Hierarchical spatial sampling reveals factors influencing arbuscular mycorrhizal fungus diversity in Côte d'Ivoire cocoa plantations

While many molecular studies have documented arbuscular mycorrhizal fungi (AMF) communities in temperate ecosystems, very few studies exist in which molecular techniques have been used to study tropical AMF communities. Understanding the composition of AMF communities in tropical areas gains special relevance as crop productivity in typically low fertility tropical soils can be improved with the use of AMF. We used a hierarchical sampling approach in which we sampled soil from cocoa (Theobroma cacao L.) plantations nested in localities, and in which localities were nested within each of three regions of Côte d'Ivoire. This sampling strategy, combined with 18S rRNA gene sequencing and a dedicated de novo OTU-picking model, allowed us to study AMF community composition and how it is influenced at different geographical scales and across environmental gradients. Several factors, including pH, influenced overall AMF alpha diversity and differential abundance of specific taxa and families of the Glomeromycotina. Assemblages and diversity metrics at the local scale did not reliably predict those at regional scales. The amount of variation explained by soil, climate, and geography variables left a large proportion of the variance to be explained by other processes, likely happening at smaller scales than the ones considered in this study. Gaining a better understanding of processes involved in shaping tropical AMF community composition and AMF establishment are much needed and could allow for the development of sustainable, productive tropical agroecosystems.

The phenotype caused by recessive variations in SLC25A22: Report of a new case and literature review

We describe the clinical, electroencephalography (EEG), and developmental features of a patient with developmental and epileptic encephalopathy due to a homozygous pathogenic variation of mitochondrial glutamate/H⁺ symporter SLC25A22. Epilepsy began during the first week of life with focal onset seizures. Interictal EEG revealed a suppression-burst pattern with extensive periods of non-activity. The prospective follow-up confirmed developmental encephalopathy as well as ongoing active epilepsy and almost no sign of development at 8 years of age. We confirm in the following paper that SLC25A22 recessive variations may cause a severe developmental and epileptic encephalopathy characterized by a suppression-burst pattern. On the basis of an in-depth literature review, we also provide an overview of this rare genetic cause of neonatal onset epilepsy.

Within-species phylogenetic relatedness of a common mycorrhizal fungus affects evenness in plant communities through effects on dominant species

Arbuscular mycorrhizal fungi (AMF) have been shown to influence plant community structure and diversity. Studies based on single plant-single AMF isolate experiments show that within AMF species variation leads to large differential growth responses of different plant species. Because of these differential effects, genetic differences among isolates of an AMF species could potentially have strong effects on the structure of plant communities. We tested the hypothesis that within species variation in the AMF Rhizophagus irregularis significantly affects plant community structure and plant co-existence. We took advantage of a recent genetic characterization of several isolates using double-digest restriction-site associated DNA sequencing (ddRADseq). This allowed us to test not only for the impact of within AMF species variation on plant community structure but also for the role of the R. irregularis phylogeny on plant community metrics. Nine isolates of R. irregularis, belonging to three different genetic groups (Gp1, Gp3 and Gp4), were used as either single inoculum or as mixed diversity inoculum. Plants in a mesocosm representing common species that naturally co-exist in European grasslands were inoculated with the different AMF treatments. We found that within-species differences in R. irregularis did not strongly influence the performance of individual plants or the structure of the overall plant community. However, the evenness of the plant community was affected by the phylogeny of the fungal isolates, where more closely-related AMF isolates were more likely to affect plant community evenness in a similar way compared to more genetically distant isolates. This study underlines the effect of within AMF species variability on plant community structure. While differential effects of the AMF isolates were not strong, a single AMF species had enough functional variability to change the equilibrium of a plant community in a way that is associated with the evolutionary history of the fungus.

Plant species distributions along environmental gradients: do belowground interactions with fungi matter?

The distribution of plants along environmental gradients is constrained by abiotic and biotic factors. Cumulative evidence attests of the impact of biotic factors on plant distributions, but only few studies discuss the role of belowground communities. Soil fungi, in particular, are thought to play an important role in how plant species assemble locally into communities. We first review existing evidence, and then test the effect of the number of soil fungal operational taxonomic units (OTUs) on plant species distributions using a recently collected dataset of plant and metagenomic information on soil fungi in the Western Swiss Alps. Using species distribution models (SDMs), we investigated whether the distribution of individual plant species is correlated to the number of OTUs of two important soil fungal classes known to interact with plants: the Glomeromycetes, that are obligatory symbionts of plants, and the Agaricomycetes, that may be facultative plant symbionts, pathogens, or wood decayers. We show that including the fungal richness information in the models of plant species distributions improves predictive accuracy. Number of fungal OTUs is especially correlated to the distribution of high elevation plant species. We suggest that high elevation soil show greater variation in fungal assemblages that may in turn impact plant turnover among communities. We finally discuss how to move beyond correlative analyses, through the design of field experiments manipulating plant and fungal communities along environmental gradients.

