Multilocus Genotypes of the Wheat Leaf Rust Fungus Puccinia triticina in Worldwide Regions Indicate Past and Current Long-Distance Migration

Many plant pathogenic fungi have a global distribution across diverse ecological zones and agricultural production systems. Puccinia triticina, the wheat leaf rust fungus, is a major pathogen in many wheat production areas of the world. The objective of this research was to determine the genetic relatedness of P. triticina in different worldwide regions. A total of 831 single-uredinial isolates collected from 11 regions were characterized for multilocus genotype at 23 simple sequence repeat loci and for virulence to 20 lines of wheat with single genes for leaf rust resistance. A total of 424 multilocus genotypes and 497 virulence phenotypes were found. All populations had high heterozygosity and significant correlation between virulence and molecular variation, which indicated clonal reproduction. The populations from North America and South America, Central Asia and Russia, and the Middle East and Europe were closely related for multilocus genotypes and many individual isolates from other continental regions were closely related. Twenty-seven multilocus genotypes were found in more than one continental region, and 13 of these had isolates with identical virulence phenotypes. The wide geographic distribution of identical and highly related multilocus genotypes of P. triticina indicated past and more recent migration events facilitated by the spread of clonally produced urediniospores.

Mutations in AIFM1 cause an X-linked childhood cerebellar ataxia partially responsive to riboflavin

BACKGROUND

AIFM1 encodes a mitochondrial flavoprotein with a dual role (NADH oxidoreductase and regulator of apoptosis), which uses riboflavin as a cofactor. Mutations in the X-linked AIFM1 were reported in relation to two main phenotypes: a severe infantile mitochondrial encephalomyopathy and an early-onset axonal sensorimotor neuropathy with hearing loss. In this paper we report two unrelated males harboring AIFM1 mutations (one of which is novel) who display distinct phenotypes including progressive ataxia which partially improved with riboflavin treatment.

METHODS

For both patients trio whole exome sequencing was performed. Validation and segregation were performed with Sanger sequencing. Following the diagnosis, patients were treated with up to 200 mg riboflavin/day for 12 months. Ataxia was assessed by the ICARS scale at baseline, and 6 and 12 months following treatment.

RESULTS

Patient 1 presented at the age of 5 years with auditory neuropathy, followed by progressive ataxia, vermian atrophy and axonal neuropathy. Patient 2 presented at the age of 4.5 years with severe limb and palatal myoclonus, followed by ataxia, cerebellar atrophy, ophthalmoplegia, sensorineural hearing loss, hyporeflexia and cardiomyopathy. Two deleterious missense mutations were found in the AIFM1 gene: p. Met340Thr mutation located in the FAD dependent oxidoreductase domain and the novel p. Thr141Ile mutation located in a highly conserved DNA binding motif. Ataxia score, decreased by 39% in patient 1 and 20% in patient 2 following 12 months of treatment.

CONCLUSION

AIFM1 mutations cause childhood cerebellar ataxia, which may be partially treatable in some patients with high dose riboflavin.

Microcephaly, intractable seizures and developmental delay caused by biallelic variants in TBCD: further delineation of a new chaperone-mediated tubulinopathy

Microtubule dynamics play a crucial role in neuronal development and function, and several neurodevelopmental disorders have been linked to mutations in genes encoding tubulins and functionally related proteins. Most recently, variants in the tubulin cofactor D (TBCD) gene, which encodes one of the five co-chaperones required for assembly and disassembly of α/β-tubulin heterodimer, were reported to underlie a recessive neurodevelopmental/neurodegenerative disorder. We report on five patients from three unrelated families, who presented with microcephaly, intellectual disability, intractable seizures, optic nerve pallor/atrophy, and cortical atrophy with delayed myelination and thinned corpus callosum on brain imaging. Exome sequencing allowed the identification of biallelic variants in TBCD segregating with the disease in the three families. TBCD protein level was significantly reduced in cultured fibroblasts from one patient, supporting defective TBCD function as the event underlying the disorder. Such reduced expression was associated with accelerated microtubule re-polymerization. Morpholino-mediated TBCD knockdown in zebrafish recapitulated several key pathological features of the human disease, and TBCD overexpression in the same model confirmed previous studies documenting an obligate dependency on proper TBCD levels during development. Our findings confirm the link between inactivating TBCD variants and this newly described chaperone-associated tubulinopathy, and provide insights into the phenotype of this disorder.

Mitochondrial epileptic encephalopathy, 3-methylglutaconic aciduria and variable complex V deficiency associated with TIMM50 mutations

Mitochondrial encephalopathies are a heterogeneous group of disorders that, usually carry grave prognosis. Recently a homozygous mutation, Gly372Ser, in the TIMM50 gene, was reported in an abstract form, in three sibs who suffered from intractable epilepsy and developmental delay accompanied by 3-methylglutaconic aciduria. We now report on four patients from two unrelated families who presented with severe intellectual disability and seizure disorder, accompanied by slightly elevated lactate level, 3-methylglutaconic aciduria and variable deficiency of mitochondrial complex V. Using exome analysis we identified two homozygous missense mutations, Arg217Trp and Thr252Met, in the TIMM50 gene. The TIMM50 protein is a subunit of TIM23 complex, the mitochondrial import machinery. It serves as the major receptor in the intermembrane space, binding to proteins which cross the mitochondrial inner membrane on their way to the matrix. The mutations, which affected evolutionary conserved residues and segregated with the disease in the families, were neither present in large cohorts of control exome analyses nor in our ethnic specific exome cohort. Given the phenotypic similarity, we conclude that missense mutations in TIMM50 are likely manifesting by severe intellectual disability and epilepsy accompanied by 3-methylglutaconic aciduria and variable mitochondrial complex V deficiency. 3-methylglutaconic aciduria is emerging as an important biomarker for mitochondrial dysfunction, in particular for mitochondrial membrane defects.

