Results of Genome-Wide Analyses on Neurodevelopmental Phenotypes at Four-Year Follow-Up following Cardiac Surgery in Infancy

Background

Adverse neurodevelopmental sequelae are reported among children who undergo early cardiac surgery to repair congenital heart defects (CHD). APOE genotype has previously been determined to contribute to the prediction of these outcomes. Understanding further genetic causes for the development of poor neurobehavioral outcomes should enhance patient risk stratification and improve both prevention and treatment strategies.

Methods

We performed a prospective observational study of children who underwent cardiac surgery before six months of age; this included a neurodevelopmental evaluation between their fourth and fifth birthdays. Attention and behavioral skills were assessed through parental report utilizing the Attention Deficit-Hyperactivity Disorder-IV scale preschool edition (ADHD-IV), and Child Behavior Checklist (CBCL/1.5-5), respectively. Of the seven investigated, three neurodevelopmental phenotypes met genomic quality control criteria. Linear regression was performed to determine the effect of genome-wide genetic variation on these three neurodevelopmental measures in 316 subjects.

Results

This genome-wide association study identified single nucleotide polymorphisms (SNPs) associated with three neurobehavioral phenotypes in the postoperative children ADHD-IV Impulsivity/Hyperactivity, CBCL/1.5-5 PDPs, and CBCL/1.5-5 Total Problems. The most predictive SNPs for each phenotype were: a LGALS8 intronic SNP, rs4659682, associated with ADHD-IV Impulsivity (P = 1.03×10⁻⁶); a PCSK5 intronic SNP, rs2261722, associated with CBCL/1.5-5 PDPs (P = 1.11×10⁻⁶); and an intergenic SNP, rs11617488, 50 kb from FGF9, associated with CBCL/1.5-5 Total Problems (P = 3.47×10⁻⁷). 10 SNPs (3 for ADHD-IV Impulsivity, 5 for CBCL/1.5-5 PDPs, and 2 for CBCL/1.5-5 Total Problems) had p<10⁻⁵.

Conclusions

No SNPs met genome-wide significance for our three neurobehavioral phenotypes; however, 10 SNPs reached a threshold for suggestive significance (p<10⁻⁵). Given the unique nature of this cohort, larger studies and/or replication are not possible. Studies to further investigate the mechanisms through which these newly identified genes may influence neurodevelopment dysfunction are warranted.     

DNA barcoding the native flowering plants and conifers of Wales

We present the first national DNA barcode resource that covers the native flowering plants and conifers for the nation of Wales (1143 species). Using the plant DNA barcode markers rbcL and matK, we have assembled 97.7% coverage for rbcL, 90.2% for matK, and a dual-locus barcode for 89.7% of the native Welsh flora. We have sampled multiple individuals for each species, resulting in 3304 rbcL and 2419 matK sequences. The majority of our samples (85%) are from DNA extracted from herbarium specimens. Recoverability of DNA barcodes is lower using herbarium specimens, compared to freshly collected material, mostly due to lower amplification success, but this is balanced by the increased efficiency of sampling species that have already been collected, identified, and verified by taxonomic experts. The effectiveness of the DNA barcodes for identification (level of discrimination) is assessed using four approaches: the presence of a barcode gap (using pairwise and multiple alignments), formation of monophyletic groups using Neighbour-Joining trees, and sequence similarity in BLASTn searches. These approaches yield similar results, providing relative discrimination levels of 69.4 to 74.9% of all species and 98.6 to 99.8% of genera using both markers. Species discrimination can be further improved using spatially explicit sampling. Mean species discrimination using barcode gap analysis (with a multiple alignment) is 81.6% within 10×10 km squares and 93.3% for 2×2 km squares. Our database of DNA barcodes for Welsh native flowering plants and conifers represents the most complete coverage of any national flora, and offers a valuable platform for a wide range of applications that require accurate species identification.     

Permissible variation in the 3' non-coding region of the haemagglutinin genome segment of the H5N1 candidate influenza vaccine virus NIBRG-14 [corrected

The candidate H5N1 vaccine virus NIBRG-14 was created in response to a call from the World Health Organisation in 2004 to prepare candidate vaccine viruses (CVVs) to combat the threat of an H5N1 pandemic. NIBRG-14 was created by reverse genetics and is composed of the neuraminidase (NA) and modified haemagglutinin (HA) genes from A/Vietnam/1194/2004 and the internal genes of PR8, a high growing laboratory adapted influenza A(H1N1) strain. Due to time constraints, the non-coding regions (NCRs) of A/Vietnam/1194/2004 HA were not determined prior to creating NIBRG-14. Consequently, the sequence of the primers used to clone the modified A/Vietnam/1194/2004 HA was based upon previous experience of cloning H5N1 viruses. We report here that the HA 3' NCR sequence of NIBRG-14 is different to that of the parental wild type virus A/Vietnam/1194/2004; however this does not appear to impact on its growth or antigen yield. We introduced additional small changes into the 3'NCR of NIBRG-14; these had only minor effects on viral growth and antigen content. These findings may serve to assure the influenza vaccine community that generation of CVVs using best-guess NCR sequences, based on sequence alignments, are likely to produce robust viruses.     