System size effects on gyrokinetic turbulence

The scaling of turbulence-driven heat transport with system size in magnetically confined plasmas is reexamined using first-principles based numerical simulations. Two very different numerical methods are applied to this problem, in order to resolve a long-standing quantitative disagreement, which may have arisen due to inconsistencies in the geometrical approximation. System size effects are further explored by modifying the width of the strong gradient region at fixed system size. The finite width of the strong gradient region in gyroradius units, rather than the finite overall system size, is found to induce the diffusivity reduction seen in global gyrokinetic simulations.

Tokamak magnetohydrodynamic equilibrium states with axisymmetric boundary and a 3D helical core

Magnetohydrodynamic (MHD) equilibrium states with imposed axisymmetric boundary are computed in which a spontaneous bifurcation develops to produce an internal three-dimensional (3D) configuration with a helical structure in addition to the standard axisymmetric system. Equilibrium states with similar MHD energy levels are shown to develop very different geometric structures. The helical equilibrium states resemble saturated internal kink mode structures.

Bilateral periventricular nodular heterotopia in France: frequency of mutations in FLNA, phenotypic heterogeneity and spectrum of mutations

Bilateral periventricular nodular heterotopia (BPNH) is the most common form of periventricular heterotopia. Mutations in FLNA, encoding filamin A, are responsible for the X linked dominant form of BPNH (FLNA-BPNH). Recently, atypical phenotypes including BPNH with Ehlers-Danlos syndrome (BPNH-EDS) have been recognised. A total of 44 FLNA mutations have so far been reported in this phenotype. Most of these mutations lead to a truncated protein, but few missense mutations have also been described. Here, the results of a mutation screening conducted in a series of 32 BPNH patients with the identification of 12 novel point mutations in 15 patients are reported. Nine mutations were truncating, while three were missense. Three additional patients with BPNH-EDS and a mutation in FLNA are described. No phenotype-genotype correlations could be established, but these clinical data sustain the importance of cardiovascular monitoring in FLNA-BPNH patients.

Novel FOXG1 mutations associated with the congenital variant of Rett syndrome

BACKGROUND

Rett syndrome is a severe neurodevelopmental disorder representing one of the most common genetic causes of mental retardation in girls. The classic form is caused by MECP2 mutations. In two patients affected by the congenital variant of Rett we have recently identified mutations in the FOXG1 gene encoding a brain specific transcriptional repressor, essential for early development of the telencephalon.

METHODS

60 MECP2/CDKL5 mutation negative European Rett patients (classic and variants), 43 patients with encephalopathy with early onset seizures, and four atypical Rett patients were analysed for mutations in FOXG1.

RESULTS AND CONCLUSIONS

Mutations have been identified in four patients, independently classified as congenital Rett variants from France, Spain and Latvia. Clinical data have been compared with the two previously reported patients with mutations in FOXG1. In all cases hypotonia, irresponsiveness and irritability were present in the neonatal period. At birth, head circumference was normal while a deceleration of growth was recognised soon afterwards, leading to severe microcephaly. Motor development was severely impaired and voluntary hand use was absent. In contrast with classic Rett, patients showed poor eye contact. Typical stereotypic hand movements with hand washing and hand mouthing activities were present continuously. Some patients showed abnormal movements of the tongue and jerky movements of the limbs. Brain magnetic resonance imaging showed corpus callosum hypoplasia in most cases, while epilepsy was a variable sign. Scoliosis was present and severe in the older patients. Neurovegetative symptoms typical of Rett were frequently present.

Role of plasma elongation on turbulent transport in magnetically confined plasmas

The theoretical study of plasma turbulence is of central importance to fusion research. Experimental evidence indicates that the confinement time results mainly from the turbulent transport of energy, the magnitude of which depends on the turbulent state resulting from nonlinear saturation mechanisms, in particular, the self-generation of coherent macroscopic structures and large scale flows. Plasma geometry has a strong impact on the structure and magnitude of these flows and also modifies the mode linear growth rates. Nonlinear global gyrokinetic simulations in realistic tokamak magnetohydrodynamic equilibria show how plasma shape can control the turbulent transport. Results are best described in terms of an effective temperature gradient. With increasing plasma elongation, the nonlinear critical effective gradient is not modified while the stiffness of transport is decreasing.

Periventricular heterotopia, mental retardation, and epilepsy associated with 5q14.3-q15 deletion

BACKGROUND

Periventricular heterotopia (PH) is an etiologically heterogeneous disorder characterized by nodules of neurons ectopically placed along the lateral ventricles. Most affected patients have seizures and their cognitive level varies from normal to severely impaired. At present, two genes have been identified to cause PH when mutated. Mutations in FLNA (Xq28) and ARFGEF2 (20q13) are responsible for X-linked bilateral PH and a rare autosomal recessive form of PH with microcephaly. Chromosomal rearrangements involving the 1p36, 5p15, and 7q11 regions have also been reported in association with PH but the genes implicated remain unknown. Fourteen additional distinct anatomoclinical PH syndromes have been described, but no genetic insights into their causes have been gleaned.

