Meeting the challenge of interpreting high-resolution single nucleotide polymorphism array data in prenatal diagnosis: does increased diagnostic power outweigh the dilemma of rare variants?

OBJECTIVE: Several studies have already shown the superiority of chromosomal microarray analysis (CMA) compared with conventional karyotyping for prenatal investigation of fetal ultrasound abnormality. This study used very high-resolution single nucleotide polymorphism (SNP) arrays to determine the impact on detection rates of all clinical categories of copy number variations (CNVs), and address the issue of interpreting and communicating findings of uncertain or unknown clinical significance, which are to be expected at higher frequency when using very high-resolution CMA. DESIGN: Prospective validation study. SETTING: Tertiary clinical genetics centre. POPULATION: Women referred for further investigation of fetal ultrasound anomaly. METHODS: We prospectively tested 104 prenatal samples using both conventional karyotyping and high-resolution arrays. MAIN OUTCOME MEASURES: The detection rates for each clinical category of CNV. RESULTS: Unequivocal pathogenic CNVs were found in six cases, including one with uniparental disomy (paternal UPD 14). A further four cases had a 'likely pathogenic' finding. Overall, CMA improved the detection of 'pathogenic' and 'likely pathogenic' abnormalities from 2.9% (3/104) to 9.6% (10/104). CNVs of 'unknown' clinical significance that presented interpretational difficulties beyond results from parental investigations were detected in 6.7% (7/104) of samples. CONCLUSIONS: Increased detection sensitivity appears to be the main benefit of high-resolution CMA. Despite this, in this cohort there was no significant benefit in terms of improving detection of small pathogenic CNVs. A potential disadvantage is the high detection rate of CNVs of 'unknown' clinical significance. These findings emphasise the importance of establishing an evidence-based policy for the interpretation and reporting of CNVs, and the need to provide appropriate pre- and post-test counselling.

A fluorescence-based screen for ribosome binding antibiotics.

The development of new antibacterial agents has become necessary to treat the large number of emerging bacterial strains resistant to current antibiotics. Despite the different methods of resistance developed by these new strains, the A-site of the bacterial ribosome remains an attractive target for new antibiotics. To develop new drugs that target the ribosomal A-site, a high-throughput screen is necessary to identify compounds that bind to the target with high affinity. To this end, we present an assay that uses a novel fluorescein-conjugated neomycin (F-neo) molecule as a binding probe to determine the relative binding affinity of a drug library. We show here that the binding of F-neo to a model Escherichia coli ribosomal A-site results in a large decrease in the fluorescence of the molecule. Furthermore, we have determined that the change in fluorescence is due to the relative change in the pK(a) of the probe resulting from the change in the electrostatic environment that occurs when the probe is taken from the solvent and localized into the negative potential of the A-site major groove. Finally, we demonstrate that F-neo can be used in a robust, highly reproducible assay, determined by a Z'-factor greater than 0.80 for 3 consecutive days. The assay is capable of rapidly determining the relative binding affinity of a compound library in a 96-well plate format using a single channel electronic pipette. The current assay format will be easily adaptable to a high-throughput format with the use of a liquid handling robot for large drug libraries currently available and under development.

The course of posttraumatic stress symptoms and functional impairment following a disaster: what is the lasting influence of acute versus ongoing traumatic events and stressors?