A New Rust Disease on Wild Coffee (Psychotria nervosa) Caused by Puccinia mysuruensis sp. nov

Psychotria nervosa, commonly called "wild coffee" (Rubiaceae), is an important ethno-medicinal plant in India. In 2010, a new rust disease of P. nervosa was observed in three regions of Mysore District, Karnataka (India), with disease incidence ranging from 58 to 63%.Typical symptoms of the rust disease on wild coffee were prominently visible during the early monsoon season (May to June), with chlorotic spots on the adaxial and black pustules (telia) on the abaxial leaf surface. Telia produced abundant teliospores, which were bicelled, pedicillate, and measured 33 to 45 by 19 to 30 μm. The germination of teliospores produced a typical metabasidium bearing four basidiospores, each containing two haploid nuclei. Spore stages of the wild coffee rust pathogen were studied using artificially inoculated healthy wild coffee plants with germinated teliospores. Only telia were observed on the inoculated plants, indicating that this rust fungus has an abbreviated microcyclic life cycle that includes only teliospores and basidiospores. Phylogenetic analysis based on internal transcribed spacer and partial large subunit (LSU) sequence data showed that the wild coffee rust pathogen is related to Macruropyxis fraxini, Puccinia bartholomaei, P. choridis, and P. sparganioidis. The herbarium sample of P. psychotriae was examined and was shown to be different with respect to telium size and teliospore dimensions (24 to 32 by 13 to 18 μm). Therefore, the rust pathogen causing wild coffee rust is a new species, P. mysuruensis sp. nov.

Creatine transporter deficiency: Novel mutations and functional studies

X-linked cerebral creatine deficiency (MIM 300036) is caused by deficiency of the creatine transporter encoded by the SLC6A8 gene. Here we report three patients with this condition from Israel. These unrelated patients were evaluated for global developmental delays and language apraxia. Borderline microcephaly was noted in one of them. Diagnosis was prompted by brain magnetic resonance imaging and spectroscopy which revealed normal white matter distribution, but absence of the creatine peak in all three patients. Biochemical testing indicated normal plasma levels of creatine and guanidinoacetate, but an increased urine creatine/creatinine ratio. The diagnosis was confirmed by demonstrating absent ([14])C-creatine transport in fibroblasts. Molecular studies indicated that the first patient is hemizygous for a single nucleotide change substituting a single amino acid (c.619 C > T, p.R207W). Expression studies in HeLa cells confirmed the causative role of the R207W substitution. The second patient had a three base pair deletion in the SLC6A8 gene (c.1222_1224delTTC, p.F408del) as well as a single base change (c.1254 + 1G > A) at a splicing site in the intron-exon junction of exon 8, the latter occurring de novo. The third patient, had a three base pair deletion (c.1006_1008delAAC, p.N336del) previously reported in other patients with creatine transporter deficiency. These three patients are the first reported cases of creatine transporter deficiency in Israel.

SLC1A4 mutations cause a novel disorder of intellectual disability, progressive microcephaly, spasticity and thin corpus callosum

Two unrelated patients, presenting with significant global developmental delay, severe progressive microcephaly, seizures, spasticity and thin corpus callosum (CC) underwent trio whole-exome sequencing. No candidate variant was found in any known genes related to the phenotype. However, crossing the data of the patients illustrated that they both manifested pathogenic variants in the SLC1A4 gene which codes the ASCT1 transporter of serine and other neutral amino acids. The Ashkenazi patient is homozygous for a deleterious missense c.766G>A, p.(E256K) mutation whereas the Ashkenazi-Iraqi patient is compound heterozygous for this mutation and a nonsense c.945delTT, p.(Leu315Hisfs*42) mutation. Structural prediction demonstrates truncation of significant portion of the protein by the nonsense mutation and speculates functional disruption by the missense mutation. Both mutations are extremely rare in general population databases, however, the missense mutation was found in heterozygous mode in 1:100 Jewish Ashkenazi controls suggesting a higher carrier rate among Ashkenazi Jews. We conclude that SLC1A4 is the disease causing gene of a novel neurologic disorder manifesting with significant intellectual disability, severe postnatal microcephaly, spasticity and thin CC. The role of SLC1A4 in the serine transport from astrocytes to neurons suggests a possible pathomechanism for this disease and implies a potential therapeutic approach.

The neuropsychological profile of patients with 3-methylglutaconic aciduria type III, Costeff syndrome

Costeff syndrome is a rare genetic neuro-ophthalmological syndrome consisting of early-onset bilateral optic atrophy along with a progressive complex motor disorder with elevated levels of urinary 3-methylglutaconic acid and 3-methylglutaric acid. While borderline to mild cognitive deficits have been considered to be common in patients with this syndrome, a comprehensive cognitive assessment has never been performed. The aim of the current study was to explore the cognitive profile associated with Costeff syndrome. Sixteen adult patients diagnosed with Costeff syndrome were administered a neuropsychological test battery that was composed of standardized verbal tests adapted for the blind. General intelligence ranged from average to borderline, with a group mean consistent with intact general cognitive functioning (VIQmean  = 85, z = -1) in the low-average range of the general population. The auditory immediate and delayed memory indexes were in the average range and were significantly higher than the general cognitive functioning, whereas the working memory index was significantly lower than the general cognitive functioning. Adult patients with Costeff syndrome have intact global cognition and learning abilities and strong auditory memory performance. © 2015 Wiley Periodicals, Inc.