METHODS

We report the clinical and imaging features of three unrelated patients with epilepsy, mental retardation, and bilateral PH in the walls of the temporal horns of the lateral ventricles, associated with a de novo deletion of the 5q14.3-15 region. We used microarray-based comparative genomic hybridization to define the boundaries of the deletions.

RESULTS

The three patients shared a common deleted region spanning 5.8 Mb and containing 14 candidate genes.

CONCLUSION

We identified a new syndrome featuring bilateral periventricular heterotopia (PH), mental retardation, and epilepsy, mapping to chromosome 5q14.3-q15. This observation reinforces the extreme clinical and genetic heterogeneity of PH. Array comparative genomic hybridization is a powerful diagnostic tool for characterizing causative chromosomal rearrangements of limited size, identifying potential candidate genes for, and improving genetic counseling in, malformations of cortical development.

Refinement of cortical dysgeneses spectrum associated with TUBA1A mutations

OBJECTIVE

We have recently shown that de novo mutations in the TUBA1A gene are responsible for a wide spectrum of neuronal migration disorders. To better define the range of these abnormalities, we searched for additional mutations in a cohort of 100 patients with lissencephaly spectrum for whom no mutation was identified in DCX, LIS1 and ARX genes and compared these data to five previously described patients with TUBA1A mutations.

RESULTS

We detected de novo TUBA1A mutations in six patients and highlight the existence of a prominent form of TUBA1A related lissencephaly. In four patients, the mutations identified, c.1190T>C (p.L397P), c.1265G>A (p.R422H), c.1264C>T (p.R422C), c.1306G>T (p.G436R), have not been reported before and in two others, the mutation corresponds to a recurrent missense mutation, c.790C>T (p.R264C), likely to be a hot spot of mutation. All together, it emerges that the TUBA1A related lissencephaly spectrum ranges from perisylvian pachygyria, in the less severe form, to posteriorly predominant pachygyria in the most severe, associated with dysgenesis of the anterior limb of the internal capsule and mild to severe cerebellar hypoplasia. When compared with a large series of lissencephaly of other origins (ILS17, ILSX or unknown origin), these features appear to be specific to TUBA1A related lissencephaly. In addition, TUBA1A mutated patients share a common clinical phenotype that consists of congenital microcephaly, mental retardation and diplegia/tetraplegia.

CONCLUSIONS

Our data highlight the presence of consistent and specific abnormalities that should allow the differentiation of TUBA1A related lissencephalies from those related to LIS1, DCX and ARX genes.

Serological and molecular comparison of Mannheimia haemolytica and Pasteurella trehalosi strains isolated from wild and domestic ruminants in the French Alps

Over a period of 17 years, 84 bacterial isolates identified as Mannheimia haemolytica or M. glucosida, and 52 isolates identified as Pasteurella trehalosi were detected in the lungs of domestic and wild ruminants in the French Alps. The isolates were serotyped according to their surface capsular antigens, and those sharing common antigens were further characterized by pulsed field gel electrophoresis. The results showed that the bacterial isolates included in the study clustered according to the host species from which they were isolated. These findings indicate that the transmission of serotypes of M. haemolytica, M. glucosida or P. trehalosi from an animal host in which they are common to another species sharing the same geographical space may be a rare epidemiological event.

Pulsed-field gel electrophoresis profiles of aeromonads isolated from healthy and diseased Helix aspersa from French snail farms

The XbaI digestion patterns of chromosomal DNA of 42 aeromonads isolated from French breeding snails during a new epizootic disease, which rapidly progressed to death during the summer of 1994, were analyzed by pulsed-field gel electrophoresis. Biochemical identification to species level was also performed. Interestingly, we found that 76% of the aeromonads isolated from diseased snails clustered into a unique pulsotype (P1) whatever their geographic origin, and were assessed to belong to Aeromonas hydrophila. Other strains belonged to Aeromonas caviae or remained unspecified. Our results provide retrospective supplementary epidemiological evidence for implication of A. hydrophila strains in the snail summer disease.

Spectrum and distribution of MECP2 mutations in 424 Rett syndrome patients: a molecular update

Mutations in the MECP2 (Methyl-CpG-binding protein) gene have been reported to cause Rett syndrome (RTT), an X-linked progressive encephalopathy. Recent studies have identified large gene rearrangements that escape the common PCR-based mutation screening strategy and mutations in a novel MeCP2 isoform (named MECP2B). We have collected the results of MECP2 mutational analysis concerning 424 RTT patients conducted in eight laboratories in France. In total, 121 different MECP2 mutations were identified. R168X (11.5%) is the most common of MECP2 mutations, followed by R270X (9%), R255X (8.7%), T158 M (8.3%) and R306C (6.8%). Only eight mutations had relative frequency>3%. Large and complex rearrangements not previously detected using only a PCR-based strategy represent 5.8% of MECP2 mutations. On the contrary, mutation in exon 1 appears to be rare (less than 0.5%). These data demonstrate the high allelic heterogeneity of RTT in France and suggest that routine mutation screening in MECP2 should include quantitative analysis of the MECP2 gene. This study represents an important instrument for molecular diagnosis strategy and genetic counseling in RTT families.