Evolutionary associations between nectar properties and specificity in bird pollination systems

A long-standing paradigm in biology has been that hummingbirds and passerine birds select for different nectar properties in the plants they pollinate. Here we show that this dichotomy is false and a more useful distinction is that between specialized and generalized bird pollination systems. Flowers adapted for sunbirds, which are specialized passerine nectarivores, have nectar similar to that of hummingbird flowers in terms of volume (approx. 10-30 microl), concentration (approx. 15-25% w/w) and sucrose content (approx. 40-60% of total sugar). In contrast, flowers adapted to generalized bird pollinators are characterized by large volumes (approx. 40-100 microl) of extremely dilute (approx. 8-12%) nectar with minimal sucrose (approx. 0-5%). These differences in nectar traits are highly significant even when statistical analyses are based on phylogenetically separate pairwise comparisons between taxa. We present several hypotheses for the association between nectar properties and specificity in bird pollination systems.     

Bees get a head start on honey production

Nectar concentration is assumed to remain constant during transport by honeybees between flowers and hive. We sampled crop contents of nectar foragers on Aloe greatheadii var. davyana, a major winter bee plant in South Africa. The nectar is dilute (approx. 20% w/w), but the crop contents of bees captured on flowers are significantly more concentrated. In returning foragers, the concentration increases further to 38–40%, accompanied by a volume decrease. The doubling of sugar concentration suggests that nectar is regurgitated onto the tongue and evaporated during foraging and on the return flight. Processing of the dilute nectar into honey thus begins early, aided by low ambient humidities. This has implications for honeybee thermoregulation, water balance and energetics during foraging, and for the communication of nectar quality to recruits.     

How important is the relationship between Protea humiflora (Proteaceae) and its non-flying mammal pollinators?

The interaction between Protea humiflora and its non-flying mammal pollinators was investigated with the aim of quantifying the relationship for both the plants and mammals involved. We manipulated flower density by inflorescence removal and determined the effect upon mammal captures, and excluded mammals to determine their effect upon seed set. Of three mammal species captured frequently, the smallest, Acomys subspinosus (18dž SD g, Rodentia: Muridae), demonstrated the strongest relationship with P. humiflora. Breeding coincided with flowering, and pollen constituted 33.5ᆯ.5% by volume (max 80%, n=19) of winter scats. Acomys captures on control grids were twice those on inflorescence-removal grids during flowering. Aethomys namaquensis (51ᆢ g, Rodentia: Muridae) included flower products in its diet (pollen comprising 3.2dž.9% of winter scats, n=73), but captures were not affected by inflorescence removal. Aethomys is a seasonal breeder and juveniles entered the population 2 months after flowering. Elephantulus edwardii, although an insectivore (48lj g, Macroscelidea: Macroscelididae), carried more pollen grains on its nose than the rodents, acquired while foraging in inflorescences for insects. Pollen comprised 3.1LJ.4% (n=23) of winter scats. From the plant perspective, seed set was significantly reduced in caged inflorescences and in those >20 cm above the ground, presumably due to limited accessibility by terrestrial animals. We conclude that small mammals are responsible for around half (56%) of the effective seed set in P. humiflora.     

Effectiveness of appropriately trained nurses in preoperative assessment: randomised controlled equivalence/non-inferiority trial

ObjectiveTo determine whether preoperative assessments carried out by appropriately trained nurses are inferior in quality to those carried out by preregistration house officers.DesignRandomised controlled equivalence/non-inferiority trial.SettingFour NHS hospitals in three trusts. Three of the four were teaching hospitals.ParticipantsAll patients attending for assessment before general anaesthesia for general, vascular, urological, or breast surgery between April 1998 and March 1999.InterventionAssessment by one of three appropriately trained nurses or by one of several preregistration house officers.Results1907 patients were randomised, and 1874 completed the study; 926 were assessed by house officers and 948 by nurses. Overall 121/948 (13%) assessments carried out by nurses were judged to have possibly affected management compared with 138/926 (15%) of those performed by house officers. Nurses were judged to be non-inferior to house officers in assessment, although there was variation among them in terms of the quality of history taking. The house officers ordered considerably more unnecessary tests than the nurses (218/926 (24%) v 129/948 (14%).ConclusionsThere is no reason to inhibit the development of nurse led preoperative assessment provided that the nurses involved receive adequate training. However, house officers will continue to require experience in preoperative assessment.     

Estimating glycoprotein carbohydrate chain structures by lectin reactivities in polyacrylamide gels

Complex mixtures of cellular glycoproteins contain a myriad of different carbohydrate chains that cannot be easily analyzed without rigorous purification of each individual glycoprotein. We have analyzed the carbohydrate chains in complex mixtures of cellular glycoproteins by separation using sodium dodecyl-sulfate polyacrylamide gel electrophoresis and interacting the gels with several 125I-labeled lectins. By use of in situ chemical modifications of the glycoproteins after their electrophoretic separation together with the known carbohydrate-binding specifities of several lectins, it has been possible to estimate glycoprotein carbohydrate chain structures. As an example we have examined the cellular glycoproteins of a ovary-colonizing metastatic variant of B16 melanoma and report the types of carbohydrate chains that are found on various melanoma glycoproteins.     

Diuresis in the cabbage white butterfly, Pieris brassicae: Water and ion regulation and the rôle of the hindgut

The significance of diuresis in the water and ion balance of newly emerged Pieris was examined by comparing the composition of haemolymph and urine during diuresis. The high potassium content of the urine results in a marked increase in the Na/K ratio of the haemolymph. The haemolymph osmolarity is well regulated, in spite of the very hypo-osmotic urine. By means of an isolated preparation of the ileum, it was shown that rapid resorption of potassium ions by this part of the hindgut is responsible for the low osmolarity of the urine.