Genetic differentiation of Puccinia triticina populations in the Middle East and genetic similarity with populations in Central Asia

Leaf rust of wheat, caused by Puccinia triticina, is a common and widespread disease in the Middle East. The objective of this study was to determine whether genetically differentiated groups of P. triticina are present in the Middle East region and to compare the population from the Middle East with the previously characterized population from Central Asia to determine whether genetically similar groups of isolates are found in the two regions. In total, 118 isolates of P. triticina collected from common wheat and durum wheat in Egypt, Israel, Turkey, Ethiopia, and Kenya were tested for virulence on 20 lines of wheat with single genes for leaf rust resistance and for molecular genotypes with 23 simple-sequence repeat (SSR) markers. After removal of isolates with identical virulence and SSR genotype in each country, 103 isolates were retained for further analysis. Clustering of SSR genotypes based on two-dimensional principal coordinates and virulence to wheat differential lines grouped the isolates into four Middle East (ME) groups. The two largest ME groups had virulence phenotypes typical of isolates collected from common wheat and two smaller ME groups had virulence typical of isolates collected from durum wheat. All pairs of ME groups were significantly differentiated for SSR genotype based on R(ST) and F(ST) statistics, and for virulence phenotype based on Φ(PT). All ME groups had observed values of heterozygosity greater than expected and significant fixation indices that indicated the clonal reproduction of urediniospores in the overall population. Linkage disequilibria for SSR genotypes was high across the entire population. The overall values of R(ST) and F(ST) were lower when isolates were grouped by country of origin that indicated the likely migration of isolates within the region. Although the two ME groups with virulence typical of isolates from common wheat were not differentiated for SSR genotype from groups of isolates from Central Asia based on R(ST), there was no direct evidence for migration between the two regions because all ME isolates differed from the Central Asia isolates for SSR genotypes.

Glyceryl triacetate for Canavan disease: a low-dose trial in infants and evaluation of a higher dose for toxicity in the tremor rat model

Canavan disease (CD) is a fatal dysmyelinating genetic disorder associated with aspartoacylase deficiency, resulting in decreased brain acetate levels and reduced myelin lipid synthesis in the developing brain. Here we tested tolerability of a potent acetate precursor, glyceryl triacetate (GTA), at low doses in two infants diagnosed with CD, aged 8 and 13 months. Much higher doses of GTA were evaluated for toxicity in the tremor rat model of CD. GTA was given orally to the infants for up to 4.5 and 6 months, starting at 25 mg/kg twice daily, doubling the dose weekly until a maximum of 250 mg/kg reached. Wild-type and tremor rat pups were given GTA orally twice daily, initially at a dose of 4.2 g/kg from postnatal days 7 through 14, and at 5.8 g/kg from day 15 through 23, and thereafter in food (7.5%) and water (5%). At the end of the trial (approximately 90 to 120 days) sera and tissues from rats were analysed for changes in blood chemistry and histopathology. GTA treatment caused no detectable toxicity and the patients showed no deterioration in clinical status. In the high-dose animal studies, no significant differences in the mean blood chemistry values occurred between treated and untreated groups, and no lesions indicating toxicity were detectable in any of the tissues examined. Lack of GTA toxicity in two CD patients in low-dose trials, as well as in high-dose animal studies, suggests that higher, effective dose studies in human CD patients are warranted.

Genome size in natural and synthetic autopolyploids and in a natural segmental allopolyploid of several Triticeae species

Nuclear DNA amount (1C) was determined by flow cytometry in the autotetraploid cytotype of Hordeum bulbosum, in the cytologically diploidized autotetraploid cytotypes of Elymus elongatus, Hordeum murinum subsp. murinum and Hordeum murinum subsp. leporinum, in Hordeum marinum subsp. gussoneanum, in their progenitor diploid cytotypes, and in a newly synthesized autotetraploid line of E. elongatus. Several lines collected from different regions of the distribution area of every taxon, each represented by a number of plants, were analyzed in each taxon. The intracytotype variation in nuclear DNA amount of every diploid and autotetraploid cytotype was very small, indicating that no significant changes have occurred in DNA amount either after speciation or after autopolyploid formation. The autotetraploid cytotypes of H. bulbosum and the cytologically diploidized H. marinum subsp. gussoneanum had the expected additive amount of their diploid cytotypes. On the other hand, the cytologically diploidized autotetraploid cytotypes of E. elongatus and H. murinum subsp. murinum and H. murinum subsp. leporinum had considerably less nuclear DNA (10%-23%) than the expected additive value. Also, the newly synthesized autotetraploid line of E. elongatus showed similar reduction in DNA as its natural counterpart, indicating that the reduction in genome size occurred in the natural cytotype during autopolyploidization. It is suggested that the diploid-like meiotic behavior of these cytologically dipolidized autotetraploids is caused by the instantaneous elimination of a large number of DNA sequences, different sequences from different homologous pairs, leading to differentiation of the constituent genomes. The eliminated sequences are likely to include those that participate in homologous recognition and initiation of meiotic pairing. A gene system determining exclusive bivalent pairing by utilizing the differentiation between the two groups of homologues has been presumably superimposed on the DNA reduction process.

Genome size and genome evolution in diploid Triticeae species

One of the intriguing issues concerning the dynamics of plant genomes is the occurrence of intraspecific variation in nuclear DNA amount. The aim of this work was to assess the ranges of intraspecific, interspecific, and intergeneric variation in nuclear DNA content of diploid species of the tribe Triticeae (Poaceae) and to examine the relation between life form or habitat and genome size. Altogether, 438 plants representing 272 lines that belong to 22 species were analyzed. Nuclear DNA content was estimated by flow cytometry. Very small intraspecific variation in DNA amount was found between lines of Triticeae diploid species collected from different habitats or between different morphs. In contrast to the constancy in nuclear DNA amount at the intraspecific level, there are significant differences in genome size between the various diploid species. Within the genus Aegilops, the 1C DNA amount ranged from 4.84 pg in A. caudata to 7.52 pg in A. sharonensis; among genera, the 1C DNA amount ranged from 4.18 pg in Heteranthelium piliferum to 9.45 pg in Secale montanum. No evidence was found for a smaller genome size in annual, self-pollinating species relative to perennial, cross-pollinating ones. Diploids that grow in the southern part of the group's distribution have larger genomes than those growing in other parts of the distribution. The contrast between the low variation at the intraspecific level and the high variation at the interspecific one suggests that changes in genome size originated in close temporal proximity to the speciation event, i.e., before, during, or immediately after it. The possible effects of sudden changes in genome size on speciation processes are discussed.