Disruption of a new X linked gene highly expressed in brain in a family with two mentally retarded males

BACKGROUND

Mental retardation (MR) affects 2-3% of the human population and some of these cases are genetically determined. Although several genes responsible for MR have been identified, many cases have still not been explained.

METHODS

We have identified a pericentric inversion of the X chromosome inv(X)(p22.3;q13.2) segregating in a family where two male carriers have severe MR while female carriers are not affected.

RESULTS

The molecular characterisation of this inversion led us to identify two new genes which are disrupted by the breakpoints: KIAA2022 in Xq13.2 and P2RY8 in Xp22.3. These genes were not previously fully characterised in humans. KIAA2022 encodes a protein which lacks significant homology to any other known protein and is highly expressed in the brain. P2RY8 is a member of the purine nucleotide G-protein coupled receptor gene family. It is located in the pseudo-autosomal region of the X chromosome and is not expressed in brain.

CONCLUSIONS

Because the haploinsufficiency of P2RY8 in carrier mothers does not have a phenotypic consequence, we propose that the severe MR of the affected males in this family is due to the absence of the KIAA2022 gene product. However, screening 20 probands from X linked MR families did not reveal mutations in KIAA2022. Nonetheless, the high expression of this gene in fetal brain and in the adult cerebral cortex could be consistent with a role in brain development and/or cognitive function.

Delineation of the clinical phenotype associated withOPHN1 mutations based on the clinical and neuropsychological evaluation of three families

Recent reports have demonstrated that mutations in the OPHN1 gene were responsible for a syndromic rather than non-specific mental retardation. Abnormalities of the posterior fossa with cerebellar hypoplasia have been demonstrated in all male patients reported to date. We report here a new family with X-linked mental retardation due to mutation in OPHN1 and present unpublished data about two families previously reported, concerning the facial and psychological phenotype of affected males and carrier females. Our study confirms that cerebellar hypoplasia is a hallmark of this syndrome. In addition, affected males display facial similarities that can help the diagnosis. Most carrier females have mild mental retardation and subtle facial changes.

[Epigenetic study of Rett's syndrome as an adequate model for autistic disorders]

Rett's syndrome (RTT) is a severe hereditary disorder of the nervous system. MECP2 gene mutations are considered as a primary cause of the disease. In the present study, we have found MECP2 mutations in 33 (84.6%) out of 39 RTT females. We have also studied X-inactivation patterns in 70 girls with RTT. A frequency of skewed X-inactivation was 37% (26 patients), being significantly higher (p < 0.001) than that in the controls. The investigation of inactivated X chromosome origin revealed that about 33% pairs had preferentially the inactivated maternal X chromosome. An abnormal type of chromosome X inactivation was observed in all RTT females. Thus, we conclude that skewed X-inactivation may be considered as a common feature of RTT. There is unambiguous evidence that epigenetic alterations in RTT are associated with MECP2 mutations. MeCP2 protein also appears to be involved in transcriptional regulation of chromosome X genes. RTT in females without MECP2 mutations is related to the epigenetic alterations. We suggest X chromosome inactivation study in RTT females and their mothers to be informative for investigation of genetic processes in RTT girls, even in case MECP2 mutations have not been found. RTT could be considered as an appropriate model for studying epigenetic abnormalities in relation to autistic spectrum disorders.

Partial androgen insensitivity syndrome and t(X;5): are there upstream regulatory elements of the androgen receptor gene?

BACKGROUND/AIMS

Two half-brothers with similar malformed genitals, who both inherited a maternally derived t(X;5)(q13;p15) translocation, have a phenotype consistent with partial androgen sensitivity syndrome. The aim was to identify the gene disrupted by the X chromosome breakpoint.

METHODS

The breakpoint was localized using fluorescence in situ hybridization to metaphase spreads of the translocation.

RESULTS

The breakpoint on the X chromosome of the X;5 translocation was localized to a 30-kb region. This region does not contain any identified genes or transcripts. However, the breakpoint is approximately 134 kb from the 5' end of the androgen receptor (AR) gene.

CONCLUSIONS

Genetic defects of the AR gene are collectively called androgen insensitivity syndrome and include a range of phenotypes from normal males, often with associated sterility, to XY females. The phenotype seen in the males with the t(X;5) is consistent with this syndrome. The analysis of the chromosomal abnormality suggests that this translocation may remove one or more upstream regulatory elements of the AR gene that are essential for its normal expression and its role in typical external masculinization.