PURPOSE: Ongoing traumatic events and stressors, rather than acute sources of trauma, may shape long-term post-disaster mental health. The purpose of this study was to compare the influence of acute hurricane-related exposures and ongoing post-hurricane exposures on the short- and long-term course of posttraumatic stress symptoms (PTSS) and functional impairment (FI). METHODS: A random sample of adults (n = 658) in Galveston and Chambers Counties, Texas, was selected 2-6 months after Hurricane Ike and interviewed 3 times over 18 months. Hurricane-related exposures included traumatic events such as death of a family member due to the hurricane and stressors such as loss/damage to personal property due to the hurricane. Post-hurricane exposures included traumatic events such as sexual assault and stressors such as divorce or serious financial problems. RESULTS: Experiencing an acute hurricane-related traumatic event or stressor was associated with initial post-hurricane PTSS [RR = 1.92 (95% CI = 1.13-3.26) and RR = 1.62 (1.36-1.94), respectively] and FI [RR = 1.76; (1.05-2.97) and RR = 1.74 (1.46-2.08)], respectively, and acute hurricane-related stressors were associated with a higher rate of increase in FI over time [RR = 1.09; (1.01-1.19)]. In contrast, ongoing post-hurricane daily stressors were not associated within initial PTSS and FI, but were associated with PTSS and FI at the second and third interviews. CONCLUSIONS: While immediate postdisaster interventions may influence short-term mental health, investment in the prevention of ongoing stressors may be instrumental to manage long-term mental health status.

Toward in situ monitoring of water contamination by nitroenergetic compounds.

We have previously described the application of novel porous organosilicate materials to the preconcentration of nitroenergetic targets from aqueous solution prior to HPLC analysis. The performance of the sorbents and the advantages of these types of materials over commercially available solid phase extraction sorbents have been demonstrated. Here, the development of systems for application of those sorbents to in situ monitoring is described. Considerations such as column pressure, particulate filtration, and component durability are discussed. The diameter of selected column housings, the sorbent bed depth, and the frits utilized significantly impact the utility of the sorbent columns in the prototype system. The impact of and necessity for improvements in the morphological characteristics of the sorbents as they relate to reduction in column pressure are detailed. The results of experiments utilizing a prototype system are presented. Data demonstrating feasibility for use of the sorbents in preconcentration prior to ion mobility spectrometry is also presented.

Pathogenic aberrations revealed exclusively by single nucleotide polymorphism (SNP) genotyping data in 5000 samples tested by molecular karyotyping.

BACKGROUND: Several recent studies have demonstrated the use of single nucleotide polymorphism (SNP) arrays for the investigation of intellectual disability, developmental delay, autism or congenital abnormalities. In addition to LogR 'copy number' data, these arrays provide SNP genotyping data for gene level autozygosity mapping, estimating low levels of mosaicism, assessing long continuous stretches of homozygosity (LCSH), detection of uniparental disomy, and 'autozygous' regions. However, there remains little specific information on the clinical utility of this genotyping data. METHODS: Molecular karyotyping, using SNP array, was performed on 5000 clinical samples. RESULTS: Clinically significant 'LogR neutral' genotyping abnormalities were detected in 0.5% of cases. Among these were a single case of chimerism, 12 cases with low level chromosome mosaicism, and 11 cases with an LCSH associated with uniparental disomy. In addition, the genotyping data revealed several LCSH associated with clinically relevant 'recessive type' genetic defects. CONCLUSIONS: These results demonstrate the utility of SNP genotyping data for detection of clinically significant abnormalities, including chimerism/mosaicism and recessive Mendelian disorders associated with autozygosity. The incidence of clinically significant low level mosaicism inferred from these cases suggests that this has hitherto been underestimated and chromosome mosaicism frequently occurs in the absence of indicative clinical features. The growing appreciation among clinicians and demand for SNP genotyping data poses significant challenges for the interpretation of LCSH, especially where there is no detailed phenotypic description to direct laboratory analysis. Finally, reporting of unexpected or hidden consanguinity revealed by SNP array analysis raises potential ethical and legal issues.

Case report: renal cell carcinoma segregating with a t(2;3)(q37.3;q13.2) chromosomal translocation in an Ashkenazi Jewish family.

Chromosome translocations involving chromosome 3 have previously been associated with the development of renal cell carcinoma. In this report we describe an Ashkenazi Jewish family with a previously unreported balanced constitutional translocation (t(2;3)(q37.3;q13.2)) segregating with the development of clear cell renal carcinomata in three family members spanning two generations. We outline the difficulties with the clinical utility of this finding for genetic counselling and risk management strategies. We suggest that an additional renal cancer susceptibility gene may exist at 3q13.2, and review known breakpoints in the autosomes which are associated with clear cell renal cell carcinoma.

