Alpha-thalassemia intellectual disability: variable phenotypic expression among males with a recurrent nonsense mutation - c.109C>T (p.R37X)

Alpha-thalassemia intellectual disability, one of the recognizable X-linked disability syndromes, is characterized by short stature, microcephaly, distinctive facies, hypotonic appearance, cardiac and genital anomalies, and marked skewing of X-inactivation in female carriers. With the advent of next generation sequencing, mutations have been identified that result in less severe phenotypes lacking one or more of these phenotypic manifestations. Here we report five unrelated kindreds in which a c.109C>T (p.R37X) mutation segregates with a variable but overall milder phenotype. The distinctive facial appearance of alpha-thalassemia intellectual disability was present in only one of the 18 affected males evaluated beyond the age of puberty, although suggestive facial appearance was present in several during infancy or early childhood. Although the responsible genetic alteration is a nonsense mutation in exon 2 of ATRX, the phenotype appears to be partially rescued by the production of alternative transcripts and/or other molecular mechanisms.

Considering the Embryopathogenesis of VACTERL Association

The nonrandom co-occurrence of vertebral, anorectal, cardiac, tracheoesophageal, genitourinary, and limb malformations, recognized as the VACTERL association, has not been satisfactorily explained from either a causation or embryopathogenesis standpoint. Few familial cases have been identified and maternal diabetes is the only environmental influence implicated to date. Mutations in single genes have been found in a number of syndromes with one or more of the VACTERL malformations, but these syndromes usually have other features which distinguish them from the VACTERL association. Animal models have provided clues to molecular pathways that may be involved in the embryogenesis of the VACTERL structures. What is lacking is the systematic study of individual genes and pathways in well-composed cohorts of patients, which is now possible with high throughput molecular technologies.

Short-term memory deficits in carrier females with KDM5C mutations

We present the cognitive abilities of females from five families who carry a mutation in a gene (KDM5C, formerly JARIDIC or SMCX) in Xp 11.2 that encodes a transcriptional regulator with histone demethylase activity that is specific for dimethylated and trimethylated H3K4. In this report, the cognitive abilities of females who carry KDMSC mutations are compared to females who carry mutations in other genes known to cause X-linked intellectual and developmental disability (XLIDD) conditions. The KDM5C mutation carriers had higher mean scores on the abstract/visual and quantitative sections of the Stanford-Binet Intelligence Scale: Fourth Edition and lower mean short term memory scores. Implications for counseling are presented.

Phenotype and genotype in mucolipidoses II and III alpha/beta: a study of 61 probands

BACKGROUND

Mucolipidoses II and III alpha/beta (ML II and ML III) are lysosomal disorders in which the essential mannose 6-phosphate recognition marker is not synthesised on to lysosomal hydrolases and other glycoproteins. The disorders are caused by mutations in GNPTAB, which encodes two of three subunits of the heterohexameric enzyme, N-acetylglucosamine-1-phosphotransferase.

OBJECTIVES

Clinical, biochemical and molecular findings in 61 probands (63 patients) are presented to provide a broad perspective of these mucolipidoses.

METHODS

GNPTAB was sequenced in all probands and/or parents. The activity of several lysosomal enzymes was measured in plasma, and GlcNAc-1-phosphotransferase was assayed in leucocytes. Thirty-six patients were studied in detail, allowing extensive clinical data to be abstracted.

RESULTS

ML II correlates with near-total absence of phosphotransferase activity resulting from homozygosity or compound heterozygosity for frameshift or nonsense mutations. Craniofacial and orthopaedic manifestations are evident at birth, skeletal findings become more obvious within the first year, and growth is severely impaired. Speech, ambulation and cognitive function are impaired. ML III retains a low level of phosphotransferase activity because of at least one missense or splice site mutation. The phenotype is milder, with minimal delays in milestones, the appearance of facial coarsening by early school age, and slowing of growth after the age of 4 years.

CONCLUSIONS

Fifty-one pathogenic changes in GNPTAB are presented, including 42 novel mutations. Ample clinical information improves criteria for delineation of ML II and ML III. Phenotype-genotype correlations suggested in more general terms in earlier reports on smaller groups of patients are specified and extended.

