The flagellar muramidase from the photosynthetic bacterium Rhodobacter sphaeroides

We have characterized open reading frame RSP0072, which is located within the flgG operon in Rhodobacter sphaeroides. The amino acid sequence analysis of this gene product showed the presence of a soluble lytic transglycosylase domain. The deletion of the N-terminal region (90 amino acids) of the product of RSP0072 yields a leaky nonmotile phenotype, as determined by swarm assays in soft agar. Electron micrographs revealed the lack of flagella in mutant cells. The purified wild-type protein showed lytic activity on extracts of Micrococcus luteus. In contrast, no lytic activity was observed when the residues E57 or E83 were replaced by alanine. Affinity blotting suggests that the protein encoded by RSP0072 interacts with the flagellar rod-scaffolding protein FlgJ, which lacks the muramidase domain present in FlgJ of many bacteria. We propose that the product of RSP0072 is a flagellar muramidase that is exported to the periplasm via the Sec pathway, where it interacts with FlgJ to open a gap in the peptidoglycan layer for the subsequent penetration of the nascent flagellar structure.

Orbital and millennial Antarctic climate variability over the past 800,000 years

A high-resolution deuterium profile is now available along the entire European Project for Ice Coring in Antarctica Dome C ice core, extending this climate record back to marine isotope stage 20.2, approximately 800,000 years ago. Experiments performed with an atmospheric general circulation model including water isotopes support its temperature interpretation. We assessed the general correspondence between Dansgaard-Oeschger events and their smoothed Antarctic counterparts for this Dome C record, which reveals the presence of such features with similar amplitudes during previous glacial periods. We suggest that the interplay between obliquity and precession accounts for the variable intensity of interglacial periods in ice core records.

Orbital and millennial Antarctic climate variability over the past 800,000 years

A high-resolution deuterium profile is now available along the entire European Project for Ice Coring in Antarctica Dome C ice core, extending this climate record back to marine isotope stage 20.2, approximately 800,000 years ago. Experiments performed with an atmospheric general circulation model including water isotopes support its temperature interpretation. We assessed the general correspondence between Dansgaard-Oeschger events and their smoothed Antarctic counterparts for this Dome C record, which reveals the presence of such features with similar amplitudes during previous glacial periods. We suggest that the interplay between obliquity and precession accounts for the variable intensity of interglacial periods in ice core records.

Orbital and Millennial Antarctic Climate Variability over the Past 800,000 Years

A high-resolution deuterium profile is now available along the entire European Project for Ice Coring in Antarctica Dome C ice core, extending this climate record back to marine isotope stage 20.2, approximately 800,000 years ago. Experiments performed with an atmospheric general circulation model including water isotopes support its temperature interpretation. We assessed the general correspondence between Dansgaard-Oeschger events and their smoothed Antarctic counterparts for this Dome C record, which reveals the presence of such features with similar amplitudes during previous glacial periods. We suggest that the interplay between obliquity and precession accounts for the variable intensity of interglacial periods in ice core records.

A complete set of flagellar genes acquired by horizontal transfer coexists with the endogenous flagellar system in Rhodobacter sphaeroides

Bacteria swim in liquid environments by means of a complex rotating structure known as the flagellum. Approximately 40 proteins are required for the assembly and functionality of this structure. Rhodobacter sphaeroides has two flagellar systems. One of these systems has been shown to be functional and is required for the synthesis of the well-characterized single subpolar flagellum, while the other was found only after the genome sequence of this bacterium was completed. In this work we found that the second flagellar system of R. sphaeroides can be expressed and produces a functional flagellum. In many bacteria with two flagellar systems, one is required for swimming, while the other allows movement in denser environments by producing a large number of flagella over the entire cell surface. In contrast, the second flagellar system of R. sphaeroides produces polar flagella that are required for swimming. Expression of the second set of flagellar genes seems to be positively regulated under anaerobic growth conditions. Phylogenic analysis suggests that the flagellar system that was initially characterized was in fact acquired by horizontal transfer from a gamma-proteobacterium, while the second flagellar system contains the native genes. Interestingly, other alpha-proteobacteria closely related to R. sphaeroides have also acquired a set of flagellar genes similar to the set found in R. sphaeroides, suggesting that a common ancestor received this gene cluster.