Biochemical characterization of the type I inositol polyphosphate 4-phosphatase C2 domain.

Inositol polyphosphate 4 phosphatases (IP4Ps) are enzymes involved in the regulation of phosphoinositide 3-kinase lipid signaling. They catalyze the hydrolysis of the 4-position phosphate from phosphatidylinositol 3,4-bisphosphate to phosphatidylinositol 3-phosphate. In this paper we have characterized a lipid binding C2 domain located on the N-terminus of type I IP4Ps. Mutational analysis of the lipid binding loops suggests that Asp61, Asp120, Asp123, Lys122, Arg124 are involved in lipid binding in vitro. In addition, we show that this C2 domain binds calcium but calcium is not involved in lipid binding. This paper provides insight into the mechanism of membrane interaction of IP4Ps.

Substrate specificity and recognition is conferred by the pleckstrin homology domain of the Dbl family guanine nucleotide exchange factor P-Rex2.

Dbl family guanine nucleotide exchange factors (GEFs) are characterized by the presence of a catalytic Dbl homology domain followed invariably by a lipid-binding pleckstrin homology (PH) domain. To date, substrate recognition and specificity of this family of GEFs has been reported to be mediated exclusively via the Dbl homology domain. Here we report the novel and unexpected finding that, in the Dbl family Rac-specific GEF P-Rex2, it is the PH domain that confers substrate specificity and recognition. Moreover, the beta3beta4 loop of the PH domain of P-Rex2 is the determinant for Rac1 recognition, as substitution of the beta3beta4 loop of the PH domain of Dbs (a RhoA- and Cdc42-specific GEF) with that of P-Rex2 confers Rac1-specific binding capability to the PH domain of Dbs. The contact interface between the PH domain of P-Rex2 and Rac1 involves the switch loop and helix 3 of Rac1. Moreover, substitution of helix 3 of Cdc42 with that of Rac1 now enables the PH domain of P-Rex2 to bind this Cdc42 chimera. Despite having the ability to recognize this chimeric Cdc42, P-Rex2 is unable to catalyze nucleotide exchange on Cdc42, suggesting that recognition of substrate and catalysis are two distinct events. Thus substrate recognition can now be added to the growing list of functions that are being attributed to the PH domain of Dbl family GEFs.

Eczema and early solid feeding in preterm infants.

AIMS: To establish whether development of eczema is influenced by feeding practices in preterm infants, while taking account of confounding factors. METHODS: Data were assembled from 257 infants born prematurely and studied to 12 months post-term. Logistic regression analysis was performed to establish the association between feeding practices and eczema, allowing for potential confounding factors including the infants' gender, parental atopic status, social background, and parental smoking habits. RESULTS: For the development of eczema (with or without other symptoms) by 12 months post-term, the introduction of four or more solid foods by or before 17 weeks post-term was a significant risk (odds ratio 3.49). Male infants were at significantly higher risk (odds ratio 1.84). In addition, having non-atopic parents who introduced solid foods before 10 weeks post-term or having at least one atopic parent represented a significant risk scenario (odds ratio 2.94). CONCLUSIONS: Early introduction of a diverse range of solid foods may predispose the preterm infant to eczema development by 12 months post-term. Furthermore, non-atopic parents who practice early as opposed to late introduction of solid foods may be exposing preterm infants to a greater risk of eczema by 12 months post-term.

Factors affecting the introduction of complementary foods in the preterm infant.