Mutations in JARID1C are associated with X-linked mental retardation, short stature and hyperreflexia

BACKGROUND

Mutations in the JARID1C (Jumonji AT-rich interactive domain 1C) gene were recently associated with X-linked mental retardation (XLMR). Mutations in this gene are reported to be one of the relatively more common causes of XLMR with a frequency of approximately 3% in males with proven or probable XLMR. The JARID1C protein functions as a histone 3 lysine 4 (H3K4) demethylase and is involved in the demethylation of H3K4me3 and H3K4me2.

METHODS

Mutation analysis of the JARID1C gene was conducted in the following cohorts: probands from 23 XLMR families linked to Xp11.2, 92 males with mental retardation and short stature, and 172 probands from small XLMR families with no linkage information.

RESULTS

Four novel mutations consisting of two missense mutations, p.A77T and p.V504M, and two frame shift mutations, p.E468fsX2 and p.R1481fsX9, were identified in males with mental retardation. Two of the mutations, p.V504M and p.E468fsX2, are located in the JmjC domain of the JARID1C gene where no previous mutations have been reported. Additional studies showed that the missense mutation, p.V504M, was a de novo event on the grandpaternal X chromosome of the family. Clinical findings of the nine affected males from the four different families included mental retardation (100%), short stature (55%), hyperreflexia (78%), seizures (33%) and aggressive behaviour (44%). The degree of mental retardation consisted of mild (25%), moderate (12%) and severe (63%).

CONCLUSION

Based on the clinical observations, male patients with mental retardation, short stature and hyperreflexia should be considered candidates for mutations in the JARID1C gene.

Ozone uptake (flux) as it relates to ozone-induced foliar symptoms of Prunus serotina and Populus maximowiziixtrichocarpa

Field studies were conducted during 2003 and 2004 from early June to the end of August, at 20 sites of lower or higher elevation within north-central Pennsylvania, using seedlings of black cherry (Prunus serotina, Ehrh.) and ramets of hybrid poplar (Populus maximowiziixtrichocarpa). A linear model was developed to estimate the influence of local environmental conditions on stomatal conductance. The most significant factors explaining stomatal variance were tree species, air temperature, leaf vapor pressure deficit, elevation, and time of day. Overall, environmental factors explained less than 35% of the variation in stomatal conductance. Ozone did not affect gas exchange rates in either poplar or cherry. Ozone-induced foliar injury was positively correlated with cumulative ozone exposures, expressed as SUM40. Overall, the amount of foliar injury was better correlated to a flux-based approach rather than to an exposure-based approach. More severe foliar injuries were observed on plants growing at higher elevations.

Golabi-Ito-Hall syndrome results from a missense mutation in the WW domain of the PQBP1 gene

BACKGROUND

Golabi, Ito, and Hall reported a family with X linked mental retardation (XLMR), microcephaly, postnatal growth deficiency, and other anomalies, including atrial septal defect, in 1984.

METHODS

This family was restudied as part of our ongoing study of XLMR, but significant linkage to X chromosome markers could not be found. Extreme short stature and microcephaly as well as other new clinical findings were observed. Mutations in the polyglutamine tract binding protein 1 gene (PQBP1) have recently been reported in four XLMR disorders (Renpenning, Hamel cerebro-palato-cardiac, Sutherland-Haan, and Porteous syndromes) as well as in several other families. The clinical similarity of our family to these patients with mutations in PQBP1, particularly the presence of microcephaly, short stature, and atrial septal defect, prompted examination of this gene.

RESULTS

A missense mutation in PQBP1 was identified which changed the conserved tyrosine residue in the WW domain at position 65 to a cysteine (p.Y65C).

CONCLUSIONS

This is the first missense mutation identified in PQBP1 and the first mutation in the WW domain of the gene. The WW domain has been shown to play an important role in the regulation of transcription by interacting with the PPxY motif found in transcription factors. The p.Y65C mutation may affect the proper functioning of the PQBP1 protein as a transcriptional co-activator.

Disruption of DMD and deletion of ACSL4 causing developmental delay, hypotonia, and multiple congenital anomalies

We have studied a male patient with significant developmental delay, growth failure, hypotonia, girdle weakness, microcephaly, and multiple congenital anomalies including atrial (ASD) and ventricular (VSD) septal defects. Detailed cytogenetic and molecular analyses revealed three de novo X chromosome aberrations and a karyotype 46,Y,der(X)inv(X) (p11.4q11.2)inv(X)(q11.2q21.32 approximately q22.2)del(X)(q22.3q22.3) was determined. The three X chromosome aberrations in the patient include: a pericentric inversion (inv 1) that disrupted the Duchenne muscular dystrophy (DMD) gene, dystrophin, at Xp11.4; an Xq11.2q21.32 approximately q22.2 paracentric inversion (inv 2) putatively affecting no genes; and an interstitial deletion at Xq22.3 that results in functional nullisomy of several known genes, including a gene previously associated with X-linked nonsyndromic mental retardation, acyl-CoA synthetase long chain family member 4 (ACSL4). These findings suggest that the disruption of DMD and the absence of ACSL4 in the patient are responsible for neuromuscular disease and cognitive impairment.

