Genome-wide analysis of copy-number variation in humans with cleft lip and/or cleft palate identifies COBLL1, RIC1, and ARHGEF38 as clefting genes

Cleft lip with or without cleft palate (CL/P) is a common birth defect with a complex, heterogeneous etiology. It is well established that common and rare sequence variants contribute to the formation of CL/P, but the contribution of copy-number variants (CNVs) to cleft formation remains relatively understudied. To fill this knowledge gap, we conducted a large-scale comparative analysis of genome-wide CNV profiles of 869 individuals from the Philippines and 233 individuals of European ancestry with CL/P with three primary goals: first, to evaluate whether differences in CNV number, amount of genomic content, or amount of coding genomic content existed within clefting subtypes; second, to assess whether CNVs in our cohort overlapped with known Mendelian clefting loci; and third, to identify unestablished Mendelian clefting genes. Significant differences in CNVs across cleft types or in individuals with non-syndromic versus syndromic clefts were not observed; however, several CNVs in our cohort overlapped with known syndromic and non-syndromic Mendelian clefting loci. Moreover, employing a filtering strategy relying on population genetics data that rare variants are on the whole more deleterious than common variants, we identify several CNV-associated gene losses likely driving non-syndromic clefting phenotypes. By prioritizing genes deleted at a rare frequency across multiple individuals with clefts yet enriched in our cohort of individuals with clefts compared to control subjects, we identify COBLL1, RIC1, and ARHGEF38 as clefting genes. CRISPR-Cas9 mutagenesis of these genes in Xenopus laevis and Danio rerio yielded craniofacial dysmorphologies, including clefts analogous to those seen in human clefting disorders.

SPECC1L regulates palate development downstream of IRF6

SPECC1L mutations have been identified in patients with rare atypical orofacial clefts and with syndromic cleft lip and/or palate (CL/P). These mutations cluster in the second coiled-coil and calponin homology domains of SPECC1L and severely affect the ability of SPECC1L to associate with microtubules. We previously showed that gene-trap knockout of Specc1l in mouse results in early embryonic lethality. We now present a truncation mutant mouse allele, Specc1lΔC510, that results in perinatal lethality. Specc1lΔC510/ΔC510 homozygotes showed abnormal palate rugae but did not show cleft palate. However, when crossed with a gene-trap allele, Specc1lcGT/ΔC510 compound heterozygotes showed a palate elevation delay with incompletely penetrant cleft palate. Specc1lcGT/ΔC510 embryos exhibit transient oral epithelial adhesions at E13.5, which may delay shelf elevation. Consistent with oral adhesions, we show periderm layer abnormalities, including ectopic apical expression of adherens junction markers, similar to Irf6 hypomorphic mutants and Arhgap29 heterozygotes. Indeed, SPECC1L expression is drastically reduced in Irf6 mutant palatal shelves. Finally, we wanted to determine if SPECC1L deficiency also contributed to non-syndromic (ns) CL/P. We sequenced 62 Caucasian, 89 Filipino, 90 Ethiopian, 90 Nigerian and 95 Japanese patients with nsCL/P and identified three rare coding variants (p.Ala86Thr, p.Met91Iso and p.Arg546Gln) in six individuals. These variants reside outside of SPECC1L coiled-coil domains and result in milder functional defects than variants associated with syndromic clefting. Together, our data indicate that palate elevation is sensitive to deficiency of SPECC1L dosage and function and that SPECC1L cytoskeletal protein functions downstream of IRF6 in palatogenesis.

Genetic Variants and the Cortisol Response in Children: An Exploratory Study

OBJECTIVE

We examined genomic variation potentially associated with the cortisol stress response in children having a painful medical procedure.

DESIGN

Children 4-10 years old having a peripheral intravenous line inserted provided saliva samples for evaluation of the cortisol response as a biological measure of distress: two on the day of the procedure and two at home on a nonstressful day for comparison values. Children and biological parents also provided samples for genotyping of variants with known or suspected association with the cortisol stress response. Analysis included child-only association and family-based transmission disequilibrium tests (TDTs).

RESULTS

Genotype and phenotype data on the cortisol stress response were available from 326 children for child-only association analyses and 376 complete family trios for TDTs. Children were 50% female, an average of 7.5 years old, and mostly (83%) White/non-Hispanic. We identified four single-nucleotide polymorphisms (SNPs) potentially associated with the cortisol stress response: rs1176744 ( HTR3B), rs10062367 ( CRHBP), rs634479 ( OPRM1), and rs8030107 ( NTRK3). Family-based analysis identified a two-SNP haplotype in HTR1B suggestive for association with the cortisol response (rs6296, rs11568817). Allelic TDTs identified rs7897947 ( NFKB2) as potentially related to cortisol response.

