GyrB sequence analysis and MALDI-TOF MS as identification tools for plant pathogenic Clavibacter

The bacterial genus Clavibacter has only one species, Clavibacter michiganensis, containing five subspecies. All five are plant pathogens, among which three are recognized as quarantine pests (mentioned on the EPPO A2 list). Prevention of their introduction and epidemic outbreaks requires a reliable and accurate identification. Currently, identification of these bacteria is time consuming and often problematic, mainly because of cross-reactions with other plant-associated bacteria in immunological tests and false-negative results in PCR detection methods. Furthermore, distinguishing closely related subspecies is not straightforward. This study aimed at evaluating the use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and a fragment of the gyrB sequence for the reliable and fast identification of the Clavibacter subspecies. Amplification and sequencing of gyrB using a single primer set had sufficient resolution and specificity to identify each subspecies based on both sequence similarities in cluster analyses and specific signatures within the sequences. All five subspecies also generated distinct and reproducible MALDI-TOF MS profiles, with unique and specific ion peaks for each subspecies, which could be used as biomarkers for identification. Results from both methods were in agreement and were able to distinguish the five Clavibacter subspecies from each other and from representatives of closely related Rathayibacter, Leifsonia or Curtobacterium species. Our study suggests that proteomic analysis using MALDI-TOF MS and gyrB sequence are powerful diagnostic tools for the accurate identification of Clavibacter plant pathogens.     

Microduplication 22q11.2: a description of the clinical, developmental and behavioral characteristics during childhood

Microduplication 22q11.2 is a recently discovered genomic disorder. So far, targeted research on the cognitive and behavioral characteristics of individuals with this microduplication is limited. Therefore, 11 Flemish children (3-13 years old) with a microduplication 22q 1.2 were investigated in order to describe their clinical, developmental and behavioral characteristics. We measured their general intelligence, visual-motor capacities, attention, behavioral problems and characteristics of autism. In addition, there was an interview with the parents on developmental history and we reviewed available information from other specialists. The results show that the cognitive and behavioral phenotype of the children with microduplication 22q.11.2 is very wide and heterogeneous. Some of the children have a cognitively nearly normal development whereas others are more severely affected. All children had some degree of developmental delay and some of them have an intellectual disability. The most common clinical features include congenital malformations such as heart defects and cleft lip, feeding problems, hearing impairment and facial dysmorphism. The most common non-medical problems are learning difficulties, motor impairment, attention deficits, social problems and behavioral problems. There is no correlation between the size of the duplication and the phenotype.     

Recurrent De Novo Mutations in PACS1 Cause Defective Cranial-Neural-Crest Migration and Define a Recognizable Intellectual-Disability Syndrome

We studied two unrelated boys with intellectual disability (ID) and a striking facial resemblance suggestive of a hitherto unappreciated syndrome. Exome sequencing in both families identified identical de novo mutations in PACS1, suggestive of causality. To support these genetic findings and to understand the pathomechanism of the mutation, we studied the protein in vitro and in vivo. Altered PACS1 forms cytoplasmic aggregates in vitro with concomitant increased protein stability and shows impaired binding to an isoform-specific variant of TRPV4, but not the full-length protein. Furthermore, consistent with the human pathology, expression of mutant PACS1 mRNA in zebrafish embryos induces craniofacial defects most likely in a dominant-negative fashion. This phenotype is driven by aberrant specification and migration of SOX10-positive cranial, but not enteric, neural-crest cells. Our findings suggest that PACS1 is necessary for the formation of craniofacial structures and that perturbation of its functions results in a specific syndromic ID phenotype.     

Relationship between bacterial community composition and bottom-up versus top-down variables in four eutrophic shallow lakes

Bacterial community composition was monitored in four shallow eutrophic lakes during one year using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified prokaryotic rDNA genes. Of the four lakes investigated, two were of the clearwater type and had dense stands of submerged macrophytes while two others were of the turbid type characterized by the occurrence of phytoplankton blooms. One turbid and one clearwater lake had high nutrient levels (total phosphorus, >100 micro g liter(-1)) while the other lakes had relatively low nutrient levels (total phosphorus, <100 micro g liter(-1)). For each lake, seasonal changes in the bacterial community were related to bottom-up (resources) and top-down (grazers) variables by using canonical correspondence analysis (CCA). Using an artificial model dataset to which potential sources of error associated with the use of relative band intensities in DGGE analysis were added, we found that preferential amplification of certain rDNA genes over others does not obscure the relationship between bacterial community composition and explanatory variables. Besides, using this artificial dataset as well as our own data, we found a better correlation between bacterial community composition and explanatory variables by using relative band intensities compared to using presence/absence data. While bacterial community composition was related to phytoplankton biomass in the high-nutrient lakes no such relation was found in the low-nutrient lakes, where the bacterial community is probably dependent on other organic matter sources. We used variation partitioning to evaluate top-down regulation of bacterial community composition after bottom-up regulation has been accounted for. Using this approach, we found no evidence for top-down regulation of bacterial community composition in the turbid lakes, while grazing by ciliates and daphnids (Daphnia and Ceriodaphnia) was significantly related to changes in the bacterial community in the clearwater lakes. Our results suggest that in eutrophic shallow lakes, seasonality of bacterial community structure is dependent on the dominant substrate source as well as on the food web structure.     

Numb: "Adapting" notch for endocytosis

During sensory organ precursor divisions in Drosophila, the numb gene product segregates asymmetrically into one of the two daughter cells, to which it confers a specific fate by inhibiting Notch signaling. In this issue of Developmental Cell, Berdnik et al. show that Numb recruits alpha-Adaptin and that this physical interaction plays a role in downregulating Notch, presumably by stimulating endocytosis of Notch.     