Predicting activities without computing descriptors: graph machines for QSAR

We describe graph machines, an alternative approach to traditional machine-learning-based QSAR, which circumvents the problem of designing, computing and selecting molecular descriptors. In that approach, which is similar in spirit to recursive networks, molecules are considered as structured data, represented as graphs. For each example of the data set, a mathematical function (graph machine) is built, whose structure reflects the structure of the molecule under consideration; it is the combination of identical parameterised functions, called "node functions" (e.g. a feedforward neural network). The parameters of the node functions, shared both within and across the graph machines, are adjusted during training with the "shared weights" technique. Model selection is then performed by traditional cross-validation. Therefore, the designer's main task consists in finding the optimal complexity for the node function. The efficiency of this new approach has been demonstrated in many QSAR or QSPR tasks, as well as in modelling the activities of complex chemicals (e.g. the toxicity of a family of phenols or the anti-HIV activities of HEPT derivatives). It generally outperforms traditional techniques without requiring the selection and computation of descriptors.

Transcriptional specificity of RpoN1 and RpoN2 involves differential recognition of the promoter sequences and specific interaction with the cognate activator proteins

The four RpoN factors of Rhodobacter sphaeroides are functionally specialized. In this bacterium, RpoN1 and RpoN2 are specifically required for the transcription of the nitrogen fixation and flagellar genes, respectively. Analysis of the promoter sequences recognized by each of these RpoN proteins revealed some significant differences. To investigate the functional relevance of these differences, the flagellar promoter fliOp was sequentially mutagenized to resemble the nitrogen fixation promoter nifUp. Our results indicate that the promoter sequences recognized by these sigma factors have diverged enough so that particular positions of the promoter sequence are differentially recognized. In this regard, we demonstrate that the identity of the -11-position is critical for promoter discrimination by RpoN1 and RpoN2. Accordingly, purified RpoN proteins with a deletion of Region I, which has been involved in the recognition of the -11-position, did not show differential binding of fliOp and nifUp promoters. Substitution of the flagellar enhancer region located upstream fliOp by the enhancer region of nifUp allowed us to demonstrate that RpoN1 and RpoN2 interact specifically with their respective activator protein. In conclusion, two different molecular mechanisms underlie the transcriptional specialization of these sigma factors.

The flagellar hierarchy of Rhodobacter sphaeroides is controlled by the concerted action of two enhancer-binding proteins

The expression of the bacterial flagellar genes follows a hierarchical pattern. In Rhodobacter sphaeroides the flagellar genes encoding the hook and basal body proteins are expressed from sigma54-dependent promoters. This type of promoters is always regulated by transcriptional activators that belong to the family of the enhancer-binding proteins (EBPs). We searched for possible EBPs in the genome of R. sphaeroides and mutagenized two open reading frames (ORFs) (fleQ and fleT), which are in the vicinity of flagellar genes. The resulting mutants were non-motile and could only be complemented by the wild-type copy of the mutagenized gene. Transcriptional fusions showed that all the flagellar sigma54-dependent promoters with exception of fleTp, required both transcriptional activators for their expression. Interestingly, transcription of the fleT operon is only dependent on FleQ, and FleT has a negative effect. Both activators were capable of hydrolysing ATP, and were capable of promoting transcription from the flagellar promoters at some extent. Electrophoretic mobility shift assays suggest that only FleQ interacts with DNA whereas FleT improves binding of FleQ to DNA. A four-tiered flagellar transcriptional hierarchy and a regulatory mechanism based on the intracellular concentration of both activators and differential enhancer affinities are proposed.

Clinical Performance with the Levitronix Centrimag Short-term Ventricular Assist Device

BACKGROUND

The Levitronix ventricular assist device (VAD) is a centrifugal pump designed for extracorporeal support and that operates without mechanical bearings or seals. The rotor is magnetically levitated so that rotation is achieved without friction or wear, which seems to minimize blood trauma and mechanical failure. The aim of this study is to report our early results with the Levitronix Centrimag device.

METHODS

Between June 2003 and April 2005, 18 patients (pts) were supported using the Levitronix at our institution. Fourteen were male. Mean age was 40.3 +/- 18.3 (range 8 to 64) years. Indications for support at implantation were: post-cardiotomy cardiogenic shock in 12 cases (Group A), and bridge to decision regarding long-term ventricular support in 6 cases (Group B).

RESULTS

Mean support time was 14.2 +/- 15.2 days for all patients (range 1 to 64 days). Operative (30-day) mortality was 50% (9 pts). Six pts were in Group A and 3 pts were in Group B. Overall, 6 pts (33%) were discharged home and are presently alive and well (mean follow-up 13 months, range 5 to 17 months). Bleeding requiring re-operation occurred in 8 cases (44%), cerebral thromboembolism in 1 and pulmonary embolism in 1. There were no device failures.