Physiological and foliar symptom response in the crowns of Prunus serotina, Fraxinus americana and Acer rubrum canopy trees to ambient ozone under forest conditions

The crowns of five canopy dominant black cherry (Prunus serotina Ehrh.), five white ash (Fraxinus americana L.), and six red maple (Acer rubrum L.) trees on naturally differing environmental conditions were accessed with scaffold towers within a mixed hardwood forest stand in central Pennsylvania. Ambient ozone concentrations, meteorological parameters, leaf gas exchange and leaf water potential were measured at the sites during the growing seasons of 1998 and 1999. Visible ozone-induced foliar injury was assessed on leaves within the upper and lower crown branches of each tree. Ambient ozone exposures were sufficient to induce typical symptoms on cherry (0-5% total affected leaf area, LAA), whereas foliar injury was not observed on ash or maple. There was a positive correlation between increasing cumulative ozone uptake (U) and increasing percent of LAA for cherry grown under drier site conditions. The lower crown leaves of cherry showed more severe foliar injury than the upper crown leaves. No significant differences in predawn leaf water potential (psi(L)) were detected for all three species indicating no differing soil moisture conditions across the sites. Significant variation in stomatal conductance for water vapor (g(wv)) was found among species, soil moisture, time of day and sample date. When comparing cumulative ozone uptake and decreased photosynthetic activity (P(n)), red maple was the only species to show higher gas exchange under mesic vs. drier soil conditions (P < 0.05). The inconsistent differences in gas exchange response within the same crowns of ash and the uncoupling relationship between g(wv) and P(n) demonstrate the strong influence of heterogeneous environmental conditions within forest canopies.

Responses of hybrid poplar clones and red maple seedlings to ambient O(3) under differing light within a mixed hardwood forest

The responses of ramets of hybrid poplar (Populus spp.) (HP) clones NE388 and NE359, and seedlings of red maple (Acer rubrum, L.) to ambient ozone (O(3)) were studied during May-September of 2000 and 2001 under natural forest conditions and differing natural sunlight exposures (sun, partial shade and full shade). Ambient O(3) concentrations at the study site reached hourly peaks of 109 and 98 ppb in 2000 and 2001, respectively. Monthly 12-h average O(3) concentrations ranged from 32.3 to 52.9 ppb. Weekly 12-h average photosynthetically active radiation (PAR) within the sun, partial shade and full shade plots ranged from 200 to 750, 50 to 180, and 25 to 75 micromol m(-2) s(-1), respectively. Ambient O(3) exposure induced visible foliar symptoms on HP NE388 and NE359 in both growing seasons, with more severe injury observed on NE388 than on NE359. Slight foliar symptoms were observed on red maple seedlings during the 2001 growing season. Percentage of total leaf area affected (%LAA) was positively correlated with cumulative O(3) exposures. More severe foliar injury was observed on plants grown within the full shade and partial shade plots than those observed on plants grown within the sun plot. Lower light availability within the partial shade and full shade plots significantly decreased net photosynthetic rate (Pn) and stomatal conductance (g(wv)). The reductions in Pn were greater than reductions in g(wv), which resulted in greater O(3) uptake per unit Pn in plants grown within the partial shade and full shade plots. Greater O(3) uptake per unit Pn was consistently associated with more severe visible foliar injury in all species and/or clones regardless of differences in shade tolerance. These studies suggest that plant physiological responses to O(3) exposure are likely complicated due to multiple factors under natural forest conditions.