Nuclear DNA amount and genome downsizing in natural and synthetic allopolyploids of the generaAegilopsandTriticum

Recent molecular studies in the genera Aegilops and Triticum showed that allopolyploidization (interspecific or intergeneric hybridization followed by chromosome doubling) generated rapid elimination of low-copy or high-copy, non-coding and coding DNA sequences. The aims of this work were to determine the amount of nuclear DNA in allopolyploid species of the group and to see to what extent elimination of DNA sequences affected genome size. Nuclear DNA amount was determined by the flow cytometry method in 27 natural allopolyploid species (most of which were represented by several lines and each line by several plants) as well as 14 newly synthesized allopolyploids (each represented by several plants) and their parental plants. Very small intraspecific variation in DNA amount was found between lines of allopolyploid species collected from different habitats or between wild and domesticated forms of allopolyploid wheat. In contrast to the constancy in nuclear DNA amount at the intraspecific level, there are significant differences in genome size between the various allopolyploid species, at both the tetraploid and hexaploid levels. In most allopolyploids nuclear DNA amount was significantly less than the sum of DNA amounts of the parental species. Newly synthesized allopolyploids exhibited a similar decrease in nuclear DNA amount in the first generation, indicating that genome downsizing occurs during and (or) immediately after the formation of the allopolyploids and that there are no further changes in genome size during the life of the allopolyploids. Phylogenetic considerations of the origin of the B genome of allopolyploid wheat, based on nuclear DNA amount, are discussed.

Genetics of resistance to wheat leaf rust, stem rust, and powdery mildew in Aegilops sharonensis

Aegilops sharonensis (Sharon goatgrass) is a wild relative of wheat and a rich source of genetic diversity for disease resistance. The objectives of this study were to determine the genetic basis of leaf rust, stem rust, and powdery mildew resistance in A. sharonensis and also the allelic relationships between genes controlling resistance to each disease. Progeny from crosses between resistant and susceptible accessions were evaluated for their disease reaction at the seedling and/or adult plant stage to determine the number and action of genes conferring resistance. Two different genes conferring resistance to leaf rust races THBJ and BBBB were identified in accessions 1644 and 603. For stem rust, the same single gene was found to confer resistance to race TTTT in accessions 1644 and 2229. Resistance to stem rust race TPMK was conferred by two genes in accessions 1644 and 603. A contingency test revealed no association between genes conferring resistance to leaf rust race THBJ and stem rust race TTTT or between genes conferring resistance to stem rust race TTTT and powdery mildew isolate UM06-01, indicating that the respective resistance genes are not linked. Three accessions (1644, 2229, and 1193) were found to carry a single gene for resistance to powdery mildew. Allelism tests revealed that the resistance gene in accession 1644 is different from the respective single genes present in either 2229 or 1193. The simple inheritance of leaf rust, stem rust, and powdery mildew resistance in A. sharonensis should simplify the transfer of resistance to wheat in wide crosses.

Resistance of Sharon Goatgrass (Aegilops sharonensis) to Fungal Diseases of Wheat

Sharon goatgrass (Aegilops sharonensis) is a wild relative of wheat that is native to Israel and Lebanon. The importance of A. sharonensis as a source of new resistance genes for wheat warrants additional research on the characterization of accessions for economically important genes. Thus, the objectives of this study were to evaluate a collection of A. sharonensis accessions for resistance to seven important fungal diseases of wheat and assess the phenotypic diversity of the germplasm for disease reaction. The frequency of resistance in A. sharonensis was highest to powdery mildew (79 to 83%) and leaf rust (60 to 77%). Resistance to stem rust also was common, although the percentage of resistant accessions varied markedly depending on the pathogen race-from 13% to race TTTT to 72% to race QCCJ. The frequency of resistance was intermediate to stripe rust (45%) and low to tan spot (15 to 29%) and spot blotch (0 to 34%). None of the A. sharonensis accessions was resistant to Fusarium head blight. Many of the accessions tested exhibited heterogeneous reactions (i.e., had both resistant and susceptible plants) to one or more of the diseases, suggesting that heterozygosity may be present at some resistance loci. Substantial variation was observed in the level of diversity to individual diseases because Shannon's Equitability index ranged from 0.116 (for Fusarium head blight) to 0.994 (for tan spot). A high level of diversity was found both between and within collection sites. Moreover, differences in the geographic distribution of resistant accessions were observed. For example, accessions from northern Israel generally were less diverse and less resistant to leaf rust and stripe rust than accessions from more southern locations. Four A. sharonensis accessions were highly resistant to most of the diseases evaluated and may provide a source of unique resistance genes for introgression into cultivated wheat.

Audiometric and imaging characteristics of distal renal tubular acidosis and deafness

Objective:

Primary distal renal tubular acidosis with sensorineural hearing loss is a rare autosomal recessive disease, usually caused by mutations in the ATP6V1B1 gene. The aim of this study was to characterise the phenotype of this disease, with emphasis on the auditory findings, in a cohort of Israeli children.

Study design:

Prospective study of five children, from three unrelated families, with distal renal tubular acidosis and bilateral sensorineural hearing loss, with mutations in the ATP6V1B1 gene.

Methods:

The following were collected from patients' medical records: biochemical and renal data, age at distal renal tubular acidosis diagnosis, and age at hearing loss. Hearing loss progression as well as current hearing status were assessed, and high resolution computed tomography of the temporal bone was performed. All patients underwent genetic testing.

Results:

Four patients were diagnosed with distal renal tubular acidosis before the age of six months and one at 24 months. All had the classical findings of low blood pH and inappropriately high urine pH. Hearing loss was diagnosed between the ages of three months and two years. The hearing loss was bilateral, asymmetrical and progressive, occasionally with a conductive component. Two children underwent cochlear implantation, at ages 10 and 15 years. High resolution computed tomography, performed in four patients between the ages of 2.5 and 15 years, showed bilaterally enlarged vestibular aqueducts. This was the only radiological abnormality in the inner ear in all cases. A different mutation in the ATP6V1B1 gene was found in each family.