OBJECTIVES: The aim of the study was to identify current infant feeding practices among carers of preterm infants. DESIGN: Structured interviews on milk and complementary feeding practices were conducted with mothers of preterm infants at intervals until infants were 12 months corrected age. SETTING: Recruitment took place in three local Surrey hospitals over a 2 y period. SUBJECTS: Two-hundred and fifty-three preterm infants (139 male, 114 female) including 33 sets of twins and three sets of triplets were recruited. RESULTS: Forty-nine percent of the preterm infant group received first solid foods (the commencement of 'weaning') before the current Department of Health (DoH) guideline. The mean+/-s.e.m. weaning age from birth was 17.1+/-0.23 weeks. Ninety-five percent of the infants were weaned before the DoH guideline when the data was examined from term (mean 11.5+/-s.e.m. 0.21 weeks). Twenty-one percent were weaned before the DoH guideline for preterm infants which is that 'the infant weighs at least 5 kg' (mean 5.61+/-s.e.m. 0.01 kg). Human milk-fed infants were significantly lighter at weaning than combined milk-fed infants (5.32+/-0.12 vs 5.72+/-0.01 kg; P<0.05) even though they were weaned at a similar age. Infant formula-fed infants (mean weaning age from term 10.2+/-0.47 weeks) were weaned significantly earlier than both human milk-fed (11.9+/-0.49 weeks; P<0.05) and combined milk-fed (11.9+/-0.25 weeks; P<0.005) infants. CONCLUSIONS: The introduction of complementary foods varied widely between carers of preterm infants and compliance with DoH guidelines was poor. Further studies on preterm infants are necessary to see if weaning practices affect long-term growth and morbidity and to provide a basis for the development of appropriate recommendations. SPONSORSHIP: This work was funded by the MAFF Food Intolerance Programme.

Postdisaster stress in the United States and Mexico: a cross-cultural test of the multicriterion conceptual model of posttraumatic stress disorder.

Data on symptoms of posttraumatic stress disorder (PTSD) were collected 6 months after Hurricanes Paulina (N = 200; Mexico) and Andrew (non-Hispanic n = 270; United States) using the Revised Civilian Mississippi Scale. A 4-factor measurement model that represented the accepted multicriterion conceptualization of PTSD fit the data of the U.S. and Mexican samples equally well. The 4 factors of Intrusion, Avoidance, Numbing, and Arousal correlated significantly and equivalently with severity of trauma in each sample. A single construct explained much of the covariance of the symptom factors in each sample. However, modeling PTSD as a unidimensional construct masked differences between samples in symptom severity. With severity of trauma controlled, the Mexican sample was higher in Intrusion and Avoidance, whereas the U.S. sample was higher in Arousal. The results suggest that PTSD is a meaningful construct to study in Latin American societies.

Genome of the bacterium Streptococcus pneumoniae strain R6.

Streptococcus pneumoniae is among the most significant causes of bacterial disease in humans. Here we report the 2,038,615-bp genomic sequence of the gram-positive bacterium S. pneumoniae R6. Because the R6 strain is avirulent and, more importantly, because it is readily transformed with DNA from homologous species and many heterologous species, it is the principal platform for investigation of the biology of this important pathogen. It is also used as a primary vehicle for genomics-based development of antibiotics for gram-positive bacteria. In our analysis of the genome, we identified a large number of new uncharacterized genes predicted to encode proteins that either reside on the surface of the cell or are secreted. Among those proteins there may be new targets for vaccine and antibiotic development.

Identification of a novel spliceoform of inositol polyphosphate 4-phosphatase type Ialpha expressed in human platelets: structure of human inositol polyphosphate 4-phosphatase type I gene.

