Structures and roles of BcsD and partner scaffold proteins in proteobacterial cellulose secretion

Cellulose is the world's most abundant biopolymer, and similar to its role as a cell wall component in plants, it is a prevalent constituent of the extracellular matrix in bacterial biofilms. Although bacterial cellulose (BC) was first described in the 19th century, it was only recently revealed that it is produced by several distinct types of Bcs secretion systems that feature multiple accessory subunits in addition to a catalytic BcsAB synthase tandem. We recently showed that crystalline cellulose secretion in the Gluconacetobacter genus (α-Proteobacteria) is driven by a supramolecular BcsH-BcsD scaffold-the "cortical belt"-which stabilizes the synthase nanoarrays through an unexpected inside-out mechanism for secretion system assembly. Interestingly, while bcsH is specific for Gluconacetobacter, bcsD homologs are widespread in Proteobacteria. Here, we examine BcsD homologs and their gene neighborhoods from several plant-colonizing β- and γ-Proteobacteria proposed to secrete a variety of non-crystalline and/or chemically modified cellulosic polymers. We provide structural and mechanistic evidence that through different quaternary structure assemblies BcsD acts with proline-rich BcsH, BcsP, or BcsO partners across the proteobacterial clade to form synthase-interacting intracellular scaffolds that, in turn, determine the biofilm strength and architecture in species with strikingly different physiology and secreted biopolymers.

Govania unica gen. nov., sp. nov., a rare biosphere bacterium that represents a novel family in the class Alphaproteobacteria

Strain LMG 31809 ^T was isolated from a top soil sample of a temperate, mixed deciduous forest in Belgium. Comparison of its 16S rRNA gene sequence with that of type strains of bacteria with validly published names positioned it in the class Alphaproteobacteria and highlighted a major evolutionary divergence from its near neighbor species which represented species of the orders Emcibacterales and Sphingomonadales. 16S rRNA amplicon sequencing of the same soil sample revealed a highly diverse community in which Acidobacteria and Alphaproteobacteria predominated, but failed to yield amplicon sequence variants highly similar to that of strain LMG 31809 ^T. There were no metagenome assembled genomes that corresponded to the same species and a comprehensive analysis of public 16S rRNA amplicon sequencing data sets demonstrated that strain LMG 31809 ^T represents a rare biosphere bacterium that occurs at very low abundances in multiple soil and water-related ecosystems. The genome analysis suggested that this strain is a strictly aerobic heterotroph that is asaccharolytic and uses organic acids and possibly aromatic compounds as growth substrates. We propose to classify LMG 31809 ^T as a novel species within a novel genus, Govania unica gen. nov., sp. nov, within the novel family Govaniaceae of the class Alphaproteobacteria. Its type strain is LMG 31809 ^T (=CECT 30155 ^T). The whole-genome sequence of strain LMG 31809 ^T has a size of 3.21 Mbp. The G + C content is 58.99 mol%. The 16S rRNA gene and whole-genome sequences of strain LMG 31809 ^T are publicly available under accession numbers OQ161091 and JANWOI000000000, respectively.

Cyclitol metabolism is a central feature of Burkholderia leaf symbionts

The symbioses between plants of the Rubiaceae and Primulaceae families with Burkholderia bacteria represent unique and intimate plant-bacterial relationships. Many of these interactions have been identified through PCR-dependent typing methods, but there is little information available about their functional and ecological roles. We assembled 17 new endophyte genomes representing endophytes from 13 plant species, including those of two previously unknown associations. Genomes of leaf endophytes belonging to Burkholderia s.l. show extensive signs of genome reduction, albeit to varying degrees. Except for one endophyte, none of the bacterial symbionts could be isolated on standard microbiological media. Despite their taxonomic diversity, all endophyte genomes contained gene clusters linked to the production of specialized metabolites, including genes linked to cyclitol sugar analog metabolism and in one instance non-ribosomal peptide synthesis. These genes and gene clusters are unique within Burkholderia s.l. and are likely horizontally acquired. We propose that the acquisition of secondary metabolite gene clusters through horizontal gene transfer is a prerequisite for the evolution of a stable association between these endophytes and their hosts.

Ecotin: A versatile protease inhibitor of bacteria and eukaryotes

Serine protease inhibitors are a large family of proteins involved in important pathways and processes, such as inflammatory responses and blood clotting. Most are characterized by a precise mode of action, thereby targeting a narrow range of protease substrates. However, the serine-protease inhibitor ecotin is able to inhibit a broad range of serine proteases that display a wide range of specificities. This specificity is driven by special structural features which allow unique flexibility upon binding to targets. Although frequently observed in many human/animal-associated bacteria, ecotin homologs may also be found in plant-associated taxa and environmental species. The purpose of this review is to provide an update on the biological importance, role in host-microbe interactions, and evolutionary relationship between ecotin orthologs isolated from Eukaryotic and Prokaryotic species across the Tree of Life.

Whole-Genome Sequencing of Bacterial Endophytes From Fresh and Preserved Plant Specimens

Many plants harbor symbiotic bacteria in their leaves, sometimes within structures visible with the naked eye. These bacteria play critical roles for host development and defense, but are often not amenable to culture. Gaining insight into the functions of these obligate endophytic bacteria hinges on culture-independent omics approaches, which have seen tremendous development in recent years. We describe in this chapter a set of protocols for the extraction and bioinformatic analysis of bacterial genomic DNA from leaf samples of various origins, including fresh, silica-preserved, or herbarium specimens.