Conclusion:

Several types of mutations in the ATP6V1B1 gene may cause distal renal tubular acidosis and sensorineural hearing loss. Patients display a typical progressive type of hearing loss and have enlarged vestibular aqueducts, with no other abnormalities being observed on imaging.

Spatio-temporal genetic variation in populations of wild emmer wheat, Triticum turgidum ssp. dicoccoides, as revealed by AFLP analysis

Genetic structure of natural populations of wild crop relatives has been the subject of many studies. Yet, most of them focused on the assessment of spatial genetic diversity, while information on long-term variation, affected by yearly changes, has been considered only in few cases. The present study aimed therefore, to estimate the spatio-temporal genetic variation in populations of wild emmer wheat, the progenitor of domesticated wheat, and to assess the contribution of spatial versus temporal factors to the maintenance of genetic variation in a population. Single spikes were collected in the years 1988 and 2002 from plants that grew in the same sampling points, from six different habitats in the Ammiad conservation site, Eastern Galilee, Israel. Seeds were planted in a nursery and DNA was extracted from each plant and analyzed by the AFLP method. Fourteen primer combinations yielded 1,545 bands of which 50.0 and 48.8% were polymorphic in the years 1988 and 2002, respectively. Genetic diversity was much larger within populations than between populations and the temporal genetic diversity was considerably smaller than the spatial one. Nevertheless, population genetic structure may vary to some degree in different years, mainly due to fluctuations in population size because of yearly rainfall variations. This may lead to predominance of different genotypes in different years. Clustering the plants by their genetic distances grouped them according to their habitats, indicating the existence of genotype-environment affinities. The significance of the results in relation to factors affecting the maintenance of polymorphism in natural populations is discussed.

Peak bone mass in patients with phenylketonuria

OBJECTIVE

Several studies have suggested a compromised bone mass in phenylketonuria patients but most reported on heterogeneous or small patient groups. Our aim was to evaluate peak bone mass in adult PKU patients and to relate BMD to nutritional parameters.

PATIENTS AND METHODS

BMD was measured by dual-energy x-ray absorptiometry in 31 adult PKU patients (18 female), mean age 25 +/- 5.3 years. Nutritional intake was calculated based on food diaries. Diet adherence was determined based on patients' report.

RESULTS

Mean blood phenylalanine (Phe) concentration was 968 +/- 526 micromol/L (16 +/- 8.7 mg/dl). Eight patients (32.2%) met the recommended blood Phe concentration of <726 micromol/L (<12 mg/dl), and there was no significant difference in Phe concentrations between diet-adherent and non-adherent patients. Osteopenia was detected in 11 patients (38.7%), while osteoporosis was detected in 2 patients (6.5%). No correlation was found between BMD and age, blood minerals, Phe, vitamin D and alkaline phosphatase levels, calcium and protein intake, body mass index, and body fat percentage.

CONCLUSIONS

Peak bone mass is decreased in PKU patients. Possible explanations include long-standing dietary deficiency in protein, calcium, vitamin D or trace elements, or a primary defect in bone turnover inherent to the disease itself. Our data do not favour any of these hypotheses. Further studies are needed to elucidate the cause of low bone density in PKU patients.

Infusion of platelets transiently reduces nucleoside overload in MNGIE

Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) is caused by thymidine phosphorylase (TP) deficiency, which leads to toxic accumulations of thymidine (dThd) and deoxyuridine (dUrd). In this work, we report that infusion of platelets from healthy donors to patients with MNGIE restored transiently circulating TP and reduced plasma dThd and dUrd levels, suggesting that treatments to achieve permanent restoration of circulating TP such as allogeneic stem cell transplantation or gene transfer might be therapeutic.

Spore dimensions of Puccinia species of cereal hosts as determined by image analysis

Digital image analysis was used to measure dimensions of spores produced by Puccinia coronata, P. graminis, P. hordei, P. recondita, P. striiformis and P. triticina. Included were teliospores, basidiospores, urediniospores and, except for P. striiformis, pycniospores and aeciospores. Length, width and projection area of spores were measured with NIH Image or Scion software. By using limits on size, spores were automatically selected and measured, except for teliospores, which required manual elimination of the pedicel and separation of images of adhering spores. Length and width were determined as the major and minor axes of the best fitting ellipse for each spore. This procedure gave values for length and width close to results obtained with an ocular micrometer. Projection area was determined as the number of pixels within spore boundaries multiplied by the area represented by each pixel, giving values that are not feasible to obtain accurately with an ocular micrometer. Of the species studied, spores of P. recondita had the largest dimensions, P. triticina had the smallest. The rank of the six species based on increasing width, length or projection area was almost the same, using each spore type except pycniospores. Generally, differences of 5% in a given spore dimension between two species were significant. Differences between species were greater with basidiospores and aeciospores than with other spore types. Teliospores were unique in that length and width were negatively correlated, resulting in less variation in area than in length or width. The results indicate that image analysis is useful for measuring spore dimensions, that projection area of spores is a useful added parameter for characterizing rust species and that dimensions of teliospores, basidiospores, aeciospores and urediniospores each are potentially useful for differentiating species.