Tokamak equilibria with reversed current density

Observations of nearly zero toroidal current in the central region of tokamaks (the "current hole") raises the question of the existence of toroidal equilibria with very low or reversed current in the core. The solutions of the Grad-Shafranov equilibrium equation with hollow toroidal current density profile including negative current density in the plasma center are investigated. Solutions of the corresponding eigenvalue problem provide simple examples of such equilibrium configurations. More realistic equilibria with toroidal current density reversal are computed using a new equilibrium problem formulation and computational algorithm which do not assume nested magnetic surfaces.

[Genotype-phenotype correlations in Rett syndrome: the study of Russian cohort of patients]

Rett syndrome (RTT) is a severe neurodevelopmental disorder caused by mutations in methyl-CpG-binding protein 2 gene (MECP2). We carried out a mutations analysis in Russian cohort of patients with RTT. MECP2 mutations were found in 23 of 28 RTT girls and one boy (82%). Thirteen different types of mutations have been identified: 6 nonsense, 5 missense and 2 deletions in MECP2 gene. In typical RTT form, most frequent mutations were R255X (5 cases) and T158M (4 cases). A boy with classical clinical picture of RTT had R270X mutation. Skewed inactivation of chromosome x has been found in 2 of 27 RTT girls with classical RTT form and "forme fruste". The data obtained imply possible correlations between genotype and phenotype in RTT.

Abnormal expression of the KLF8 (ZNF741) gene in a female patient with an X;autosome translocation t(X;21)(p11.2;q22.3) and non-syndromic mental retardation

Non-syndromic X linked mental retardation (MRX) is a heterogeneous group of conditions in which all patients have mental retardation as the only constant phenotypic feature. We have identified a female patient with mental retardation and a balanced translocation involving chromosomes X and 21, t(X;21)(p11.2;q22.3). Physical mapping of the translocation breakpoint on the human X chromosome was performed using fluorescence in situ hybridisation. We have mapped the X chromosome breakpoint to a 21 kb DNA fragment upstream of the first exon of the KLF8 (ZNF741) gene in Xp11.21. We have subsequently shown that the KLF8 transcript is no longer detected in cells from the patient, although KLF8 expression is otherwise normally present in control lymphoblasts. Mutation screening of probands from 20 unrelated XLMR families linked to the proximal short arm of the human X chromosome failed to show any mutation in the coding region of the KLF8 gene.

Segregation of a totally skewed pattern of X chromosome inactivation in four familial cases of Rett syndrome without MECP2 mutation: implications for the disease

BACKGROUND

Rett syndrome is a neurodevelopmental disorder affecting only girls; 99.5% of Rett syndrome cases are sporadic, although several familial cases have been reported. Mutations in the MECP2 gene were identified in approximately 70-80% of sporadic Rett syndrome cases.

METHODS

We have screened the MECP2 gene coding region for mutations in five familial cases of Rett syndrome and studied the patterns of X chromosome inactivation (XCI) in each girl.

RESULTS

We found a mutation in MECP2 in only one family. In the four families without mutation in MECP2, we found that (1) all mothers exhibit a totally skewed pattern of XCI; (2) six out of eight affected girls also have a totally skewed pattern of XCI; and (3) it is the paternally inherited X chromosome which is active in the patients with a skewed pattern of XCI. Given that the skewing of XCI is inherited in our families, we genotyped the whole X chromosome using 32 polymorphic markers and we show that a locus potentially responsible for the skewed XCI in these families could be located on the short arm of the X chromosome.

CONCLUSION

These data led us to propose a model for familial Rett syndrome transmission in which two traits are inherited, an X linked locus abnormally escaping X chromosome inactivation and the presence of a skewed XCI in carrier women.

Mapping of X chromosome inversion breakpoints [inv(X)(q11q28)] associated with FG syndrome: a second FG locus [FGS2]?

FG syndrome is an X-linked condition comprising mental retardation, congenital hypotonia, macrocephaly, distinctive facial changes, and constipation or anal malformations. In a linkage analysis, we mapped a major FG syndrome locus [FGS1] to Xq13, between loci DXS135 and DXS1066. The same data, however, clearly demonstrated genetic heterogeneity. Recently, we studied a French family in which an inversion [inv(X)(q12q28)] segregates with clinical symptoms of FG syndrome. This suggests that one of the breakpoints corresponds to a second FG syndrome locus [FGS2]. We report the results of fluorescence in situ hybridization analysis performed in this family using YACs and cosmids encompassing the Xq11q12 and Xq28 regions. Two YACs, one positive for the DXS1 locus at Xq11.2 and one positive for the color vision pigment genes and G6PD loci at Xq28, were found to cross the breakpoints, respectively. We postulate that a gene might be disrupted by one of the breakpoints.

Two affected boys in a Rett syndrome family: clinical and molecular findings

BACKGROUND

The authors report a family in which two boys had severe neonatal encephalopathy of unknown origin. They both presented with the same condition and died of severe apnea before they were 1 year old. Their sister has a classic form of Rett syndrome.