Rhizobium leguminosarum symbiovar viciae strains are natural wheat endophytes that can stimulate root development

Although rhizobia that establish a nitrogen-fixing symbiosis with legumes are also known to promote growth in non-legumes, studies on rhizobial associations with wheat roots are scarce. We searched for Rhizobium leguminosarum symbiovar viciae (Rlv) strains naturally competent to endophytically colonize wheat roots. We isolated 20 strains from surface-sterilized wheat roots, and found a low diversity of Rlv compared to that observed in the Rlv species complex. We tested the ability of a subset of these Rlv for wheat root colonization when co-inoculated with other Rlv. Only a few strains, including those isolated from wheat roots, and one strain isolated from pea nodules, were efficient in colonizing roots in co-inoculation conditions, while all the strains tested in single strain inoculation conditions were found to colonize the surface and interior of roots. Furthermore, Rlv strains isolated from wheat roots were able to stimulate root development and early arbuscular mycorrhizal fungi colonization. These responses were strain and host genotype dependent. Our results suggest that wheat can be an alternative host for Rlv; nevertheless, there is a strong competition between Rlv strains for wheat root colonization. In addition, we showed that Rlv are endophytic wheat root bacteria with potential ability to modify wheat development.

Patterns of transmission and horizontal gene transfer in the Dioscorea sansibarensis leaf symbiosis revealed by whole-genome sequencing

Leaves of the wild yam species Dioscorea sansibarensis display prominent forerunner or "drip" tips filled with extracellular bacteria of the species Orrella dioscoreae.¹ This species of yam is native to Madagascar and tropical Africa and reproduces mainly asexually through aerial bulbils and underground tubers, which also contain a small population of O. dioscoreae.^2,3 Despite apparent vertical transmission, the genome of O. dioscoreae does not show any of the hallmarks of genome erosion often found in hereditary symbionts (e.g., small genome size and accumulation of pseudogenes).^4-6 We investigated here the range and distribution of leaf symbiosis between D. sansibarensis and O. dioscoreae using preserved leaf samples from herbarium collections that were originally collected from various locations in Africa. We recovered DNA from the extracellular symbiont in all samples, showing that the symbiosis is widespread throughout continental Africa and Madagascar. Despite the degraded nature of this DNA, we constructed 17 symbiont genomes using de novo methods without relying on a reference. Phylogenetic and genomic analyses revealed that horizontal transmission of symbionts and horizontal gene transfer have shaped the evolution of the symbiont. These mechanisms could help explain lack of signs of reductive genome evolution despite an obligate host-associated lifestyle. Furthermore, phylogenetic analysis of D. sansibarensis based on plastid genomes revealed a strong geographical clustering of samples and provided evidence that the symbiosis originated at least 13 mya, earlier than previously estimated.³.

Paenibacillus foliorum sp. nov., Paenibacillus phytohabitans sp. nov., Paenibacillus plantarum sp. nov., Paenibacillus planticolens sp. nov., Paenibacillus phytorum sp. nov. and Paenibacillus germinis sp. nov., isolated from the Arabidopsis thaliana phyllosphere

Six endospore-forming, Gram-stain-positive or variable, motile, rod-shaped, aerobic or facultatively anaerobic bacteria with different MALDI-TOF mass spectra (MS) were isolated from the phyllosphere of Arabidopsis thaliana plants grown in plant chambers after inoculation of surface sterilized seeds with a top soil microbial cell suspension. They were identified as members of the genus Paenibacillus through comparison with a commercial MALDI-TOF MS database and comparative 16S rRNA gene sequencing. Their genome sequences comprised multiple biosynthetic gene clusters and suggested they have unexplored biotechnological potential. Analyses of average nucleotide identity values between these strains and the type strains of their nearest neighbour species demonstrated that they represented a novel Paenibacillus species each. A detailed phenotypic comparison yielded distinctive biochemical characteristics for each of these novel species. We therefore propose to classify that these isolates into six novel species within genus Paenibacillus, for which we propose the names Paenibacillus foliorum sp. nov., Paenibacillus phytohabitans sp. nov., Paenibacillus plantarum sp. nov., Paenibacillus planticolens sp. nov., Paenibacillus phytorum sp. nov. and Paenibacillus germinis sp. nov., with strains LMG 31456^T (=R-74617^T=CECT 30138^T), LMG 31459^T (=R-74621^T=CECT 30135^T), LMG 31461^T (=R-74618^T=CECT 30133^T), LMG 31457^T (=R-74619^T=CECT 30137^T), LMG 31458^T (=R-74620^T=CECT 30136^T) and LMG 31460^T (=R-74622^T=CECT 30134^T) as the type strains, respectively.

Pedobacter gandavensis sp. nov., Pedobacter foliorum sp. nov. and Pedobacter planticolens sp. nov., isolated from leaves of Arabidopsis thaliana