Resistance to Leaf Rust, Stripe Rust, and Stem Rust in Aegilops spp. in Israel

In all, 1,323 single plant accessions of Aegilops bicornis, A. kotschyi, A. longissima, A. ovata, A. searsii, A. sharonensis, A. speltoides, and A. variabilis collected from 18 regions in Israel and 2 adjacent regions in Lebanon and Egypt were evaluated for leaf rust (Puccinia triticina) and stripe rust (P. striiformis) resistance in field plots and for seedling resistance to leaf rust and stem rust (P. graminis f. sp. tritici) in greenhouse tests. Nearly all accessions of A. speltoides were highly resistant to leaf rust, stripe rust, and stem rust. A. longissima and A. ovata were highly resistant to stripe rust, whereas A. bicornis and A. kotschyi were highly susceptible. A. searsii was highly susceptible to stem rust, but 24 to 51% of accessions of A. bicornis, A. longissima, A. ovata, and A. variabilis were resistant to stem rust. Except for A. ovata and A. speltoides, more than 95% of the Aegilops accessions were susceptible to leaf rust caused by P. recondita alternating on Anchusa spp. Only Aegilops ovata was susceptible to P. recondita from Echium spp. A. bicornis, A. koschyi, and A. searsii were highly susceptible as seedlings to common wheat leaf rust caused by P. triticina. Most accessions of A. variabilis and about half of the accessions of A. longissima had good seedling resistance to P. triticina. Few accessions of A. ovata showed seedling resistance to the P. triticina population in Israel, but 30% were resistant to U.S. isolates. In field tests, A. bicornis showed high susceptibility to common wheat leaf rust, but more than 90% of the accessions of the other Aegilops spp. developed little or no leaf rust on adult plants. The Aegilops spp. in Israel and adjoining countries provide a rich and varied source of rust resistance for wheat breeding.

Leaf Rust and Stem Rust Resistance in Triticum dicoccoides Populations in Israel

A total of 742 single plant accessions of Triticum dicoccoides were collected from 26 locations in Israel. All accessions were evaluated for leaf rust (Puccinia triticina) resistance in field plots at Tel Aviv, and subsets of 284 and 468 accessions were tested in the greenhouse in Tel Aviv and St. Paul, MN, respectively, for seedling resistance to leaf rust; 460 accessions were also tested for seedling resistance to stem rust (Puccinia graminis f. sp. tritici) in St. Paul. One accession was highly resistant to leaf rust in seedling tests in Tel Aviv, and 21 others had moderately susceptible to moderately resistant seedling resistance. Four accessions were highly resistant to leaf rust in seedling tests in St. Paul, and 11 were resistant to at least one stem rust race. Adult resistance to leaf rust was more common than seedling resistance among the accessions; 21 accessions had less than 25% leaf rust severity in field plots compared with 80 to 90% severity for highly susceptible accessions. Most of the accessions with effective adult plant resistance came from two nearby locations in Upper Galilee, a region where populations of T. dicoccoides are most extensive and genetically diverse. These accessions may provide valuable new partial resistance genes for durable protection against leaf rust in cultivated wheat.

Virulence associations in oat crown rust

ABSTRACT Isolates of Puccinia coronata obtained from natural populations of Avena sterilis in Israel, winter oat (A. sativa) cultivars in Texas, and spring oat cultivars in the Northern Plains states of Minnesota, North Dakota, and South Dakota were analyzed for significance of pairwise virulence associations. Isolates from all three regions were tested on 25 oat lines with single P. coronata (Pc) genes for crown rust resistance from A. sterilis and one line with a Pc gene from A. sativa. Isolates from Israel were tested also on 11 Iowa backcross lines with undesignated crown rust resistance genes from A. sterilis. Four associated virulence groups were identified from significant positive virulence associations that were consistent across all three regions. Group 38 included virulence to Pc-38, Pc-39, Pc-55, Pc-63, and Pc-71; group 45 included virulence to Pc-45, Pc-46, Pc-48, Pc-52, Pc-54, and Pc-57; group 58 included virulence to Pc-35, Pc-40, Pc-58, and Pc-59; and group 61 included virulence to Pc- 36, Pc-51, Pc-56, Pc-60, and Pc-61. Virulence to Pc-70 showed the strongest association to virulences in group 38 but also showed significant association with virulence to Pc-45, Pc-35, and Pc-58. Virulences in group 61 were consistently negatively associated with virulences in group 38 in each region. In Israel, virulences to five of the Iowa lines showed positive associations to virulences in group 61 and negative associations to virulences in groups 38 and 45. Close similarity of reactions of nearly all isolates to Pc-39, Pc-55, and Pc-71 suggest that these genes may be identical or nearly identical alleles.

Genetic Variation and Virulence on Lr26 in Puccinia triticina

ABSTRACT The genetic relationships between isolates of Puccinia triticina virulent on wheat with the Lr26 resistance gene were studied. The diversity within and between isolates of P. triticina from Israel, Europe, and the United States was determined by virulence on near-isogenic Thatcher lines and by random amplified polymorphic DNA. According to the molecular markers, isolates that were virulent on Lr26 had diversity levels similar to those of Lr26 nonpathogenic isolates. Distances between subpopulations of isolates virulent and avirulent on Lr26 varied and were unrelated to the Lr26 virulence phenotype. Cluster analysis suggested four groups, three of which were closely associated with the geographical origin of the isolates-Israel, the United States, and Europe. All four groups included both Lr26 virulent and avirulent pathotypes. The results showed that Lr26 virulent rust pathotypes are as genetically dissimilar as the rest of the population. The cluster analysis showed that the rust population in Israel includes at least two different subpopulations, both of which contain Lr26 virulent and Lr26 avirulent isolates.

Morphology, life cycle biology, and DNA sequence analysis of rust fungi on garlic and chives from california

ABSTRACT In the late 1990s, commercial garlic fields in California (CA) were devastated by an outbreak of rust caused by Puccinia allii. We compared collections of the pathogen from garlic (Allium sativum) and chives (A. schoenoprasum) in central CA and Oregon (OR) to collections from garlic and leek (A. porrum and A. ampeloprasum) in the Middle East. Teliospores from the CA and OR collections were smaller in length, width, and projected cross-sectional area compared with collections from the Middle East. CA and OR collections had a shortened life cycle, in which pycnia and aecia were not formed. Germinating teliospores produced a two-celled promycelium, resulting in two basidiospores, each initially with two nuclei, indicating that this rust was homothallic. In addition, the morphology of the substomatal vesicles was different between the CA-OR (fusiform) and the Middle Eastern (bulbous) collections. DNA sequence analysis of the nuclear ribosomal internal transcribed spacer region showed that the CA and OR rust collections formed a well-supported cluster distinct from the Middle Eastern and European samples. These results suggest that the rust on garlic and chives in CA and OR is a different species than the rust fungus on garlic and leek in the Middle East.