METHODS

Because mutations in the methyl-CpG-binding protein 2 (MECP2) gene have been identified in 70 to 80% of the sporadic cases of Rett syndrome, the authors looked for a mutation in the MECP2 gene in this family.

RESULTS

The authors identified a missense mutation (T158M) in the affected girl and subsequently showed that one of her affected brothers, for whom DNA was available, carried the same mutation. The mother of the patients is a carrier of the T158M mutation. X-chromosome inactivation studies showed that the mother has a completely skewed X-chromosome inactivation pattern that favors the expression of the normal allele; this explains why she does not exhibit any phenotypic manifestation. In addition, the MECP2 mutation appeared on the grandpaternal X chromosome in this family.

CONCLUSIONS

An MECP2 mutation can be identified in boys, even though they do not present a Rett syndrome phenotype.

Molecular characterization of a new human T-box gene (TBX22) located in xq21.1 encoding a protein containing a truncated T-domain

We are conducting a systematic transcriptional mapping of the Xq12-q21 region of the human X chromosome in order to identify new genes potentially involved in X-linked mental retardation phenotypes. In silico analysis using the sequence of the genomic clones originating from this region of the human X chromosome allowed us to characterize a new gene belonging to the T-box family of transcriptional regulators. These genes were shown to be critical for proper development of both vertebrates and invertebrates. We show here that this new gene, called TBX22, is composed of seven exons spanning 8.7 kilobases of genomic DNA in Xq21.1. The TBX22 mRNA is 2099 base pairs long and encodes a 400-amino-acids protein containing a T-domain in its NH(2)-terminal region which has the unique feature of missing 20 amino-acids relative to the other known T-domains. TBX22 transcripts were exclusively found in a human fetal cDNA library and no homologous gene could be detected in the mouse genome. In addition, phylogenetic studies performed using all the known T-domain-containing proteins show that TBX22 is not directly related to any of them. These data indicate that TBX22 may be the first identified member of a new family of T-domain-containing proteins.

MECP2 mutations account for most cases of typical forms of Rett syndrome

Rett syndrome (RTT) is a severe progressive neurological disorder that affects almost exclusively females, with an estimated prevalence of approximately one in 10 000-15 000 female births. Most cases are sporadic, but several reports about familial recurrence support X-linked dominant inheritance with male lethality. The gene responsible for this disorder, MECP2, was recently identified by candidate gene strategy. Mutations were detected in <25% of RTT cases in this first report. To characterize the spectrum of mutations in the MECP2 gene in RTT patients, we selected 46 typical RTT patients and performed mutation screening by denaturing gradient gel electrophoresis combined with direct sequencing. We identified 30 mutations, accounting for 65% of RTT patients. They include 12 novel mutations (11 located in exon 3 and one in exon 2). Mutations, such as R270X and frameshift deletions in a (CCACC) (n) rich region, have been found with multiple recurrences. Most of the mutations were de novo, except in one family where the non-affected transmitter mother exhibited a bias of X inactivation. Although this study showed that MECP2 mutations account for most cases of typical forms of RTT (65%) and mutations in non-coding regions cannot be excluded for the remaining cases, an alternative hypothesis that takes into account the homogeneous phenotype and exclusive involvement of females, could be the implication in RTT of a putative second X-linked gene.

Ribotyping and rapid identification of Staphylococcus xylosus by 16-23S spacer amplification

Ninety-five strains of Staphylococcus xylosus isolated from goat milk, French sausage or mice were analyzed together with 35 Staphylococcus type strains by 16-23S spacer amplification and ribotyping. The results obtained by PCR amplification of the 16-23S spacer region permitted the distinction of each type strain and additionally generated a DNA banding pattern characteristic for 93 of the 95 Staphylococcus xylosus strains. Ribotyping proved to be an efficient epidemiological tool for Staphylococcus xylosus species as it clustered the 95 strains into 23 distinct types.

Detection of Escherichia coli O157:H7 in heifers' faecal samples using an automated immunoconcentration system

Pre-treatment of a 5-h enrichment culture with an automated immunoconcentration (ICE) system greatly improved the isolation of Escherichia coli O157:H7 from spiked heifer faecal samples. Enrichment samples plated directly onto sorbitol MacConkey agar (SMAC) and SMAC agar supplemented with cefixime and potassium tellurite (CT-SMAC) showed recovery rates of 8% and 56%, respectively. However, after ICE treatment, E. coli O157:H7 was recovered from 92% of the samples on SMAC and 100% on CT-SMAC. Immunoconcentration analysis of heifers' faecal samples collected from a slaughter-house in France, during March to June 1998, showed that 1% (three of 300) was positive for E. coli O157:H7. Phenotypic and genotypic analysis showed that all three isolates carried both the O157 and H7 antigens, did not ferment sorbitol or had beta-glucuronidase activity and carried trait virulence factors for E. coli O157:H7 (uidA allele, eaeA and pO157 plasmid). However, only one strain was toxigenic and this strain produced a single toxin, namely verotoxin 2.