Three rod-shaped, non-spore-forming, yellow or pale-yellow pigmented bacteria with distinct MALDI-TOF mass spectra were isolated from the phyllosphere of Arabidopsis thaliana seedlings. Their 16S rRNA gene sequences demonstrated that these isolates belong to the genus Pedobacter. The nearest phylogenetic neighbours of strain LMG 31462^T were Pedobacter steynii DSM 19110^T (98.3 % 16S rRNA sequence similarity) and Pedobacter caeni LMG 22862^T (98.3 %); the nearest phylogenetic neighbours of strain LMG 31463^T were Pedobacter panaciterrae Gsoil 042^T (98.3 %) and Pedobacter nutrimenti DSM 27372^T (98.1 %); and the nearest phylogenetic neighbours of strain LMG 31464^T were Pedobacter boryungensis BR-9^T (99.0 %) and Pedobacter daejeonensis THG-DN3.18^T (98.7 %). Average nucleotide identity analyses between the whole genome sequences of the three strains and of the type strains of their respective nearest-neighbour taxa yielded values well below the species delineation threshold and thus confirmed that the three strains represented a novel Pedobacter species each. An extensive phenotypic comparison and an analysis of whole-cell fatty acid components yielded distinctive phenotypic characteristics for each of these strains. We therefore propose to classify these isolates as three novel species, for which we propose the names Pedobacter gandavensis with LMG 31462^T (=R-74704^T=CECT 30149^T) as the type strain, Pedobacter foliorum with LMG 31463^T (=R-74623^T=CECT 30150^T) as the type strain and Pedobacter planticolens with LMG 31464^T (=R-74626^T=CECT 30151^T) as the type strain.

Induction of antibiotic specialized metabolism by co-culturing in a collection of phyllosphere bacteria

A diverse set of bacteria live on the above-ground parts of plants, composing the phyllosphere, and play important roles for plant health. Phyllosphere microbial communities assemble in a predictable manner and diverge from communities colonizing other plant organs or the soil. However, how these communities differ functionally remains obscure. We assembled a collection of 258 bacterial isolates representative of the most abundant taxa of the phyllosphere of Arabidopsis and a shared soil inoculum. We screened the collection for the production of metabolites that inhibit the growth of Gram-positive and Gram-negative bacteria either in isolation or in co-culture. We found that isolates capable of constitutive antibiotic production in monoculture were significantly enriched in the soil fraction. In contrast, the proportion of binary cultures resulting in the production of growth inhibitory compounds differed only marginally between the phyllosphere and soil fractions. This shows that the phyllosphere may be a rich resource for potentially novel molecules with antibiotic activity, but that production or activity is dependent upon induction by external signals or cues. Finally, we describe the isolation of antimicrobial acyloin metabolites from a binary culture of Arabidopsis phyllosphere isolates, which inhibit the growth of clinically relevant Acinetobacter baumannii.

PaSiT: a novel approach based on short-oligonucleotide frequencies for efficient bacterial identification and typing

MOTIVATION

One of the most widespread methods used in taxonomy studies to distinguish between strains or taxa is the calculation of average nucleotide identity. It requires a computationally expensive alignment step and is therefore not suitable for large-scale comparisons. Short oligonucleotide-based methods do offer a faster alternative but at the expense of accuracy. Here, we aim to address this shortcoming by providing a software that implements a novel method based on short-oligonucleotide frequencies to compute inter-genomic distances.

RESULTS

Our tetranucleotide and hexanucleotide implementations, which were optimized based on a taxonomically well-defined set of over 200 newly sequenced bacterial genomes, are as accurate as the short oligonucleotide-based method TETRA and average nucleotide identity, for identifying bacterial species and strains, respectively. Moreover, the lightweight nature of this method makes it applicable for large-scale analyses.

AVAILABILITY AND IMPLEMENTATION

The method introduced here was implemented, together with other existing methods, in a dependency-free software written in C, GenDisCal, available as source code from https://github.com/LM-UGent/GenDisCal. The software supports multithreading and has been tested on Windows and Linux (CentOS). In addition, a Java-based graphical user interface that acts as a wrapper for the software is also available.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Introducing SPeDE: High-Throughput Dereplication and Accurate Determination of Microbial Diversity from Matrix-Assisted Laser Desorption-Ionization Time of Flight Mass Spectrometry Data

The isolation of microorganisms from microbial community samples often yields a large number of conspecific isolates. Increasing the diversity covered by an isolate collection entails the implementation of methods and protocols to minimize the number of redundant isolates. Matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry methods are ideally suited to this dereplication problem because of their low cost and high throughput. However, the available software tools are cumbersome and rely either on the prior development of reference databases or on global similarity analyses, which are inconvenient and offer low taxonomic resolution. We introduce SPeDE, a user-friendly spectral data analysis tool for the dereplication of MALDI-TOF mass spectra. Rather than relying on global similarity approaches to classify spectra, SPeDE determines the number of unique spectral features by a mix of global and local peak comparisons. This approach allows the identification of a set of nonredundant spectra linked to operational isolation units. We evaluated SPeDE on a data set of 5,228 spectra representing 167 bacterial strains belonging to 132 genera across six phyla and on a data set of 312 spectra of 78 strains measured before and after lyophilization and subculturing. SPeDE was able to dereplicate with high efficiency by identifying redundant spectra while retrieving reference spectra for all strains in a sample. SPeDE can identify distinguishing features between spectra, and its performance exceeds that of established methods in speed and precision. SPeDE is open source under the MIT license and is available from https://github.com/LM-UGent/SPeDEIMPORTANCE Estimation of the operational isolation units present in a MALDI-TOF mass spectral data set involves an essential dereplication step to identify redundant spectra in a rapid manner and without sacrificing biological resolution. We describe SPeDE, a new algorithm which facilitates culture-dependent clinical or environmental studies. SPeDE enables the rapid analysis and dereplication of isolates, a critical feature when long-term storage of cultures is limited or not feasible. We show that SPeDE can efficiently identify sets of similar spectra at the level of the species or strain, exceeding the taxonomic resolution of other methods. The high-throughput capacity, speed, and low cost of MALDI-TOF mass spectrometry and SPeDE dereplication over traditional gene marker-based sequencing approaches should facilitate adoption of the culturomics approach to bacterial isolation campaigns.