CONCLUSIONS

The Levitronix functioned well and proved to be useful in patients with extremely poor prognosis previously considered non-suitable for a long-term assist device. The device was technically easy to implant and manage. There was no device dysfunction and complications were acceptable or consistent with other devices. Survival to explant or a definitive procedure (VAD or transplantation) was encouraging.

La paragonimose pleuropulmonaire

Paragonimiasis is a food borne zoonosis due to a trematode belonging to the genus Paragonimus. Although present throughout the world, about 90% of the cases occur in Asia where around 20 million people are infected. The parasitic cycle is complex with two different intermediate hosts. Man is infected by ingesting the raw or undercooked flesh of the second host - a freshwater crab or prawn - or possibly of a paratenic mammal host (wild boar), which contains the infective larval stage metacercariae that reaches the lung which is the main target organ. Epidemiological, pathological, and clinical aspects are reviewed. The main symptoms are protracted cough, and recurrent "benign" hemoptysis. Abnormal pleuro-pulmonary imaging features are constant, but protean and non-specific, leading to frequent confusion with tuberculosis. Diagnosis is easily achieved by ova search in the sputum or pleural fluid, or by serology. Evolution is usually considered benign, although not well known. Finally, praziquantel is the effective first choice treatment. Some paradoxical aspects of this disease are underlined such as: underdiagnosis despite a very simple diagnostic procedure, or opposite tendencies according to location, either extinction or re-emergence.

Biochemical study of multiple CheY response regulators of the chemotactic pathway of Rhodobacter sphaeroides

The six copies of the response regulator CheY from Rhodobacter sphaeroides bind to the switch protein FliM. Phosphorylation by acetyl phosphate (AcP) was detected by tryptophan fluorescence quenching in three of the four CheYs that contain this residue. Autophosphorylation with Ac(32)P was observed in five CheY proteins. We also show that all of the cheY genes are expressed simultaneously; therefore, in vivo all of the CheY proteins could bind to FliM to control the chemotactic response. Consequently, we hypothesize that in this complex chemotactic system, the binding of some CheY proteins to FliM, does not necessarily imply switching of the flagellar motor.

Probable allergic reaction to cyclosporin and early formation of thrombi on a pulmonary artery catheter: two unusual complications during bilateral lung transplantation

We describe a patient who had two rare complications (a probable allergic reaction to cyclosporin and the early formation of a right atrial thrombus) during bilateral sequential single lung transplantation performed under the one anaesthetic. The thrombus, discovered at the end of the procedure, was then removed under cardiopulmonary bypass. Peroperative transoesophageal echocardiography was useful in providing critical diagnostic and therapeutic information.

Characterization of the flgG operon of Rhodobacter sphaeroides WS8 and its role in flagellum biosynthesis

In this work, we show evidence regarding the functionality of a large cluster of flagellar genes in Rhodobacter sphaeroides. The genes of this cluster, flgGHIJKL and orf-1, are mainly involved in the formation of the basal body, and flgK and flgL encode the hook-associated proteins HAP1 and HAP3. In general, these genes showed a good similarity as compared with those reported for Salmonella enterica. However, flgJ and flgK showed particular features that make them unique among the flagellar sequences already reported. flgJ is only a third of the size reported for flgJ from Salmonella; whereas flgK is about three times larger than any other flgK sequence previously known. Our results indicate that both genes are functional, and their products are essential for flagellar assembly. In contrast, the interruption of orf-1, did not affect motility suggesting that this sequence, if functional, is not indispensable for flagellar assembly. Finally, we present genetic evidence suggesting that the flgGHIJKL genes are expressed as a single transcriptional unit depending on the sigma-54 factor.

The four different sigma(54) factors of Rhodobacter sphaeroides are not functionally interchangeable

The sigma(54) factor is highly conserved in a large number of bacterial species. From the complete genome sequence of Rhodobacter sphaeroides, it was possible to identify four different sequences encoding potentially functional sigma(54) factors. In this work, we provide evidence that one of these copies (rpoN2) is specifically required to express the flagellar genes in this bacterium. A mutant strain carrying a lesion in the rpoN2 gene was unable to swim even though the RpoN1 and RpoN3 proteins were present in the cytoplasm. The possibility that the different copies of the sigma(54) factor might be specific for the transcription of a particular subset of sigma(54) promoters was reinforced by the fact that a mutant strain carrying a lesion in rpoN1 showed a severe growth defect in nitrogen-free culture medium, even though the rpoN2 and rpoN4 genes were actively transcribed from a plasmid or from the chromosome. Different mechanisms that might be responsible for this specificity are discussed.