Linkage of X-linked myopathy with excessive autophagy (XMEA) to Xq28

X-linked myopathy with excessive autophagy (XMEA, MIM 310440) is a rare inherited mild myopathy. We have used 32 polymorphic markers spanning the entire X chromosome to exclude most of the chromosome except the Xq28 region in a large XMEA family. Using three additional families for linkage analysis, we have obtained a significant two-point lod score with marker DXS1183 (Z = 2.69 at theta = 0). Multipoint linkage analysis confirmed the assignment of the disease locus with a maximal lod score of 2.74 obtained at recombination fraction zero. Linkage of XMEA to the Xq28 region is thus firmly established. In addition, we have ruled out the Emery-Dreifuss muscular dystrophy to be allelic with XMEA by direct sequencing of the emerin gene in three of our families.

Evidence that a dodecamer duplication in the gene HOPA in Xq13 is not associated with mental retardation

A recent study suggested that a dodecamer duplication in exon 42 of the HOPA gene in Xq13 may be a significant factor in the etiology of X-linked mental retardation. In an effort to investigate this possibility, we determined the incidence of the dodecamer duplication in cohorts of non-fragile X males with mental retardation from three countries, cohorts of fragile X males from two countries, 43 probands from families with X-linked mental retardation and control cohorts from three countries. The duplication was found in 3.6-4.0% of male patients from two non-fragile X groups (Italy and South Carolina), in 1.2% from another non-fragile X group (South Africa), but in no male patients from families with X-linked mental retardation (South Carolina). The dodecamer duplication was also found in several white males with fragile X syndrome from France (5%) and South Africa (22.2%). Additionally, the duplication was found in 1.5% of South Carolinian newborn males, 2.5% South Carolinian male college students, 5% Italian male controls and 4.5% of the white South African controls. None of the black South African non-fragile X individuals with mental retardation, the fragile X or the control samples tested carried the duplication, suggesting that the duplication is rare in the black South African population. The incidence of the duplication was not significantly different between any of the groups in the study. Therefore, results of our studies in four different populations do not corroborate the findings of the previous study, and indicate that the HOPA dodecamer duplication does not convey an increased susceptibility to mental retardation.

Two unrelated patients with inversions of the X chromosome and non-specific mental retardation: physical and transcriptional mapping of their common breakpoint region in Xq13.1

Two unrelated mildly retarded males with inversions of the X chromosome and non-specific mental retardation (MRX) are described. Case 1 has a pericentric inversion 46,Y,inv(X) (p11.1q13.1) and case 2 a paracentric inversion 46,Y,inv(X) (q13.1q28). Both male patients have severe learning difficulties. The same chromosomal abnormalities were found in their mothers who are intellectually normal. Fluorescence in situ hybridisation mapping showed a common area of breakage of each of the inverted chromosomes in Xq13.1 near DXS131 and DXS162. A detailed long range restriction map of the breakpoint region was constructed using YAC, PAC, and cosmid clones. We show that the two inverted chromosomes break within a short 250 kb region. Moreover, a group of ESTs corresponding to an as yet uncharacterised gene was mapped to the same critical interval. We hypothesise that the common inversion breakpoint region of the two cases in Xq13.1 may contain a new MRX gene.

Characterization of xnp-1, a Caenorhabditis elegans gene similar to the human XNP/ATR-X gene

We report the characterization of a new Caenorhabditis elegans gene, xnp-1, that encodes the closest known non-mammalian relative of the human XNP/ATR-X protein. Mutations in the corresponding gene lead to mental retardation in humans. The nematode gene is composed of 10 exons, and we show that a 4.3kb transcript is produced from the xnp-1 locus. The 1359 residue XNP-1 protein is 33.6% identical and 52.2% similar to the human XNP/ATR-X protein. In two regions of more than 250 amino acids, the proteins display 70% identity. The human and nematode proteins are putative DNA helicases and contain the seven characteristic domains of this family of proteins. In addition to the fact that similar proteins are encoded by the nematode and human gene, they share a partially identical genomic structure. These data indicate that xnp-1 and XNP/ATR-X have diverged from the same ancestral DNA helicase gene and may therefore have conserved similar functions at the cellular level.

Transcript map of the human chromosome Xq11-Xq21 region: localization of 33 novel genes and one pseudogene

The human Xq11-Xq21.3 region has been implicated in several inherited disorders including dystonia-parkinsonism (DYT3), sideroblastic anemia and several specific and non-specific forms of mental retardation (MR) syndromes. As part of a positional cloning effort to identify MR genes, we have generated a YAC-based transcript map. We first constructed a YAC/STS framework by extending previously published contigs. This framework map consists of a minimal set of 119 clones, covering approximately 20 Megabases (Mb) and allowing the precise ordering of 71 STSs between DXS136 and DXS472. This YAC contig was then used to define the positions of genes and expressed sequence tags (ESTs) assigned to the Xcen-Xq21.3 region. In addition to the genes previously localized to this part of the X chromosome, 18 transcription units corresponding to additional known genes or gene family members, one pseudogene and 15 novel transcripts were mapped. This transcriptional map incorporates 51 transcription units and provides a useful resource of candidate genes for some of the disorders assigned to this region of the X chromosome.