Five-year mortality in patients with diabetic foot ulcer during 2009-2010 was lower than expected

AIM

Mortality rates are decreasing in patients with diabetes. However, as this observation also concerns patients with diabetic foot ulcer (DFU), additional data are needed. For this reason, our study evaluated the 5-year mortality rate in patients with DFU during 2009-2010 and identified risk factors associated with mortality.

METHODS

Consecutive patients who attended a clinic for new DFU during 2009-2010 were followed until healing and at 1 year. Data on mortality were collected at year 5. Multivariate Cox proportional-hazards model was used to identify mortality risk factors.

RESULTS

A total of 347 patients were included: mean age was 65±12 years, diabetes duration was 16 [10; 27] years; 13% were on dialysis; and 7% had an organ transplant. At 5 years, 49 patients (14%) were considered lost to follow-up. Total mortality rate at 5 years was 35%, and 16% in patients with neuropathy. On multivariate analyses, mortality was positively associated with: age [hazard ratio (HR): 1.05 (1.03-1.07), P<0.0001]; duration of diabetes [HR: 1.02 (1.001-1.03], P=0.03]; PEDIS perfusion grade 2 vs. 1 [HR: 2.35 (1.28-4.29), P=0.006)]; PEDIS perfusion grade 3 vs. 1 [HR: 3.14 (1.58-6.24), P=0.001); and ulcer duration at year 1 [HR 2.09 (1.35-3.22), P=0.0009].

CONCLUSION

Mortality rates were not as high as expected despite the large number of comorbidities, suggesting that progress has been made in the health management of these patients. In particular, patients with neuropathic foot ulcer had a survival rate of 84% at 5 years.

Synthesis and Biological Evaluation of the Novel Growth Inhibitor Streptol Glucoside, Isolated from an Obligate Plant Symbiont

The plant Psychotria kirkii hosts an obligatory bacterial symbiont, Candidatus Burkholderia kirkii, in nodules on their leaves. Recently, a glucosylated derivative of (+)-streptol, (+)-streptol glucoside, was isolated from the nodulated leaves and was found to possess a plant growth inhibitory activity. To establish a structure-activity relationship study, a convergent strategy was developed to obtain several pseudosugars from a single synthetic precursor. Furthermore, the glucosylation of streptol was investigated in detail and conditions affording specifically the α or β glucosidic anomer were identified. Although (+)-streptol was the most active compound, its concentration in P. kirkii plant leaves extract was approximately ten-fold lower than that of (+)-streptol glucoside. These results provide compelling evidence that the glucosylation of (+)-streptol protects the plant host against the growth inhibitory effect of the compound, which might constitute a molecular cornerstone for this successful plant-bacteria symbiosis.

The course of apathy in late-life depression treated with electroconvulsive therapy; a prospective cohort study

OBJECTIVES

Apathy, a lack of motivation, is frequently seen in older individuals, with and without depression, with substantial impact on quality of life. This prospective cohort study of patients with severe late-life depression treated with electroconvulsive therapy (ECT) aims to study the course of apathy and the predictive value of vascular burden and in particular white matter hyperintensities on apathy course.

METHODS

Information on apathy (defined by a score of >13 on the Apathy Scale), depression severity, vascular burden, and other putative confounders was collected in at 2 psychiatric hospitals on patients with late-life depression (aged 55 to 87 years, N = 73). MRI data on white matter hyperintensities were available in 52 patients. Possible risk factors for apathy post-ECT were determined using regression analyses.

RESULTS

After treatment with ECT, 52.0% (26/50) of the depression remitters still suffered from clinically relevant apathy symptoms. In the entire cohort, more patients remained apathetic (58.9%) than depressed (31.5%). Presence of apathy post-ECT was not associated with higher age, use of benzodiazepines, or severity of apathy and depression at baseline. Less response in depressive symptomatology after ECT predicted post-treatment apathy. The presence of vascular disease, diabetes mellitus and smoking, and white matter hyperintensities in the brain was not associated with post-treatment apathy.

CONCLUSIONS

Apathy may perpetuate in individual patients, despite remission of depressive symptoms. In this cohort of patients with late-life depression, post-ECT apathy is not associated with white matter hyperintensities.

In silico clinical trials for pediatric orphan diseases

To date poor treatment options are available for patients with congenital pseudarthrosis of the tibia (CPT), a pediatric orphan disease. In this study we have performed an in silico clinical trial on 200 virtual subjects, generated from a previously established model of murine bone regeneration, to tackle the challenges associated with the small, pediatric patient population. Each virtual subject was simulated to receive no treatment and bone morphogenetic protein (BMP) treatment. We have shown that the degree of severity of CPT is significantly reduced with BMP treatment, although the effect is highly subject-specific. Using machine learning techniques we were also able to stratify the virtual subject population in adverse responders, non-responders, responders and asymptomatic. In summary, this study shows the potential of in silico medicine technologies as well as their implications for other orphan diseases.