Inositol polyphosphate 4-phosphatases (IP4Ps) are enzymes involved in the regulation of phosphoinositide 3-kinase (PI3K) signaling. IP4Ps catalyze the hydrolysis of the D-4 position phosphoester of the PI3K generated lipid second messenger, phosphatidylinositol 3,4-bisphosphate. Western blot analysis detected the expression of a novel 110 kDa form of IP4P type Ialpha in mouse spleen, heart, lung, and uterus. In addition, the 110 kDa form of IP4P type Ialpha was found to be the major form of this enzyme expressed in human platelets, MEG-01 megakaryocytes and Jurkat T-cells. RT-PCR analysis of MEG-01 megakaryocytes and Jurkat T-cells indicates that the 110-kDa form of IP4P Ialpha is derived from an alternatively spliced mRNA that encodes an additional internal domain of 40 amino acids not present in the two previously described brain IP4P Ialpha spliceoforms. The predicted molecular mass of this spliceoform is 109,968 Da, consistent with its apparent molecular mass estimated by Western blot analysis. The novel domain is proline rich and contains a PEST sequence characteristic of proteins that are rapidly degraded by the calpain family of proteases. Analysis of genomic DNA sequence indicates that the IP4P type I gene consists of 25 exons and that this novel spliceoform is obtained as a result of an unusual type of differential splicing involving the use of an alternative 5'-GU donor splice site during the excision of intron 15. In addition, we show that all three known spliceoforms of IP4P Ialpha result from alternative splicing involving exon 15 and 16 indicating that structural variability in this region of the enzyme may be important for its function.

Characterization of an adapter subunit to a phosphatidylinositol (3)P 3-phosphatase: identification of a myotubularin-related protein lacking catalytic activity.

The D3-phosphoinositides act as second messengers by recruiting, and thereby activating, diverse signaling proteins. We have previously described the purification of a rat phosphatidylinositol 3-phosphate [PtdIns(3)P] 3-phosphatase, comprising a heterodimer of a 78-kDa adapter subunit in complex with a 65-kDa catalytic subunit. Here, we have cloned and characterized the cDNA encoding the human 3-phosphatase adapter subunit (3-PAP). Sequence alignment showed that 3-PAP shares significant sequence similarity with the protein and lipid 3-phosphatase myotubularin, and with several other members of the myotubularin gene family including SET-binding factor 1. However, unlike myotubularin, 3-PAP does not contain a consensus HCX(5)R catalytic motif. The 3-PAP sequence contains several motifs that predict interaction with proteins containing Src homology-2 (SH2) domains, phosphotyrosine-binding (PTB) domains, members of the 14-3-3 family, as well as proteins with SET domains. Northern blot analysis identified two transcripts (5.5 kb and 2.5 kb) with highest abundance in human liver, kidney, lung, and placenta. 3-PAP immunoprecipitates isolated from platelet cytosol hydrolyzed the D3-phosphate from PtdIns(3)P and PtdIns 3,4-bisphosphate [PtdIns(3,4)P(2)]. However, insect cell-expressed 3-PAP recombinant protein was catalytically inactive, confirming our prior prediction that this polypeptide represents an adapter subunit.

A qualitative analysis of posttraumatic stress among Mexican victims of disaster.

In unstructured interviews, 24 Mexicans described survivors' responses to disasters in Guadalajara, Jalisco (n = 9), Homestead, Florida (n = 6), and Puerto Angel, Oaxaca (n = 9). This analysis assessed the extent to which symptom descriptions corresponded to the 17 criterion symptoms of PTSD. Nineteen participants (79%) mentioned from 1 to 9 criterion symptoms. Event-related distress, hypervigilance, recurrent recollections, and avoiding reminders were described most often. Only 3 criterion symptoms were never described. Twenty participants (83%) provided 109 separate expressions that could not be classified specifically as criterion symptoms. These phrases were sorted by 9 independent Mexican volunteers and cluster analyzed. Clusters composed of ataques de nervios, depression, lasting trauma, and somatic complaints provided the best description of the data.

Inositol polyphosphate 4-phosphatase type I regulates cell growth downstream of transcription factor GATA-1.

Megakaryocytes lacking transcription factor GATA-1 fail to complete maturation in vivo and hyperproliferate. To define how GATA-1 regulates megakaryocyte cell growth we searched for mRNA transcripts expressed in primary wild-type, but not GATA-1(-), megakaryocytes. One differentially expressed transcript encodes inositol polyphosphate 4-phosphatase type I (4-Ptase I). This enzyme hydrolyses phosphatidylinositol 3,4-bisphosphate and also has lesser activity against soluble analogues of this lipid, inositol 3, 4-bisphosphate and inositol 1,3,4-triphosphate. Reintroduction of 4-Ptase I into both primary GATA-1(-) and wild-type megakaryocytes significantly retards cell growth, suggesting that absence of 4-Ptase I may contribute to the hyperproliferative phenotype of GATA-1(-) megakaryocytes. Overexpression of 4-Ptase I also markedly reduces growth of NIH 3T3 fibroblasts. Taken together, these data indicate that 4-Ptase I is a regulator of cell proliferation.