CONCLUSIONS

Findings provide preliminary evidence for genes potentially important in cortisol response to an acute stressor in children in the serotonin, dopamine, and brain-derived neurotrophic factor pathways, the hypothalamic-pituitary-adrenal axis, and the inflammatory response. Combined with analyses of related phenotypes and clinical data, these results could help identify patients at increased risk of adverse responses to painful medical procedures who might benefit from tailored interventions.

Identification of 16q21 as a modifier of nonsyndromic orofacial cleft phenotypes

Orofacial clefts (OFCs) are common, complex birth defects with extremely heterogeneous phenotypic presentations. Two common subtypes-cleft lip alone (CL) and CL plus cleft palate (CLP)-are typically grouped into a single phenotype for genetic analysis (i.e., CL with or without cleft palate, CL/P). However, mounting evidence suggests there may be unique underlying pathophysiology and/or genetic modifiers influencing expression of these two phenotypes. To this end, we performed a genome-wide scan for genetic modifiers by directly comparing 450 CL cases with 1,692 CLP cases from 18 recruitment sites across 13 countries from North America, Central or South America, Asia, Europe, and Africa. We identified a region on 16q21 that is strongly associated with different cleft type (P = 5.611 × 10^-8 ). We also identified significant evidence of gene-gene interactions between this modifier locus and two recognized CL/P risk loci: 8q21 and 9q22 (FOXE1) (P = 0.012 and 0.023, respectively). Single nucleotide polymorphism (SNPs) in the 16q21 modifier locus demonstrated significant association with CL over CLP. The marker alleles on 16q21 that increased risk for CL were found at highest frequencies among individuals with a family history of CL (P = 0.003). Our results demonstrate the existence of modifiers for which type of OFC develops and suggest plausible elements responsible for phenotypic heterogeneity, further elucidating the complex genetic architecture of OFCs.

The Use of Variant Maps to Explore Domain-Specific Mutations of FGFR1

Here we describe the genotype-phenotype correlations of diseases caused by variants in Fibroblast Growth Factor Receptor 1 ( FGFR1) and report a novel, de novo variant in FGFR1 in an individual with multiple congenital anomalies. The proband presented with bilateral cleft lip and palate, malformed auricles, and bilateral ectrodactyly of his hands and feet at birth. He was later diagnosed with diabetes insipidus, spastic quadriplegia, developmental delay, agenesis of the corpus callosum, and enlargement of the third cerebral ventricle. We noted the substantial phenotypic overlap with individuals with Hartsfield syndrome, the rare combination of holoprosencephaly and ectrodactyly. Sequencing of FGFR1 identified a previously unreported de novo variant in exon 11 (p.Gly487Cys), which we modeled to determine its predicted effect on the protein structure. Although it was not predicted to significantly alter protein folding stability, it is possible this variant leads to the formation of nonnative intra- or intermolecular disulfide bonds. We then mapped this and other disease-associated variants to a 3-dimensional model of FGFR1 to assess which protein domains harbored the highest number of pathogenic changes. We observed the greatest number of variants within the domains involved in FGF binding and FGFR activation. To further explore the contribution of each variant to disease, we recorded the phenotype resulting from each FGFR1 variant to generate a series of phenotype-specific protein maps and compared our results to benign variants appearing in control databases. It is our hope that the use of phenotypic maps such as these will further the understanding of genetic disease in general and diseases caused by variation in FGFR1 specifically.

Relationship of Genetic Variants With Procedural Pain, Anxiety, and Distress in Children

OBJECTIVE

This study used a candidate gene approach to examine genomic variation associated with pain, anxiety, and distress in children undergoing a medical procedure.

STUDY DESIGN

Children aged 4-10 years having an IV catheter insertion were recruited from three Midwestern children's hospitals. Self-report measures of pain, anxiety, and distress were obtained as well as an observed measure of distress. Samples were collected from children and biological parents for analysis of genomic variation. Genotyped variants had known or suspected association with phenotypes of interest. Analyses included child-only association and family-based transmission disequilibrium tests.

RESULTS

Genotype and phenotype data were available from 828 children and 376 family trios. Children were 50% male, had a mean age of 7.2 years, and were 84% White/non-Hispanic. In family-based analysis, one single-nucleotide polymorphism (SNP; rs1143629, interleukin ( IL1B) 1β) was associated with observed child distress at Bonferroni-corrected levels of significance ( p = .00013), while two approached significance for association with high state anxiety (rs6330 Nerve Growth Factor, Beta Subunit, [ NGFB]) and high trait anxiety (rs6265 brain-derived neurotrophic factor [ BDNF]). In the child-only analysis, multiple SNPs showed nominal evidence of relationships with phenotypes of interest. rs6265 BDNF and rs2941026 cholecystokinin B receptor had possible relationships with trait anxiety in child-only and family-based analyses.

