simple anterior tibial external fixation frame

Tibial external fixation frames were constructed on aluminum tube simulating tibia bone. A 20-mm gap was left at the fracture site in order to measure the structural stiffness of the frame rather than the aluminum tube. The performance of the frames were experimentally evaluated and quantified using tests which simulated the loading conditions encountered in normal walking. These included axial compression, anteroposterior (AP) bending, lateral bending and torsional loading of the frame. The parameters studied were (a) number of fixation pins, (b) number of connecting rods and (c) location of clamps on the pins. Four constants were evaluated from these tests using various structural configurations of the frames; these resulted in four stiffness coefficients in compression, AP bending, lateral bending and torsion. Stiffnesses of various frames with different geometric configurations were compared by comparing their appropriate stiffness coefficients. Such comparison can set forth a quantitative guideline in selecting a suitable frame configuration for the type of injury and condition of fracture pattern. This type of quantitative analysis can also be useful in modifying the frame during the postoperative bone healing process.

Bilateral facet dislocations in the thoracolumbar spine

Bilateral facet dislocation represents approximately 11% of all thoracolumbar spine injuries requiring surgical stabilization. The injury can be caused by either flexion distraction (29/30 cases) or by pure distraction (1/30). Recognition of the injury is possible on plain radiographs, and confirmed by the empty facet sign on the computed tomography (CT) scan. In contradistinction to other major spine injuries, the majority of patients present with complete neurologic lesions (21/30). Recovery of patients with incomplete lesions is frequent (5/6); however, recovery from complete lesions did not occur. Compression instrumentation is recommended for patients with complete lesions because it is stable and requires no external immobilization. Distraction instrumentation that imparts significant extension is advised for patients with incomplete lesions. It is safe and reliable, and eliminates the posterior bulging of the injured disc that can occur with compression. For low lumbar injuries where compression is desirable in order to achieve the shortest possible instrumentation, a discectomy is recommended.

Multiplanar computed tomography: a multidimensional tool for evaluation and treatment of acetabular fractures

Fractures of the acetabulum present a formidable diagnostic and therapeutic challenge. Improved management has decreased the mortality associated with these injuries. Prolonged survival of the severely injured has raised the associated morbidity. To improve diagnosis and treatment in these patients, computed tomography with multiplanar reconstructions has been utilized in the pre- and post-operative period in 30 patients. This refinement provides a precise, accurate, and reproducible method of establishing the diagnostic data base. Consequently it is possible to better define the pathoanatomy, make decisions as to the best technique for intervention, and facilitate execution of these techniques by improved preoperative planning and postintervention assessment. It is concluded that computed tomography with multiplanar reconstructions optimizes the ability to manage these injuries.

[Psychological disorders of students and university results]

Many epidemiological studies demonstrate the importance of psychological disorders among college and university students. Those disorders have an impact upon the academic performance and may lead to dropping out. The aim of this research is to study the possible relations between the incidence of psychological troubles and the evolution of the academic performance. The sample is constituted by 45 first year students of the Université du Québec à Trois-Rivières. Each subject has answered the psychological and psychiatric inventory built up by Bernot et al. (1969) (Psychorater). The academic performance evolution has been scored by comparing, for each student, the mark means obtained at the first three sessions. Cross-sessions comparisons have made possible to divide the sample into four subgroups: "in regression", "with relatively stable performances", "in progression" and "dropouts". The results show a statistically significative relation between, on the one hand, the university adaptation difficulties leading to dropping out and, on the other hand, the "impulsivity-instability" dimension and the "family, professional and social adaptation troubles". Excluding the dropout subjects, it is not possible, however, to correlate the variations in the academic performance and the incidence of psychological troubles found with the Psychorater.

Pure thoracolumbar facet dislocation: clinical features and CT appearance

The use of computed tomography (CT) in demonstrating pure dislocations of the thoracolumbar facets and in predicting the prognosis of this injury was evaluated and compared with radiography retrospectively. The records of 29 patients with pure thoracolumbar bilateral facet dislocation who were admitted to the trauma unit over a 4-year period were reviewed. Twenty-two patients (76%) had a complete neurologic loss that remained complete following immediate surgical stabilization; five (17%) had an incomplete neurologic loss, and two (7%) were normal neurologically. Plain radiographs of the spine, including anteroposterior and lateral views, documented the level and type of fracture but failed to depict the full extent of bony ad soft-tissue injuries. CT provided essential additional information, particularly regarding the status of the posterior elements of the vertebrae and the adequacy of the spinal canal. Pure thoracolumbar facet dislocations have a characteristic appearance on axial CT scans. Sagittal reformation through CT is essential in the evaluation of this type of spinal injury.