PA26 is a candidate gene for heterotaxia in humans: identification of a novel PA26-related gene family in human and mouse

Heterotaxia is an aetiologically heterogeneous condition caused by an abnormal left-right axis formation, resulting in reversed left-right polarity of one or more organ systems. In a patient with heterotaxia and a de novo reciprocal translocation t(6;18)(q21;q21), we found that the PA26 gene was disrupted by the 6q21 breakpoint. Northern blot analysis showed decreased expression of the PA26 gene in an Epstein-Barr virus-transformed cell line of this patient. During early embryogenesis of Xenopus, the orthologue of PA26, XPA26 is exclusively expressed in the notochord, a midline structure. This further supports a possible role of PA26 in human situs determination. Mutation analysis of human PA26 gene in 40 unrelated individuals with unexplained heterotaxia failed to identify mutations, indicating that PA26 mutations are not a frequent cause of heterotaxia in humans. Analysis of the PA26 gene structure resulted in the identification of a novel PA26-related gene family, which we have named the sestrin family, and which comprises three closely related genes in human and in mouse.     

Xp22.3; Yq11.2 chromosome translocation and its clinical manifestations

We report clinical and molecular investigations in a boy with karyotype 46,Y,der(X)t(X;Y)(qter-->p22.3::q11.21-->qter) and his mother with karyotype 46,X,der(X)t(X;Y)(qter-->p22.3::q11.21-->qter). Haplo-insufficiency for the Xp22.3-->pter chromosomal region in the boy resulted in postnatal growth retardation, developmental delay, partial ichthyosis and facial dysmorphism, but normal external genitals. His mother has a normal phenotype with normal stature and gonadal function but borderline intelligence. FISH-analysis showed a duplication of the Y-heterochromatin probe in the proband and a deletion of the Y933D4 probe in his mother. Molecular investigations situated the Xp22.3 breakpoint between DXS278 and the KAL gene and the Yq11.21 breakpoint between the DYS391 and DYS390 in the proband and his mother. X-inactivation study was performed by analysis of the polymorphic CAG-repeat in the androgen-receptor gene as described showing a normal random (40% versus 60%) inactivation pattern in the mother. The manifestations in male and female with loss of the Xp22.3-->pter and gain of the Yq11.21-->qter chromosomal region are discussed.     

What exactly was wrong with the Trilucent breast implants? A unifying hypothesis

Trilucent soybean oil-filled breast implants were initially announced as the ultimate prostheses for breast augmentation. However, after an increasing number of reports of local complications and hazardous metabolites attributable to lipid oxidation, first the United Kingdom Medical Devices Agency and later the Belgian National Ministry of Health urged all plastic surgeons to contact their patients and advise them to have the implants removed and, if desired, replaced with another type of prosthesis. In our plastic surgery department, 13 patients received bilateral implants with triglyceride-filled prostheses between February and July of 1996, for primary breast augmentation or replacement of previously implanted prostheses. For 12 of those 13 patients, the prostheses have been explanted, because of unilateral breast enlargement attributable to a ruptured prosthesis for five patients and following the recommendation of the Belgian National Ministry of Health for the other seven patients. Before explantation, all patients underwent standard clinical examinations, with assessments of breast shape, volume, and firmness. Blood analyses were performed, with a special focus on liver enzymes, as were urinalyses. Magnetic resonance imaging scans were obtained before explantation; for two patients, the scans revealed a fluid level separating two liquid layers in an intact prosthesis. This is the first report of such a finding. The removed implants were examined for any damage or shell deterioration and for changes in color and viscosity, the weights and volumes were measured and compared with the initial values for the implanted prostheses, and complete biochemical analyses of the accumulated fluid in cases of ruptured prostheses and of the filler material in cases of intact prostheses were performed. This small but well-documented series illustrates the multitude of problems associated with triglyceride-filled implants, including bleeding of the triglyceride filler; shell deterioration, as indicated by a loss of texture and extreme fragility of the implant (with rupture or delamination with a simple finger touch); an increase in osmotic pressure exerted by the degraded filler material; progressive weakening of the outer silicone shell, with influx of plasma proteins of up to 750 kDa, eventually resulting in rupture of the prosthesis; a lack of oxidative stability and the formation of toxic oxidation products; a lack of biocompatibility, with the formation of insoluble organic soap-like material; and a pronounced inflammatory reaction. It is concluded that the sequential and/or simultaneous occurrence of (1) implant bleeding, (2) lipid infiltration of the silicone elastomer, and (3) inflammation attributable to oxidation products provides an overall explanation or unifying hypothesis for the wide variety of adverse events related to soybean oil-filled implants.     

Parenting, family contexts, and personality characteristics in youngsters with VCFS

Parenting, family contexts, and personality characteristics in youngsters with VCFS: The personality profiles for 48 youths with Velo-Cardio-Facial syndrome (VCFS) were described using the California Child Q-Set (CCQ). Associations between personality characteristics and parenting (i.e., Control and Warmth vs. Anger) and family contexts (i.e., Experienced Family Stress, Marital Conflict and Parental Consistency) were investigated. Personality characteristics were found to be related to parenting (in particular, Parental Warmth vs. Anger) but not to family contexts. Parents who reported more Parental Warmth (and less Anger) in interactions had children with higher Agreeableness, Conscientiousness and Emotional Stability and with lower Irritability and Dependency. Parental Control was positively related to children's Dependency and negatively to children's Conscientiousness. Compared to fathers, mothers exerted more Control. Differences in parenting and family contexts were related to the mode of inheritance but not to IQ, age, gender, and cardiac defects. Families in which a familial deletion occurred reported higher levels of Marital Conflict and lower Warmth in the parent-child interactions.