Comparative Genomics of Burkholderia singularis sp. nov., a Low G+C Content, Free-Living Bacterium That Defies Taxonomic Dissection of the Genus Burkholderia

Four Burkholderia pseudomallei-like isolates of human clinical origin were examined by a polyphasic taxonomic approach that included comparative whole genome analyses. The results demonstrated that these isolates represent a rare and unusual, novel Burkholderia species for which we propose the name B. singularis. The type strain is LMG 28154T (=CCUG 65685T). Its genome sequence has an average mol% G+C content of 64.34%, which is considerably lower than that of other Burkholderia species. The reduced G+C content of strain LMG 28154T was characterized by a genome wide AT bias that was not due to reduced GC-biased gene conversion or reductive genome evolution, but might have been caused by an altered DNA base excision repair pathway. B. singularis can be differentiated from other Burkholderia species by multilocus sequence analysis, MALDI-TOF mass spectrometry and a distinctive biochemical profile that includes the absence of nitrate reduction, a mucoid appearance on Columbia sheep blood agar, and a slowly positive oxidase reaction. Comparisons with publicly available whole genome sequences demonstrated that strain TSV85, an Australian water isolate, also represents the same species and therefore, to date, B. singularis has been recovered from human or environmental samples on three continents.

Characterization of the emerging zoonotic pathogen Arcobacter thereius by whole genome sequencing and comparative genomics

Four Arcobacter species have been associated with human disease, and based on current knowledge, these Gram negative bacteria are considered as potential food and waterborne zoonotic pathogens. At present, only the genome of the species Arcobacter butzleri has been analysed, and still little is known about their physiology and genetics. The species Arcobacter thereius has first been isolated from tissue of aborted piglets, duck and pig faeces, and recently from stool of human patients with enteritis. In the present study, the complete genome and analysis of the A. thereius type strain LMG24486^T, as well as the comparative genome analysis with 8 other A. thereius strains are presented. Genome analysis revealed metabolic pathways for the utilization of amino acids, which represent the main source of energy, together with the presence of genes encoding for respiration-associated and chemotaxis proteins. Comparative genome analysis with the A. butzleri type strain RM4018 revealed a large correlation, though also unique features. Furthermore, in silico DDH and ANI based analysis of the nine A. thereius strains disclosed clustering into two closely related genotypes. No discriminatory differences in genome content nor phenotypic behaviour were detected, though recently the species Arcobacter porcinus was proposed to encompass part of the formerly identified Arcobacter thereius strains. The report of the presence of virulence associated genes in A. thereius, the presence of antibiotic resistance genes, verified by in vitro susceptibility testing, as well as other pathogenic related relevant features, support the classification of A. thereius as an emerging pathogen.

Comparative genomics of Burkholderia multivorans, a ubiquitous pathogen with a highly conserved genomic structure

The natural environment serves as a reservoir of opportunistic pathogens. A well-established method for studying the epidemiology of such opportunists is multilocus sequence typing, which in many cases has defined strains predisposed to causing infection. Burkholderia multivorans is an important pathogen in people with cystic fibrosis (CF) and its epidemiology suggests that strains are acquired from non-human sources such as the natural environment. This raises the central question of whether the isolation source (CF or environment) or the multilocus sequence type (ST) of B. multivorans better predicts their genomic content and functionality. We identified four pairs of B. multivorans isolates, representing distinct STs and consisting of one CF and one environmental isolate each. All genomes were sequenced using the PacBio SMRT sequencing technology, which resulted in eight high-quality B. multivorans genome assemblies. The present study demonstrated that the genomic structure of the examined B. multivorans STs is highly conserved and that the B. multivorans genomic lineages are defined by their ST. Orthologous protein families were not uniformly distributed among chromosomes, with core orthologs being enriched on the primary chromosome and ST-specific orthologs being enriched on the second and third chromosome. The ST-specific orthologs were enriched in genes involved in defense mechanisms and secondary metabolism, corroborating the strain-specificity of these virulence characteristics. Finally, the same B. multivorans genomic lineages occur in both CF and environmental samples and on different continents, demonstrating their ubiquity and evolutionary persistence.

Molecular mechanisms underlying the close association between soil Burkholderia and fungi

Bacterial species belonging to the genus Burkholderia have been repeatedly reported to be associated with fungi but the extent and specificity of these associations in soils remain undetermined. To assess whether associations between Burkholderia and fungi are widespread in soils, we performed a co-occurrence analysis in an intercontinental soil sample collection. This revealed that Burkholderia significantly co-occurred with a wide range of fungi. To analyse the molecular basis of the interaction, we selected two model fungi frequently co-occurring with Burkholderia, Alternaria alternata and Fusarium solani, and analysed the proteome changes caused by cultivation with either fungus in the widespread soil inhabitant B. glathei, whose genome we sequenced. Co-cultivation with both fungi led to very similar changes in the B. glathei proteome. Our results indicate that B. glathei significantly benefits from the interaction, which is exemplified by a lower abundance of several starvation factors that were highly expressed in pure culture. However, co-cultivation also gave rise to stress factors, as indicated by the increased expression of multidrug efflux pumps and proteins involved in oxidative stress response. Our data suggest that the ability of Burkholderia to establish a close association with fungi mainly lies in the capacities to utilize fungal-secreted metabolites and to overcome fungal defense mechanisms. This work indicates that beneficial interactions with fungi might contribute to the survival strategy of Burkholderia species in environments with sub-optimal conditions, including acidic soils.

[Macro replantation of upper extremity. Update and review of the long-term functional results]

Confronted with increasing problems of financing in health care, some question the relevance of certain interventions of high technicality. Today, the limiting factor for practitioners is not any longer situated at the technical and technological level (the survival of macro replantations is assured in 85-90%) but moves slowly and surely towards the economic level. It is true that medicine has a price and that if a technique is expensive, it should at least be justified at the human level and superior to other less expensive therapeutic options which are available. In this article, we will first focus on the long-term outcome of patients and also on the functional benefit which brings them replantation compared to patients who underwent a regularization of their stump and possibly a reconstruction enabling them to be correctly fitted with a prosthesis.