Patterns of Virulence in Natural Populations of Puccinia coronata on Wild Oat in Israel and in Agricultural Populations on Cultivated Oat in the United States

ABSTRACT Crown rust (Puccinia coronata) in indigenous populations of Avena sterilis has been cited as an example of stability of wild pathosystems that consist of natural mixtures of resistance and virulence. This study confirmed that virulence/avirulence polymorphisms in P. coronata on A. sterilis in Israel are highly diverse and that super races do not dominate. Isolates of P. coronata from Israel in 1991 to 1996 were polymorphic for virulence to 35 of 36 differential oat lines with resistance genes from A. sterilis. On average, isolates of P. coronata were more highly virulent to differentials with Pc genes from A. sterilis accessions from Israel than to differentials with Pc genes from other countries. Isolates from Israel also were more virulent on average to 10 additional differentials with Pc genes derived from A. sativa than to differentials with Pc genes from A. sterilis. Frequencies of virulence were usually higher in collections of P. coronata from Israel than in collections from cultivated oat in the United States, even though several of the Pc genes in the differentials have been used extensively in American oat cultivars. Mean virulence complexity of P. coronata from eight regions of Israel was not correlated with the distribution of resistance among collections of A. sterilis from previous surveys in the same areas, probably because pathogen migration between regions within Israel is sufficient to obscure effects of selection locally.

The influence of space in genetic-environmental relationships when environmental heterogeneity and seed dispersal occur at similar scale

We tested the importance of microenvironmental topographic parameters as predictors of emmer wheat genetic variation using three classes of single-locus (or at most several-loci) genetic markers (allozymes, glutenins, and qualitative traits) and two classes of markers of polygenic inheritance (phenological and morphological traits). Canonical correspondence analysis (CCA) and redundancy analysis (RDA) detected a significant effect of spatially structured environmental variation on genetic differences between plants for allozymes, glutenins, and quantitative morphological and phenological traits. However, after removing a spatial component of variation in partial CCA and partial RDA, the relationship of the remaining environmental variation with these genetic markers could be explained by chance alone, allowing us to rule out microniche topographic specialization in emmer wheat. Topographic autocorrelation exhibited a certain degree of similarity with genetic marker autocorrelation, indicating similar scales of environmental heterogeneity and seed flow. The detected population genetic structure agrees with one expected under isolation by distance as a result of limited gene flow. A negative relationship of genetic similarity with the logarithm of distance between plants was detected for both molecular markers and quantitative traits, which differed in the strength but not the pattern of association.

CTNS mutations in African American patients with cystinosis

Cystinosis, an autosomal recessive lysosomal storage disorder, is rarely diagnosed in African Americans. The disease results from mutations in the gene CTNS; at least 55 such mutations have been reported. By far the most common is a 57,257-bp deletion of Northern European origin encompassing most of the CTNS gene. We performed mutation analysis on DNA from four African American patients with cystinosis. In one individual with classical, nephropathic cystinosis, we identified a new molecular defect, i.e., a homozygous GT-->CC substitution at the +5 position of IVS 5 of CTNS (IVS 5+5 GT-->CC). The out-of-frame splicing of exon 5 creates a null allele consistent with the patient's severe phenotype. Two patients were heterozygous and one homozygous for the common 57-kb deletion allele, reflecting the admixture of African and Northern European gene pools in North America. The two African Americans heterozygous for the 57-kb deletion were also hemizygous for a 928G-->A change, associated with ocular or nonnephropathic cystinosis. These two individuals are the only known African Americans with ocular cystinosis. We conclude that the diagnosis of cystinosis should be entertained in African Americans with symptoms of the disease, and that mutation analysis for the 57-kb deletion should be considered in this group of patients.

A new genetic isolate of gray platelet syndrome (GPS): clinical, cellular, and hematologic characteristics

Gray platelet syndrome (GPS) is a disorder characterized by thrombocytopenia and large platelets that lack alpha granules and their contents. We describe two siblings with GPS who are members of a Moslem Bedouin genetic isolate. The children, an 8-year-old girl and a 5-year-old boy, had characteristic pale blue platelets lacking alpha granules on electron microscopy. Platelet aggregation studies were normal. The girl underwent a bone marrow aspiration and biopsy which showed mild myelofibrosis and extensive emperipolesis, i.e., the passage of other hematopoietic cells through megakaryocytes. Both children lacked high-molecular-weight multimers of von Willebrand factor (vWF) and had reduced activity and antigens of vWf. Platelet activation was approximately normal when ADP was employed as agonist, but significantly impaired using the thrombin receptor-activating peptide (TRAP). These findings are explained in light of the mechanism of action of each agonist. In addition, we propose that the emperipolesis was caused by increased P-selectin in megakaryocytes, and resulted in release of fibroblastic growth factors, explaining the myelofibrosis. The detailed description of these cases provides a basis for future differentiation of the various types of GPS, and for our current attempts to isolate the gene causing GPS in this genetic isolate.

Characterization of the murine gene corresponding to human Hermansky-Pudlak syndrome type 3: exclusion of the Subtle gray (sut) locus

Hermansky-Pudlak syndrome (HPS) consists of oculocutaneous albinism and a bleeding diathesis due to absent platelet dense bodies. In addition to exhibiting considerable phenotypic variation, this autosomal recessive disorder displays locus heterogeneity. One causative gene is HPS1, coding for a protein of unknown function and resulting in HPS-1 disease, common in northwest Puerto Rico. A second HPS-causing gene is ADTB3A, coding for the beta3A subunit of adaptor complex-3 (AP-3, a coat protein complex) and resulting in HPS-2 disease. Each of these HPS subtypes has a murine counterpart, specifically pale ear for HPS-1 and pearl for HPS-2. Recently, the HPS3 gene, responsible for HPS-3 disease in a genetic isolate of central Puerto Rico, was isolated and characterized. Its location on human chromosome 3q24 suggested that the mouse model corresponding to HPS-3 disease might be subtle gray. To examine this possibility, we determined the mouse HPS3 sequence, its genomic organization, and its amino acid sequence, which shares 95.8% identity with the human protein. We demonstrated that the subtle gray mouse produces a normal size and amount of HPS3 mRNA and has an entirely normal sequence in every exon and intron/exon boundary. Furthermore, subtle gray exhibits a normal contingent of platelet dense bodies. Together, these data eliminate subtle gray as a murine model for HPS-3 disease and suggest that other mouse models be examined.