Influence of light fleck and low light on foliar injury and physiological responses of two hybrid poplar clones to ozone

Five-month old hybrid poplar clones NE388 and NE359 were exposed to square-wave 30, 55, and 80 ppb O(3) (8 h/day, 7 day/week) under constant high light (HL) and light fleck (LF) during 28 May-29 June 1999, and exposed to 30 and 55 ppb O(3) under HL, LF, and constant low light (LL) during 22 May-28 June 2000 within Continuously Stirred Tank Reactors (CSTR) in a greenhouse. Ramets of these two hybrid clones received similar total photosynthetically active radiation (PAR) within the LF and LL treatments. Visible foliar symptoms, leaf gas exchange, and growth were measured. More severe O(3) induced foliar symptoms were observed on ramets within the LF and LL treatments than within the HL treatment for both clones. The LF treatment resulted in significantly greater foliar injury than the LL treatment for NE388. The LF and LL treatments generally resulted in lower photosynthetic rates (Pn) for both clones, but did not affect stomatal conductance (g(wv)); therefore, the ratios of g(wv)/Pn and the O(3) uptake/Pn were greatest in plants grown under the LF treatment, followed by those grown under LL treatment; plants grown under HL had the lowest ratios of g(wv)/Pn and O(3) uptake/Pn. Greater ratios of g(wv)/Pn and O(3) uptake/Pn were consistently associated with more severe visible foliar symptoms. The negative impacts of the LF treatment on growth were greater than those of the LL treatment. Results indicate that not only the integral, but also the pattern of photo flux density, may affect carbon gain in plants. Increased foliar injury may be expected under light fleck conditions due to the limited repair capacity as a result of continuity of O(3) uptake while photosynthesis decreases under LL conditions.

Clinical and molecular contributions to the understanding of X-linked mental retardation

X-linked mental retardation (XLMR) was first recognized in the 1940s, long before any human genes had been mapped. It is now estimated that XLMR has a prevalence of 2.6 cases per 1,000 population, accounting for over 10% of all cases of mental retardation. It is likely that over 150 genes are associated with XLMR. Fragile X syndrome, the most common form of XLMR, has a prevalence of about 1 in 4,000 males. Clinically, XLMR exists in syndromic (mental retardation with other somatic, neurological, behavioral, or metabolic findings) and nonsyndromic (mental retardation without other distinguishing features) forms. However, recent findings have caused this distinction to become blurred as mutations in some genes have been found in both syndromic and nonsyndromic XLMR. Progress in XLMR gene identification has allowed some insight into various pathways and cellular activities involved in developing cognitive functions. The genes involve signaling pathways, transcription factors, cytoskeletal organization, cell adhesion and migration, and maintenance of the cell membrane potential.

Appressorium Formation and Tomato Fruit Infection by Colletotrichum coccodes

Tomato fruit grown for commercial processing are harvested when the majority of the fruit are at the full, red-ripe stage of development. At this physiological stage, marketable yields often are reduced significantly by Colletotrichum coccodes. Appressorium formation and the infection of tomato fruit by C. coccodes were investigated in controlled-environment experiments. Conidia of C. coccodes were subjected to five temperature treatments (10 to 34°C with 6°C increments), and eight incubation periods (3 to 24 h with 3-h increments). The highest proportion of conidia that formed appressoria occurred at 16 and 22°C. Appressoria were formed within as few as 6 h of incubation at 16, 22, and 28°C. In contrast, incubation periods of at least 15 and 18 h were required for appressoria to form at 34 and 10°C, respectively. Appressorium formation was significantly reduced by 0.1 to 0.2 ppm of the fungicide chlorothalonil, and no appressoria formed at concentrations >0.4 ppm. When tomato fruit were inoculated with C. coccodes at three inoculum densities (2 × 10⁵, 6 × 10⁵, and 10 × 10⁵ conidia/ml) and incubated in dew chambers for 8, 16, and 24 h at 5°C increments from 15 to 35°C, there was no significant interaction among inoculum density, dew period, and temperature. In general, across all inoculum densities and dew periods, anthracnose severity levels were greater for each 5°C increase in temperature from 15°C until its maximum level was observed at 30°C. However, when the fruit were exposed to 35°C, disease development was minimal. At temperatures from 15 to 30°C anthracnose severity increased proportionally as dew-period duration and inoculum density increased.