Help-seeking comfort and receiving social support: the role of ethnicity and context of need.

Examined help-seeking comfort and receiving social support among Latinos, African Americans, and European Americans across two contexts: in a communitywide emergency (Hurricane Andrew) and 2 years later in a nonemergency situation. In general, help-seeking comfort was a strong predictor of received support. Notwithstanding many similarities between the groups, the effects of ethnicity differed according to the context. In emergency, all groups reported similarly high levels of help-seeking comfort and received support. In nonemergency, help-seeking comfort declined for blacks and whites but not for Latinos. Although all ethnic groups reported receiving less social support in nonemergency, the decline in received support across contexts was most dramatic for Latinos. Situational, cultural, and differential resource loss explanations are offered to account for the findings.

Characterological, situational, and behavioral risk factors for motor vehicle accidents: a prospective examination.

The occurrence of motor vehicle accidents (MVAs) was studied prospectively in a sample of 500 drivers aged 19-88. Over a 4-year interval from 1991 to 1995, 36% of these drivers had a minor accident and 9% had a serious (injury-producing) accident. Data collected in 1991 demonstrated that crashes could be predicted from a combination of pre-existing characterological, situational, and behavioral risk factors, and that these risk factors largely explained sex and age differences in accident rates. The best predictors of future MVAs were younger age, high hostility in combination with poor self-esteem, residence in a larger city, recent relocation, high job stress, prior MVAs, and self-reported tendencies to speed and disregard traffic rules. Failure to wear seat belts did not predict accidents but did significantly influence the severity of accidents that did occur; that is, those who had earlier reported using seat belts 'always' were less likely than others to be injured when accidents did occur. Financial stress increased the likelihood of involvement in more serious accidents.

Inhibition of carbohydrate-mediated glucagon-like peptide-1 (7-36)amide secretion by circulating non-esterified fatty acids.

Two studies were performed to assess the entero-insular axis in simple obesity and the possible effect of variations in the level of circulating non-esterified fatty acids (NEFA) on one of the components of the entero-insular axis, glucagon-like peptide-1 [(7-36) amide]. In the first study, we compared the entero-pancreatic hormone response to oral carbohydrate in obese and lean women. Obese subjects demonstrated hyperinsulinaemia and impaired glucose tolerance but this was not associated with an increased secretion of either glucose-dependent insulinotropic polypeptide or glucagon-like peptide-1 (GLP-1). These findings therefore provide no support for the hypothesis that overactivity of the entero-insular axis contributes to the hyperinsulinaemia seen in obesity. Indeed, the plasma GLP-1 response to carbohydrate was markedly attenuated in obese subjects, confirming previous observations. In the second study, in which carbohydrate-stimulated GLP-1 responses were again evaluated in obese and lean women, circulating NEFA levels were modulated using either heparin (to increase serum NEFA) or acipimox (to reduce serum NEFA). Treatment with acipimox resulted in complete suppression of NEFA levels and in a markedly higher GLP-1 response than the response to carbohydrate alone or to carbohydrate plus heparin. We suggest that higher fasting and postprandial NEFA levels in obesity may tonically inhibit nutrient-mediated GLP-1 secretion, and that this results in attenuation of the GLP-1 response to carbohydrate. However, although serum NEFA levels post-acipimox were similarly suppressed in both lean and obese subjects, the GLP-1 response was again significantly lower in obese subjects, suggesting the possibility of an intrinsic defect of GLP-1 secretion in obesity. The reduction of GLP-1 levels in obesity may be important both in relation to its insulinotropic effect and to its postulated role as a satiety factor.