How to be a gray box: dynamic semi-physical modeling

A general methodology for gray-box, or semi-physical, modeling is presented. This technique is intended to combine the best of two worlds: knowledge-based modeling, whereby mathematical equations are derived in order to describe a process, based on a physical (or chemical, biological, etc.) analysis, and black-box modeling, whereby a parameterized model is designed, whose parameters are estimated solely from measurements made on the process. The gray-box modeling technique is very valuable whenever a knowledge-based model exists, but is not fully satisfactory and cannot be improved by further analysis (or can only be improved at a very large computational cost). We describe the design methodology of a gray-box model, and illustrate it on a didactic example. We emphasize the importance of the choice of the discretization scheme used for transforming the differential equations of the knowledge-based model into a set of discrete-time recurrent equations. Finally, an application to a real, complex industrial process is presented.

The N terminus of FliM is essential to promote flagellar rotation in Rhodobacter sphaeroides

FliM is part of the flagellar switch complex. Interaction of this protein with phospho-CheY (CheY-P) through its N terminus constitutes the main information relay point between the chemotactic system and the flagellum. In this work, we evaluated the role of the N terminus of FliM in the swimming behavior of Rhodobacter sphaeroides. Strains expressing the FliM protein with substitutions in residues previously reported in Escherichia coli as being important for interaction with CheY showed an increased stop frequency compared with wild-type cells. In accordance, we observed that R. sphaeroides cells expressing FliM lacking either the first 13 or 20 amino acids from the N terminus showed a stopped phenotype. We show evidence that FliMDelta13 and FliMDelta20 are stable proteins and that cells expressing them allow flagellin export at levels indistinguishable from those detected for the wild-type strain. These results suggest that the N-terminal region of FliM is required to promote swimming in this bacterium. The role of CheY in controlling flagellar rotation in this organism is discussed.

The hook gene (flgE) is expressed from the flgBCDEF operon in Rhodobacter sphaeroides: study of an flgE mutant

In this work we identified the flgE gene encoding the flagellar hook protein from Rhodobacter sphaeroides. Our results show that this gene is part of a flagellar cluster that includes the genes flgB, flgC, flgD, flgE, and flgF. Two different types of mutants in the flgE gene were isolated, and both showed a Fla(-) phenotype, indicating the functionality of this sequence. Complementation studies of these mutant strains suggest that flgE is included in a single transcriptional unit that starts in flgB and ends in flgF. In agreement with this possibility, a specific transcript of approximately 3.5 kb was identified by Northern blot. This mRNA is large enough to represent the complete flgBCDEF operon. FlgE showed a relatively high proline content; in particular, a region of 12 amino acids near the N terminus, in which four prolines were identified. Cells expressing a mutant FlgE protein lacking this region showed abnormal swimming behavior, and their hooks were curved. These results suggest that this region is involved in the characteristic quaternary structure of the hook of R. sphaeroides and also imply that a straight hook, or perhaps the rigidity associated with this feature, is important for an efficient swimming behavior in this bacterium.

Surgery of acute type A dissection: what have we learned during the past 25 years?