Physiological and foliar injury responses of Prunus serotina, Fraxinus americana, and Acer rubrum seedlings to varying soil moisture and ozone

Sixteen black cherry (Prunus serotina, Ehrh.), 10 white ash (Fraxinus americana, L.) and 10 red maple (Acer rubrum, L.) 1-year old seedlings were planted per plot in 1997 on a former nursery bed within 12 open-top chambers and six open plots. Seedlings were exposed to three different ozone scenarios (ambient air: 100% O3; non-filtered air: 98% ambient O3; charcoal-filtered air: 50% ambient O3) within each of two different water regimes (nine plots irrigated, nine plots non-irrigated) during three growing seasons. During the 1998 and 1999 growing season, leaf gas exchange, plant water relations, and foliar injury were measured. Climatic data,ambient- and chamber-ozone-concentrations were monitored. We found that seedlings grown under irrigated conditions had similar (in 1998) but significantly higher gas exchange rates (in 1999) than seedlings grown within non-irrigated plots among similar ozone exposures. Cherry and ash had similar ozone uptake but cherry developed more ozone-induced injury (< 34% affected leaf area, LAA) than ash (<5% LAA), while maple rarely showed foliar injury, indicating the species differed in ozone sensitivity. Significantly more severe injury on seedlings grown under irrigated conditions than seedlings grown under non-irrigated conditions demonstrated that soil moisture altered seedling responses to ambient ozone exposures.

Use of bioindicators and passive sampling devices to evaluate ambient ozone concentrations in north central Pennsylvania

Ambient concentrations of tropospheric ozone and ozone-induced injury to black cherry (Prunus serotina) and common milkweed (Asclepias syriaca) were determined in north central Pennsylvania from 29 May to 5 September 2000 and from 28 May to 18 September 2001. Ogawa passive ozone samplers were utilized within openings at 15 forested sites of which six were co-located with TECO model 49 continuous ozone monitors. A significant positive correlation was observed between the Ogawa passive samplers and the TECO model 49 continuous ozone monitors for the 2000 (r=0.959) and 2001 (r=0.979) seasons. In addition, a significant positive correlation existed in 2000 and 2001 between ozone concentration and elevation (r=0.720) and (r=0.802), respectively. Classic ozone-induced symptoms were observed on black cherry and common milkweed. In 2000, initial injury was observed in early June, whereas for the 2001 season, initial injury was initially observed in late June. During both seasons, injury was noted at most sites by mid- to late-July. Soil moisture potential was measured for the 2001 season and a significant positive relationship (P<0.001) showed that injury to black cherry was a function of cumulative ozone concentrations and available soil moisture.

A multi-variate statistical model integrating passive sampler and meteorology data to predict the frequency distributions of hourly ambient ozone (O3) concentrations

A multi-variate, non-linear statistical model is described to simulate passive O3 sampler data to mimic the hourly frequency distributions of continuous measurements using climatologic O3 indicators and passive sampler measurements. The main meteorological parameters identified by the model were, air temperature, relative humidity, solar radiation and wind speed, although other parameters were also considered. Together, air temperature, relative humidity and passive sampler data by themselves could explain 62.5-67.5% (R(2)) of the corresponding variability of the continuously measured O3 data. The final correlation coefficients (r) between the predicted hourly O3 concentrations from the passive sampler data and the true, continuous measurements were 0.819-0.854, with an accuracy of 92-94% for the predictive capability. With the addition of soil moisture data, the model can lead to the first order approximation of atmospheric O3 flux and plant stomatal uptake. Additionally, if such data are coupled to multi-point plant response measurements, meaningful cause-effect relationships can be derived in the future.

Cognitive function in Coffin-Lowry syndrome

Coffin-Lowry syndrome (CLS) is an X-linked disorder associated with mental retardation, distinctive facies and hands, hypotonia, and skeletal abnormalities. The syndrome results from mutations in the RSK2 gene located in Xp22.2. Although the syndrome has been elucidated clinically, few, if any, studies have focused on the cognitive deficits of the affected males or carrier females. The subjects of the present study were selected from two African-American families who have the same missense mutation (C340T) in RSK2. The subjects included six affected males, seven carrier females, three normal males and three non-carrier (normal) females. Normal family members served as contrast/comparison cohorts to control for socio-economic, sociocultural and genetic variables which would impinge on intellectual abilities. Analysis of cognitive function, as measured by the Stanford-Binet Intelligence Scale, 4th edn, demonstrated a distinct hierarchy of abilities from normal to carrier to affected patients. The mean composite IQs of the cohorts were 90.8, 65.0 and 43.2 for normal, carrier and affected individuals, respectively. These findings lend support to the clinical concept of negative intellectual effects in carriers of certain X-linked mental retardation conditions. X-inactivation studies showed that carrier females had mild to significant skewing. Normal females in the family did not demonstrate skewing. The correlation coefficient between IQ and X-inactivation status among carriers was not significant.