Current views on calcium phosphate osteogenicity and the translation into effective bone regeneration strategies

Calcium phosphate (CaP) has traditionally been used for the repair of bone defects because of its strong resemblance to the inorganic phase of bone matrix. Nowadays, a variety of natural or synthetic CaP-based biomaterials are produced and have been extensively used for dental and orthopaedic applications. This is justified by their biocompatibility, osteoconductivity and osteoinductivity (i.e. the intrinsic material property that initiates de novo bone formation), which are attributed to the chemical composition, surface topography, macro/microporosity and the dissolution kinetics. However, the exact molecular mechanism of action is unknown. This review paper first summarizes the most important aspects of bone biology in relation to CaP and the mechanisms of bone matrix mineralization. This is followed by the research findings on the effects of calcium (Ca²⁺) and phosphate (PO₄³⁻) ions on the migration, proliferation and differentiation of osteoblasts during in vivo bone formation and in vitro culture conditions. Further, the rationale of using CaP for bone regeneration is explained, focusing thereby specifically on the material's osteoinductive properties. Examples of different material forms and production techniques are given, with the emphasis on the state-of-the art in fine-tuning the physicochemical properties of CaP-based biomaterials for improved bone induction and the use of CaP as a delivery system for bone morphogenetic proteins. The use of computational models to simulate the CaP-driven osteogenesis is introduced as part of a bone tissue engineering strategy in order to facilitate the understanding of cell-material interactions and to gain further insight into the design and optimization of CaP-based bone reparative units. Finally, limitations and possible solutions related to current experimental and computational techniques are discussed.

Exposing the third chromosome of Burkholderia cepacia complex strains as a virulence plasmid

The Burkholderia cepacia complex (Bcc) consists of 17 closely related species of opportunistic bacterial pathogens, which are particularly problematic for cystic fibrosis patients and immunocompromised individuals. Bcc genomes consist of multiple replicons, and each strain sequenced to date has three chromosomes. In addition to genes thought to be essential for survival, each chromosome carries at least one rRNA operon. We isolated three mutants during a transposon mutagenesis screen that were non-pathogenic in a Caenorhabditis elegans infection model. It was demonstrated that these mutants had lost chromosome 3 (c3), and that the observed attenuation of virulence was a consequence of this. We constructed a c3 mini-replicon and used it to cure c3 from strains of several Bcc species by plasmid incompatibility, resulting in nine c3-null strains covering seven Bcc species. Phenotypic characterization of c3-null mutants revealed that they were attenuated in virulence in multiple infection hosts (rat, zebrafish, C. elegans, Galleria mellonella and Drosophila melanogaster), that they exhibited greatly diminished antifungal activity, and that c3 was required for d-xylose, fatty acid and pyrimidine utilization, as well as for exopolysaccharide production and proteolytic activity in some strains. In conclusion, we show that c3 is not an essential chromosomal element, rather a large plasmid that encodes virulence, secondary metabolism and other accessory functions in Bcc bacteria.

Designing optimal calcium phosphate scaffold-cell combinations using an integrative model-based approach

Bone formation is a very complex physiological process, involving the participation of many different cell types and regulated by countless biochemical, physical and mechanical factors, including naturally occurring or synthetic biomaterials. For the latter, calcium phosphate (CaP)-based scaffolds have proven to stimulate bone formation, but at present still result in a wide range of in vivo outcomes, which is partly related to the suboptimal use and combination with osteogenic cells. To optimize CaP scaffold selection and make their use in combination with cells more clinically relevant, this study uses an integrative approach in which mathematical modeling is combined with experimental research. This paper describes the development and implementation of an experimentally informed bioregulatory model of the effect of calcium ions released from CaP-based biomaterials on the activity of osteogenic cells and mesenchymal stem cell driven ectopic bone formation. The amount of bone formation predicted by the mathematical model corresponds to the amount measured experimentally under similar conditions. Moreover, the model is also able to qualitatively predict the experimentally observed impaired bone formation under conditions such as insufficient cell seeding and scaffold decalcification. A strategy was designed in silico to overcome the negative influence of a low initial cell density on the bone formation process. Finally, the model was applied to design optimal combinations of calcium-based biomaterials and cell culture conditions with the aim of maximizing the amount of bone formation. This work illustrates the potential of mathematical models as research tools to design more efficient and cell-customized CaP scaffolds for bone tissue engineering applications.

[Patient complaints in a hospital emergency department in Belgium]

Patients express their dissatisfaction through complaints. This study analyzed the frequency and chief complaints of patients presenting to the emergency department (ED). The end point was find ways to improve patient satisfaction after their ED visit. In this retrospective, seven years study, we reviewed 155 chief complaints of patients presenting to the ED of a university hospital. The chief complaints were either from the patients or a family member. One hundred and fifty five chief complaints collected from 496.816 patients presenting to the ED were reviewed over a period of seven years. Complaints case rate was 3.1 per 10.000 visits. Complaints came from patients between the age of 20 to 60 years old (75.0 percent). Complains involved a physician (79.0 percent). The complaints were related a lack of communication (39.0 percent), long waiting time (14.0 percent), wrong diagnosis (22.0 percent), wrong treatment (13.0 percent) and ED disposition of the patient (12.0 percent). Two types of pathology represented more than 15 percent of the complaints: the traumatology (22.0 percent) and the psychiatry (17.0 percent). The traumatology and psychiatry represented respectively 30.0 percent and 10.0 percent of ED visits. Most complaints were addressed and resolved through a hospital mediator, Chief of service or Chief of staff. The rate of complains is low. Most complaints can be prevented if the physician improves communication with patients.