Every acute dissection involving the ascending aorta (Stanford type A) must undergo emergency surgical repair. However, the surgical techniques must vary according to the clinical presentation of the patients or the anatomical patterns observed. Furthermore, surgery is generally difficult because of the poor condition of the aortic tissues. To reduce those difficulties many technical artifacts have been described. In 1977, we proposed the use of gelatin-resorcin-formalin (GRF) biological glue to reinforce the suture areas. From January 1977 to July 1999, 212 patients (pts) (152 males and 60 females) aged from 15 to 80 years (mean age: 54 +/- 11 years) underwent an emergency operation for type A aortic dissection. One-hundred-seventy-eight pts (84%) were operated on within 4 hours after being referred to the hospital. Twenty-eight pts (13.2%) had Marfan's syndrome. In 44 patients (20.7%), the aortic valve was replaced either independently (6 cases--2.8%) or by means of a composite graft (38 cases--17.9%). Because of the location of the intimal tear, the aortic replacement was extended to the transverse arch in 61 pts (28.7%). Hospital mortality amounts to 21.6% (46 pts), 25% in pts with arch replacement and 19.4% in pts without arch replacement (n.s). Analysis of hospital mortality demonstrates that the main causes of death were cardiac tamponade, neurologic disorders and visceral malperfusion. One-hundred-sixty-six pts were discharged and surveyed from 5 months to 22 years postoperatively (mean follow-up: 85 +/- 66 months). During this period of time, 25 pts (15%) had to be reoperated for a total of 33 reoperations. Seven pts (28%) died at reoperation. Using univariate analysis, the presence of Marfan's syndrome (p < 0.05) and absence of arch replacement (p < 0.02) were determinant risk factors for reoperation. Emergency (p < 0.01) and thoraco-abdominal replacement (p < 0.04) were determinant riskfactors for death at reoperation. The freedom from reoperation (Kaplan-Meier, CI: 95%) is 96% (90-98), 87% (79-92), 80% (70-88), 66% (51-78) at 1, 5, 10 and 15 years respectively. A total of 39 pts (24.3%) died during follow-up. The presence of Marfan's syndrome (p < 0.01), reoperation (p < 0.02), stroke (p < 0.05), and cardiac failure (p < 0.05) were determinant risk factors of late mortality. The late survival rate (K-M. C.I.: 95%), including hospital mortality, is 71% (64-77), 66% (58-73), 56% (47-64), 46% (36-56), 37% (28-44) at 1, 10, 15 and 20 years, respectively. From our experience extending over more than 23 years, GRF glue has proved to be extremely useful, making the procedure much easier and safer. Nevertheless, many factors are of importance in the pre-, intra- and postoperative management of the patients. Cardiac tamponade and visceral malperfusion must be properly diagnosed and treated. During aortic repair, the main intimal tear must be resected. The transverse arch must be checked and replaced whenever necessary. The aortic valve should be preserved whenever possible. During CPB, perfusing the aorta in the regular antegrade manner seems to dramatically reduce the rate of malperfusion. The quality of the first emergency operation seems to have a major influence on the late results, especially concerning the rate of late reoperations and aortic ruptures. However, those late results depend also on the patient's basic condition, particularly in Marfan patients.

[Surgery of heart insufficiency]

Apart from heart transplantation for heart failure, the problem arises of which surgical approach should be adopted to treat this disorder. Ischemic heart disease can be surgically managed in three ways: via bypass, the Dor procedure, or by isolated or associated mitral plasty; however, cases of enlarged heart disease can only be surgically treated in two ways: i.e., by mitral plasty, or by the Batista procedure. In cases of ischemic heart disease, the following conditions must be present for coronary bypass: the patients should have an adequate contractile myocardial reserve, that is to say the left ventricle should not be greatly enlarged (< 80 mm in telediastole) or a cardiac output reserve, and there should not be any sign of over-high pulmonary hypertension (an index of > 1.6 or a pulmonary pressure of < 45); an assessment of myocardial viability should then be carried out, mainly based on a thallium fixation at rest and on echographically determined doubtamine-associated stress. In the present study, the mortality rate in a series of 260 patients was 6.3% for subjects aged under 70 years old, with an actuarial survival rate of 82% at one year post-surgery, and of 70% at five years. The Dor procedure can be used in the treatment of dyskinesia, which is now practically non-existent, but also in cases of acute akinesia with resulting left ventricular dysfunction. The aim of this technique is to alter the form of a cavity that has become ovoid to an elliptical form via the insertion of a circular endoventricular patch. The results reported for this technique show an improvement in functional class and ejection fraction. Finally, the technique for repairing mitral failure is more complicated than the two previous methods, as it requires a dynamic assessment of mitral failure, which is best carried out by an evaluation of echographically determined stress. Any mitral failure of ischemic origin of > grade 2 can be corrected during bypass surgery by ring insertion, thereby effecting a simple annuloplasty. On the other hand, the assessment of cases of enlarged heart disease is more complicated, and it is more difficult to carry out palliative surgery. The mitral plasty procedure proposed by Bolling is the technique of choice for patients with severe mitral failure, in general when the ventricle is not too enlarged. However, surgery involving the reduction in size of the left ventricle (the Batista procedure) always includes mitral plasty, and may be performed in patients with a very enlarged ventricle (> 70 mm), in general with moderate mitral failure. These two techniques have been critically assessed both as regards results and when they should be adopted, and their limitations have also been discussed. In conclusion, there are valid surgical alternatives to heart transplantation in cases of heart failure that does not respond to medical treatment, and they should probably be seriously considered before any decision is made to perform heart transplantation. These results appear encouraging, particularly in terms of functional class and left ventricular function, but there are conflicting results for hemodynamic improvement. As regards survival, it is not yet possible to propose prospective randomized trials to compare medical treatment with these surgical techniques. However, further development of these techniques is bound to occur, and an ever-widening gap will exist between the limited number of cases requiring transplantation and the more complex surgical approaches adopted in future, such as permanent circulatory backup or xenografts.