CONCLUSIONS

Exploring genomic variation furthers our understanding of pain, anxiety, and distress and facilitates genomic screening to identify children at high risk of procedural pain, anxiety, and distress. Combined with clinical observations and knowledge, such explorations could help guide tailoring of interventions to limit procedure-related distress and identify genes and pathways of interest for future genotype-phenotype studies.

Expanding the genetic and phenotypic spectrum of popliteal pterygium disorders

The popliteal pterygia syndromes are a distinct subset of the hundreds of Mendelian orofacial clefting syndromes. Popliteal pterygia syndromes have considerable variability in severity and in the associated phenotypic features but are all characterized by cutaneous webbing across one or more major joints, cleft lip and/or palate, syndactyly, and genital malformations. Heterozygous mutations in IRF6 cause popliteal pterygium syndrome (PPS) while homozygous mutations in RIPK4 or CHUK (IKKA) cause the more severe Bartsocas-Papas syndrome (BPS) and Cocoon syndrome, respectively. In this study, we report mutations in six pedigrees with children affected with PPS or BPS. Using a combination of Sanger and exome sequencing, we report the first case of an autosomal recessive popliteal pterygium syndrome caused by homozygous mutation of IRF6 and the first case of uniparental disomy of chromosome 21 leading to a recessive disorder. We also demonstrate that mutations in RIPK4 can cause features with a range of severity along the PPS-BPS spectrum and that mutations in IKKA can cause a range of features along the BPS-Cocoon spectrum. Our findings have clinical implications for genetic counseling of families with pterygia syndromes and further implicate IRF6, RIPK4, and CHUK (IKKA) in potentially interconnected pathways governing epidermal and craniofacial development.

Interferon Regulatory Factor 6 Controls Proliferation of Keratinocytes From Children With Van der Woude Syndrome

OBJECTIVE

Interferon Regulatory Factor 6 (IRF6) is critical for craniofacial development, epidermal differentiation, and tissue repair. IRF6 mutations cause Van der Woude Syndrome (VWS) and Popliteal Pterygium Syndrome. Individuals with VWS exhibit craniofacial anomalies, including cleft lip and palate and lip pits. Furthermore, they have an increased risk for wound-healing complications following surgical repair when compared with patients with nonsyndromic cleft lip and palate (NSCLP). However, nothing is known about the skin of these patients. The objective was to characterize the skin of patients with VWS. We hypothesize that IRF6 is required for proper skin homeostasis in humans.

DESIGN

Discarded tissue from a hip was collected during surgical alveolar bone graft. Samples from children with VWS harboring IRF6 mutations (n = 2) were compared with samples from children with NSCLP (n = 7). Histology was assessed following hematoxylin and eosin staining. The expressions of Proliferating Cell Nuclear Antigen, IRF6, P63, and Keratin 10 were determined by immunofluorescence. Keratinocytes were isolated and their proliferation potential was assessed by colony-forming efficiency assay.

RESULTS

Hip skin from children with VWS showed a thicker epidermis when compared with that from children with NSCLP. Proliferating Cell Nuclear Antigen staining revealed an increase in proliferation in syndromic tissues when compared with controls. However, P63 and Keratin 10 expression were similar between groups. Finally, keratinocytes from VWS showed increased long-term proliferation when compared with NSCLP.

CONCLUSIONS

These results support, in vivo and in vitro, a previously described role for IRF6 in epidermal proliferation in humans. They further demonstrate a critical function for IRF6 in cutaneous homeostasis.

A Genome-wide Association Study of Nonsyndromic Cleft Palate Identifies an Etiologic Missense Variant in GRHL3

Cleft palate (CP) is a common birth defect occurring in 1 in 2,500 live births. Approximately half of infants with CP have a syndromic form, exhibiting other physical and cognitive disabilities. The other half have nonsyndromic CP, and to date, few genes associated with risk for nonsyndromic CP have been characterized. To identify such risk factors, we performed a genome-wide association study of this disorder. We discovered a genome-wide significant association with a missense variant in GRHL3 (p.Thr454Met [c.1361C>T]; rs41268753; p = 4.08 × 10(-9)) and replicated the result in an independent sample of case and control subjects. In both the discovery and replication samples, rs41268753 conferred increased risk for CP (OR = 8.3, 95% CI 4.1-16.8; OR = 2.16, 95% CI 1.43-3.27, respectively). In luciferase transactivation assays, p.Thr454Met had about one-third of the activity of wild-type GRHL3, and in zebrafish embryos, perturbed periderm development. We conclude that this mutation is an etiologic variant for nonsyndromic CP and is one of few functional variants identified to date for nonsyndromic orofacial clefting. This finding advances our understanding of the genetic basis of craniofacial development and might ultimately lead to improvements in recurrence risk prediction, treatment, and prognosis.