[The anatomical laboratory: a tool for the trial of the new therapeutic procedures]

Since September 2009, the new anatomical department is located on the CHU building. This modern anatomical laboratory is an effective tool to design the new therapeutic procedures and to teach these procedures to practitioners.

Bacterial populations in the rhizosphere of tobacco plants producing the quorum-sensing signals hexanoyl-homoserine lactone and 3-oxo-hexanoyl-homoserine lactone

A tobacco line genetically modified to produce two N-acyl homoserine lactones and its non-transformed parental line were grown in non-sterile soil. Microbial populations inhabiting the bulk soil, and those colonizing the root system of the two tobacco lines, were analyzed using cultivation-independent (phospholipid fatty acid and denaturing gradient gel electrophoresis) and cultivation-based assays. The cell density of total cultivable bacteria, fluorescent pseudomonads, sporulated, and thermotolerant bacteria was also determined in a time-course experiment (15 weeks). A possible "rhizosphere effect" related to the development of the plant was seen. However, no dissimilarities in cell population densities or population ratios of the microbial groups were detected in the rhizosphere of the two plant lines. Similarly, bacterial communities that either produced N-acyl homoserine lactone or degraded the signal hexanoyl homoserine lactone were enumerated from the two plant lines. No noticeable differences were evidenced from one plant genotype to the other. Whilst the transgenic plants released detectable amounts of the quorum-sensing signal molecules and efficiently cross-talked with the surrounding microbial populations, the bias generated by these signals in the reported experimental conditions therefore appears to remain weak, if not non-existent.

N-hexanoyl-L-homoserine lactone, a mediator of bacterial quorum-sensing regulation, exhibits plant-dependent stability and may be inactivated by germinating Lotus corniculatus seedlings

The half-life of N-hexanoyl-l-homoserine lactone (C6-HSL) was determined under various pH and temperature conditions, and in several plant environments. C6-HSL was sensitive to alkaline pH, a process that was also temperature-dependent. In addition, C6-HSL disappeared from plant environments, i.e. axenic monocot and dicot plants cultivated under gnotobiotic, hydroponic conditions, albeit with variable kinetics. The disappearance was rapid at the root system of legume plants such as clover or Lotus, and slow or non-existent at the root system of monocots such as wheat or corn. These variable kinetics were not dependent upon pH changes that may have affected the growth media of the plants. Furthermore, C6-HSL did not accumulate in the plant, and the plant did not produce inhibitors of the C6-HSL signal. HPLC analyses revealed that C6-HSL disappeared from the media, and hence, Lotus exhibited a natural C6-HSL inactivating ability. This ability was not specific for C6-HSL and allowed the degradation of other N-acyl-homoserine lactones such as 3-oxo-C6-HSL, 3-oxo-octanoyl-HSL and 3-oxo-decanoyl-HSL. Preliminary investigation revealed that the inactivating ability is temperature-dependant and possibly of enzymatic origin.

The assimilation of gamma-butyrolactone in Agrobacterium tumefaciens C58 interferes with the accumulation of the N-acyl-homoserine lactone signal

Agrobacterium tumefaciens C58 communicates using N-acyl-homoserine lactones (acyl-HSL) and contains two lactonase-encoding genes, attM and aiiB, the products of which are capable of inactivating the acyl-HSL signal. In A. tumefaciens A6, the expression of the attKLM operon is controlled by the transcriptional repressor encoded by an adjacent gene, attJ. An attJ::Tn5 mutant does not accumulate acyl-HSL because of the constitutive expression of the lactonase AttM, the activity of which inactivates acyl-HSL. In this work, the attKLM operon of A. tumefaciens C58 was shown to be involved in an assimilative pathway of gamma-butyrolactone (GBL), gamma-hydroxybutyrate (GHB), and succinate semialdehyde (SSA), in which AttM and AttL are key enzymes for GBL and GHB assimilation. The expression of the attKLM promoter was activated in the presence of GBL, GHB, and SSA. Under these conditions, A. tumefaciens C58 did not accumulate the acyl-HSL that it naturally synthesizes, and also became able to inactivate exogenous acyl-HSL signals. Therefore, in A. tumefaciens C58, the assimilative pathway of gamma-butyrolactone interferes with the acyl-HSL signaling.

The Ti plasmid of Agrobacterium tumefaciens harbors an attM-paralogous gene, aiiB, also encoding N-Acyl homoserine lactonase activity

The Agrobacterium tumefaciens C58 genome contains three putative N-acyl homoserine lactone (acyl-HSL) hydrolases, which are closely related to the lactonase AiiA of Bacillus. When expressed in Escherichia coli, two of the putative acyl-HSL hydrolases, AttM and AiiB, conferred the ability to degrade acyl-HSLs on the host. In Erwinia strain 6276, the lactonases reduced the endogenous acyl-HSL level and the bacterial virulence in planta.