Evaluation of a mutation screening strategy for sporadic cases of ATR-X syndrome

We report on the evaluation of a strategy for screening for XNP/ATR-X mutations in males with mental retardation and associated dysmorphology. Because nearly half of the mutations in this gene reported to date fall into a short 300 bp region of the transcript, we decided to focus in this region and to extend the mutation analysis to cases with a negative family history. This study includes 21 mentally retarded male patients selected because they had severe mental retardation and a typical facial appearance. The presence of haemoglobin H or urogenital abnormalities was not considered critical for inclusion in this study. We have identified six mutations which represents a mutation detection rate of 28%. This figure is high enough for us to propose this strategy as a valid first level of screening in a selected subset of males with mental retardation. This approach is simple, does not require RNA preparation, does not involve time consuming mutation detection methods, and can thus be applied to a large number of patients at a low cost in any given laboratory.

Identification by 16S rDNA fragment amplification and determination of genetic diversity by random amplified polymorphic DNA analysis of Pasteurella pneumotropica isolated from laboratory rodents

Pasteurella pneumotropica is an opportunistic bacterium frequently isolated from colonies of various laboratory rodents. Identification of this species, including its differentiation into two distinct biotypes (Jawetz and Heyl), is usually based on the use of conventional bacteriologic methods. In this study, a 16S rDNA fragment amplification procedure was developed for use as an alternative method for identification and differentiation of P. pneumotropica. Polymerase chain reaction (PCR) products were two distinctive fragments of 937 and 564 bp specific for biotypes Jawetz and Heyl, respectively. Specificity of PCR products could be achieved by EcoRI cleavage, leading to 596 plus 341-bp and 346 plus 218-bp fragments for each of the amplification products. Use of this procedure confirmed identification of 34 field isolates and allowed definitive identification of some strains that could not have been done by use of bacteriologic examinations. Field isolates subjected to random amplified polymorphic DNA (RAPD) analysis had high genetic diversity among biotype Jawetz strains in contrast to biotype Heyl strains. In conclusion, RAPD could represent an additional means for identification of ambiguous strains of biotype Heyl and a valuable epidemiologic tool for identification of biotype Jawetz strains of P. pneumotropica.

Pulsed-field gel electrophoresis is more efficient than ribotyping and random amplified polymorphic DNA analysis in discrimination of Pasteurella haemolytica strains

One hundred thirty-three strains of Pasteurella haemolytica of both biotypes (90 and 43 strains of biotypes A and T, respectively) and almost all the serotypes were subjected to ribotyping, random amplified polymorphic DNA (RAPD) analysis, and pulsed-field gel electrophoresis (PFGE) analysis for epidemiological purposes. A total of 15 patterns recorded as ribotypes HA to HO were found for the P. haemolytica biotype A strains, with ribotypes HA, HC, and HD being encountered most often (66 strains [74%]); and 20 ribotypes, designated HA' to HT', that were clearly distinct from those observed for biotype A strains were observed for strains of biotype T. RAPD analysis generated a total of 44 (designated Rp1 to Rp44) and 15 (designated Rp1' to Rp 15') unique RAPD patterns for biogroup A and biogroup T, respectively. Analysis of the data indicated that a given combined ribotype-RAPD pattern could be observed for biotype A strains of different serotypes, whatever the zoological or geographic origin, whereas this was not the case for biotype T strains. PFGE appeared to be more efficient in strain discrimination since selected strains from various zoological or geographical origins harboring the same ribotype-RAPD group were further separated into unique entities.

Structures, sequence characteristics, and synteny relationships of the transcription factor E4TF1, the splicing factor U2AF35 and the cystathionine beta synthetase genes from Fugu rubripes

A cosmid containing the beta-amyloid precursor protein (APP) from Fugu rubripes has been completely sequenced. In addition to APP, the cosmid contains the E4TF1-60 transcription factor, the U2AF35 pre-mRNA splicing factor, and the cystathionine beta synthetase (CBS) gene. The human homologues of all four genes map to human chromosome 21 but are not clustered; APP and E4TF1-60 map within 21q21, whereas U2AF35 and CBS map approximately 20Mb distal in 21q22. 3. The protein sequences of the Fugu genes vary in their overall level of similarity to their mammalian homologues, but several regions of functional importance are almost identical. As expected, the intron/exon structures of the homologous pairs of genes are highly conserved, but there are significant differences in the compaction ratios. The introns of APP and E4TF1-60 are 49- and 24-fold smaller in Fugu than in human, and the intergenic distance is compressed at least 100-fold. For U2AF35 and CBS, the introns are compressed only five- to eightfold. These size differences were compared with those for a number of previously reported Fugu genes; in general, levels of compaction of Fugu genes are consistent with the isochore locations of the human homologues.