Replication of 13q31.1 association in nonsyndromic cleft lip with cleft palate in Europeans

Genome wide association (GWA) studies have successfully identified at least a dozen loci associated with orofacial clefts. However, these signals may be unique to specific populations and require replication to validate and extend findings as a prelude to etiologic SNP discovery. We attempted to replicate the findings of a recent meta-analysis of orofacial cleft GWA studies using four different ancestral populations. We studied 946 pedigrees (3,436 persons) of European (US white and Danish) and Asian (Japanese and Mongolian) origin. We genotyped six SNPs that represented the most significant P-value associations identified in published studies: rs742071 (1p36), rs7590268 (2p21), rs7632427 (3p11.1), rs12543318 (8q21.3), rs8001641 (13q31.1), and rs7179658 (15q22.2). We directly sequenced three non-coding conserved regions 200 kb downstream of SPRY2 in 713 cases, 438 controls, and 485 trios from the US, Mongolia, and the Philippines. We found rs8001641 to be significantly associated with nonsyndromic cleft lip with cleft palate (NSCLP) in Europeans (P-value = 4 × 10(-5), ORtransmission = 1.86 with 95% confidence interval: 1.38-2.52). We also found several novel sequence variants in the conserved regions in Asian and European samples, which may help to localize common variants contributing directly to the risk for NSCLP. This study confirms the prior association between rs8001641 and NSCLP in European populations.

Identification of functional variants for cleft lip with or without cleft palate in or near PAX7, FGFR2, and NOG by targeted sequencing of GWAS loci

Although genome-wide association studies (GWASs) for nonsyndromic orofacial clefts have identified multiple strongly associated regions, the causal variants are unknown. To address this, we selected 13 regions from GWASs and other studies, performed targeted sequencing in 1,409 Asian and European trios, and carried out a series of statistical and functional analyses. Within a cluster of strongly associated common variants near NOG, we found that one, rs227727, disrupts enhancer activity. We furthermore identified significant clusters of non-coding rare variants near NTN1 and NOG and found several rare coding variants likely to affect protein function, including four nonsense variants in ARHGAP29. We confirmed 48 de novo mutations and, based on best biological evidence available, chose two of these for functional assays. One mutation in PAX7 disrupted the DNA binding of the encoded transcription factor in an in vitro assay. The second, a non-coding mutation, disrupted the activity of a neural crest enhancer downstream of FGFR2 both in vitro and in vivo. This targeted sequencing study provides strong functional evidence implicating several specific variants as primary contributory risk alleles for nonsyndromic clefting in humans.

Using zero tillage, fertilisers and legume rotations to maintain productivity and soil fertility in opportunity cropping systems on a shallow Vertosol

The effect of 2 tillage practices (zero v. conventional), fertiliser application (nitrogen, phosphorus and zinc), and pulse–cereal rotation on changes in soil mineral nitrogen, plant-available water in the soil, grain yield and protein, and key soil fertility parameters (total nitrogen, organic carbon) in the Central Highlands of Queensland were examined between 1991 and 1998. Four pasture treatments (perennial legume, perennial grass, annual legume and legume–grass mixes) were included in January 1995, following previously unsuccessful attempts to grow lucerne and annual medics. The experiment was conducted as an opportunity cropping system on an open downs soil at Gindie that is representative of a large proportion (70%) of soils in the Central Highlands. Tillage practice did not affect the amount of mineral nitrate or the plant-available water content of the soil at planting, except in 1991 and 1998 when plant-available water content was higher under conventional tillage than zero tillage. However, zero tillage improved grain yield in 2 of 4 years (wheat in 1992; sorghum in 1996), increased uptake of nitrogen in every crop and produced greater grain protein levels in both wheat crops grown than conventional tillage. There were grain responses to nitrogen + phosphorus fertilisers (wheat in 1991 and sorghum in 1997). Grain protein was increased with applications of nitrogen regardless of whether phosphorus was added in 3 of the 4 crops planted. Sowing a pulse did not significantly increase grain yields in the following crop although it did increase soil mineral nitrogen at planting. Soil nitrate remained low in control (P0N0) plots (<39 kg N/ha) when crops were planted each year but increased significantly (average 84 kg N/ha) following a long fallow of 3.5 years resulting from drought. Plant-available water content of the soil at sowing was lower where chickpeas had been grown the previous season than with wheat. Neither tillage practice nor fertiliser application affected soil organic carbon or soil total nitrogen concentrations in the topsoil. However, all pasture treatments improved soil total nitrogen compared with continuous cropping, and with the exception of annual pasture legumes, also improved soil organic carbon after only 2 seasons. Largest improvements in soil fertility (total nitrogen and organic carbon) occurred with perennial species. It was concluded that zero tillage practices can have beneficial impacts on grain yields as well as minimising environmental degradation such as soil erosion in this region. However, if soil fertility levels are to be maintained, or improved, perennial pasture rotations will need to be used as current levels of fertiliser application or rotations with pulses had no significant beneficial effect.