Mutation of a new gene causes a unique form of Hermansky-Pudlak syndrome in a genetic isolate of central Puerto Rico

Hermansky-Pudlak syndrome (HPS) is a rare autosomal recessive disorder characterized by oculocutaneous albinism and a storage pool deficiency due to an absence of platelet dense bodies. Lysosomal ceroid lipofuscinosis, pulmonary fibrosis and granulomatous colitis are occasional manifestations of the disease. HPS occurs with a frequency of one in 1800 in north-west Puerto Rico due to a founder effect. Several non-Puerto Rican patients also have mutations in HPS1, which produces a protein of unknown function. Another gene, ADTB3A, causes HPS in the pearl mouse and in two brothers with HPS-2 (refs. 11,12). ADTB3A encodes a coat protein involved in vesicle formation, implicating HPS as a disorder of membrane trafficking. We sought to identify other HPS-causing genes. Using homozygosity mapping on pooled DNA of 6 families from central Puerto Rico, we localized a new HPS susceptibility gene to a 1.6-cM interval on chromosome 3q24. The gene, HPS3, has 17 exons, and a putative 113.7-kD product expected to reveal how new vesicles form in specialized cells. The homozygous, disease-causing mutation is a large deletion and represents the second example of a founder mutation causing HPS on the small island of Puerto Rico. We also present an allele-specific assay for diagnosing individuals heterozygous or homozygous for this mutation.

Hermansky-Pudlak syndrome and Chediak-Higashi syndrome: disorders of vesicle formation and trafficking

The rare autosomal recessive metabolic disorders Hermanky-Pudlak syndrome (HPS) and Chediak-Higashi syndrome (CHS)share the clinical findings of oculocutaneous albinism and a platelet storage pool deficiency. In addition, HPS exhibits ceroid lipofuscinosis and CHS is characterized by infections and an accelerated phase. The two disorders result from defects in vesicles of lysosomal lineage. Of the two known HPS-causing genes, HPS1 has no recognizable function, while ADTB3A codes for a subunit of an adaptor complex responsible for new vesicle formation from the trans-Golgi network. Other HPS-causing genes are likely to exist. The only known CHS-causing gene, LYST, codes for a large protein of unknown function. In general, HPS appears to be a disorder of vesicle formation and CHS a defect in vesicle trafficking. These diseases and their variants mirror a group of mouse hypopigmentation mutants. The gene productsinvolved will reveal how the melanosome, platelet dense body, and lysosome are formed and trafficked within cells.

Mutation analysis of the MCM gene in Israeli patients with mut(0) disease

Three novel mutations (IVS8+3a --> g, N219Y, and E414X) were identified in 6 unrelated patients with mut(0) methylmalonic aciduria. The presence of a wild-type along with rearranged fragments in homozygotes for the IVS8+3a --> g mutation may contribute to their later age of onset (3-11 months of age). Nonetheless, delayed onset was not associated with better neurological outcome and prolonged survival. The large number of undiagnosed dead sibs in most families suggests that the disease is largely underdiagnosed in this region.

Molecular cloning and characterization of human VPS18, VPS 11, VPS16, and VPS33

In multicellular organisms, the delivery of proteins to lysosomes is essential. Many of the genes necessary for this process have first been identified by their requirement for vacuolar delivery in yeast. A subset of these genes, the four class C vps genes, is necessary for the delivery of endocytic and biosynthetic cargo in yeast, and also in Drosophila. Here, we describe the sequence and expression pattern of four human homologs of these genes. This initial molecular description of these four genes is an important step towards their evaluation as candidate genes that may be involved in the pathogenesis of Hermansky-Pudlak syndrome-related diseases.

Pulmonary dysfunction in adults with nephropathic cystinosis

OBJECTIVE

To characterize the pulmonary dysfunction in patients with nephropathic cystinosis after renal transplantation.

DESIGN

Cross-sectional analysis of consecutive adult patients.

PATIENTS

Twelve adult, nephropathic cystinosis patients and 3 adult, ocular, nonnephropathic cystinosis patients admitted to the National Institutes of Health Clinical Center.

RESULTS

The 12 nephropathic cystinosis patients (age range, 21 to 40 years) showed an extraparenchymal pattern of restrictive lung disease, with inspiratory and expiratory dysfunction. Specifically, the mean FVC was 58% of predicted, the mean FEV(1) was 57% of predicted, and the mean total lung capacity was 66% of predicted, while the mean residual volume was normal. Furthermore, the mean maximal inspiratory pressure for the eight patients tested was 40% of predicted, and the mean maximal expiratory pressure was 26% of predicted. Two patients died of respiratory insufficiency. All the patients had lived at least 17 years, while lacking compliant cystine-depleting therapy with oral cysteamine. Seven patients had a conical chest, restricting excursion, and 10 of the 12 patients had evidence of the myopathy that typifies late cystinosis. In fact, the severity of pulmonary disease correlated directly with the severity of myopathy in our group of 12 patients. In contrast, the lung parenchyma was essentially normal, as gauged by chest radiographs and CT scans of the lung. The three patients with nonnephropathic cystinosis displayed entirely normal pulmonary function.

CONCLUSION

The distal myopathy characteristic of nephropathic cystinosis results in an extraparenchymal pattern of restrictive lung disease in adults who have not received long-term cystine depletion. Whether or not oral cysteamine therapy can prevent this complication remains to be determined.