Novel bacteria degrading N-acylhomoserine lactones and their use as quenchers of quorum-sensing-regulated functions of plant-pathogenic bacteria

Bacteria degrading the quorum-sensing (QS) signal molecule N-hexanoylhomoserine lactone were isolated from a tobacco rhizosphere. Twenty-five isolates degrading this homoserine lactone fell into six groups according to their genomic REP-PCR and rrs PCR-RFLP profiles. Representative strains from each group were identified as members of the genera Pseudomonas, Comamonas, Variovorax and Rhodococcus: all these isolates degraded N-acylhomoserine lactones other than the hexanoic acid derivative, albeit with different specificity and kinetics. One of these isolates, Rhodococcus erythropolis strain W2, was used to quench QS-regulated functions of other microbes. In vitro, W2 strongly interfered with violacein production by Chromobacterium violaceum, and transfer of pathogenicity in Agrobacterium tumefaciens. In planta, R. erythropolis W2 markedly reduced the pathogenicity of Pectobacterium carotovorum subsp. carotovorum in potato tubers. These series of results reveal the diversity of the QS-interfering bacteria in the rhizosphere and demonstrate the validity of targeting QS signal molecules to control pathogens with natural bacterial isolates.

[How I treat ... facial paralysis by hypoglosso-facial anastomosis]

Thirteen patients underwent a hypoglosso- or a spino-facial nerve anastomosis between 1990 and 1996. Facial palsy was the result of surgery in 12 cases and of radiosurgery in 1 case. The mean interval between facial palsy and anastomosis was 12 months. Facial nerve function is determined on the basis of clinical examination according to the classification of House-Brackmann and our own evaluation. According to House, 10 patients are classified grade III and 3 grade IV. Our evaluation defines in 10 grade III, 7 good results and 3 fair results. As far as the good results are concerned, the mean interval between palsy and anastomosis is short (< 3 months). The permanent eating and swallowing dysfunctions are consecutive to multiple cranial nerve deficits. The post-paralysis hemifacial spasm is facilitated by prolongated electric stimulations.

[Hypothenar hammer syndrome]

The hypothenar hammer syndrome is an uncommon but underestimated lesion of the cubital artery caused by repetitive trauma at the level of the hamate bone. It characteristically occurs in patients with a history of manual work as metal workers, carpenters and motor mechanics. We present a case of a patient who developed this syndrome following intensive use of a dig. Clinical finding, diagnosis and treatment are discussed.

Carpal tunnel syndrome in childhood: report of five new cases

Carpal tunnel syndrome is a condition rarely encountered during the growth period. We describe five new cases in two large Belgian university hospitals. One case concerned a 2-year-old child suffering from disseminated angiomatosis, an association not previously reported. Another case of mild severity corresponded to the classic association of trigger fingers and carpal tunnel syndrome. The third case was posttraumatic, and the last two cases were of the familial type that previously has been reported in four families. We discuss these observations and briefly review the literature.

[Rapid determination of bactericidal kinetics by evaluating intracellular adenosine-triphosphate in bioluminescence]

Killing kinetics measurement is usually time-consuming and tedious. Bioluminescent adenosine-triphosphate (ATP) assay, after intracellular nucleotide release by bacterial lysis, selects very quickly normal from antibiotic-modified and dead bacteria. Two simultaneous assays are performed with more and less strong lysis reagents (nucleotide releasing bacterial NRB, nucleotide releasing somatic NRS, Lumac). Bioluminescence produced in a luciferine - luciferase system is measured with Biocounter M 2010 luminometer. Differential values of two assays reflect the intracellular ATP fraction of strongest bacteria in tested cultures. Killing curves of some beta lactamines (aminopenicillin and cephalosporins) were studied with active Escherichia coli and Streptococcus pneumoniae cultures. Bactericidal action was seen within few hours, and similar variations of intracellular ATP fraction and numbers of colony-forming units obtained by reference method were observed. This method, well-suited to large series of assays and very rapid (intracellular ATP assay within one minute), performs detailed killing kinetics in real time.

[Current treatment of fresh lesions of the flexor tendons]

Different aspects of primary treatment of flexor tendon lesions are reviewed. Of outstanding importance are: adequate setting and instruments plus meticulous repair with fine material, avoidance of traumatic manipulation of structures and anatomical repair, use of dynamic mobilisation of reconstructed tendons within a team of well informed and motivated therapists.

[Current emergency treatment of lesions of the flexor tendons: anatomical, biomechanical and cicatricial aspects]

Emergency treatment of flexor tendon lesion in 1988: anatomic biomechanical and healing characteristics. Flexor tendon surgery in 1988 must take into account detailed anatomic knowledge as well as healing and biomechanical properties of flexor tendons. Application of standardised surgical technics allows reliable treatment when the surgeon is familiar with these technics and the basic knowledge they suppose. The authors detail the technics and certain details with practical goals.

Intrinsic fasciotomy. When and why?

Major trauma to the upper extremity may lead to ischemic contracture of various muscle groups, sometimes including the intrinsic muscles of the hand. The clinical consequence of such necrotic fibrosis of the intrinsics is clawing of the digits with marked stiffness. After a short anatomical review of the fascias of the intrinsics, indications and operative techniques are discussed, in parallel with clinical cases. Intrinsic fasciotomy thus appears to be a major step in the prevention of digital clawing, when associated with early physiotherapy.

The denervated first dorsal interosseous muscle flap: a case report

Coverage of a dorsal defect on the hand of a child with exposed extensor tendons was provided by a denervated first dorsal interosseous muscle and splitthickness skin grafting. We do not recommend routine use of the first dorsal interosseous muscle as a flap; however, its use in cases in which the muscle has been denervated would seem justified.