Legume and opportunity cropping systems in central Queensland. 2. Effect of legumes on following crops

Poor yields and low grain protein in cereal crops resulting from declining soil fertility, especially nitrogen (N), are major threats to the grains industry in central Queensland. The effect of 4 different pasture-ley legumes [siratro (Macroptilium atropurpureum cv. Siratro), lucerne (Medicago sativa cv. Trifecta), lablab (Lablab purpureus cv. Highworth), and desmanthus (Desmanthus virgatus cv. Marc)] on grain yield and quality of sorghum crops was compared with that of a pulse (mungbean; Vigna radiata cv. Satin) or continuous cropping with grain sorghum (Sorghum bicolor). Legume leys consistently resulted in large increases in grain yield (188–272%), N uptake by sorghum (145–345%), and grain protein (0.21–7.0% increase in grain protein) in sorghum test-crops compared with continuous sorghum crops to which no fertiliser N had been added. The positive effect of legumes persisted up to 3 sorghum test-crops after only 1 year of legumes, although by the third year the effect was comparatively small. Mungbean and lablab generally produced the largest benefit in sorghum test-crops in the first year after legumes, whereas desmanthus and lucerne produced the least benefit. Adding fertiliser N (up to 75 kg N/ha) significantly improved grain yields and N uptake of sorghum test-crops in 3 of 4 years. However, responses to fertilisers were less than those resulting from legumes, which was ascribed to increased availability of legume N to sorghum. Legumes progressively increased soil nitrate in all subsequent sorghum test-crops (compared with continuous sorghum crops), rising from 6.8–18.9 kg NO3-N/ha after 1 year of legumes to 24.2–59.6 kg NO3-N/ha after 3 years of legumes. There was little difference between the legumes in their ability to increase soil nitrate, with the exception of desmanthus, which consistently resulted in the lowest amount of soil nitrate for subsequent test-crops and lowest uptake of N by these crops. Plant-available water content (PAWC) at planting of the sorghum test-crop was only significantly (P<0.05) affected by previous species in 1997, when it was lowest in plots previously sown to siratro and lucerne and highest in sorghum and mungbean plots. In both 1996 and 1997, plots sown to sorghum had significantly higher PAWC at anthesis and grain maturity when previous plots were sorghum rather than legumes.

Changes in soil chemical and physical properties following legumes and opportunity cropping on a cracking clay soil

Incorporating legumes into the cropping system has been shown to significantly improve the nitrogen nutrition of cereal crops in Central Queensland. However, little is known about the effect of these legumes on the chemical and physical properties of soil. We examined changes in soil chemical (total nitrogen, organic carbon and pH) and physical (bulk density, cone penetrometer resistance and saturated hydraulic conductivity) properties following either continuous cropping (sorghum or mungbean) or pasture legumes (siratro, lucerne, lablab and desmanthus) over 4 years. Soil carbon was also fractionated using a KMnO4 oxidation procedure which classifies the soil carbon into either labile or non-labile pools. All pasture legumes except desmanthus increased soil total nitrogen in the topsoil (0–10 cm) after only 2 years compared with sorghum. Total nitrogen in the soil did not significantly change under mungbean. Soil organic carbon progressively increased under siratro, desmanthus and sorghum but remained unchanged under the other legumes. Before the experiment, the percentage of total soil carbon classified as labile (oxidised by 333 mmol KMnO4/L) ranged from 14 to 17%. The amount of labile carbon increased by 17% after 3 years of siratro, remained unchanged under desmanthus and sorghum, and decreased under the annual legumes and lucerne. Non-labile carbon remained either unchanged or increased under all legumes, whereas it tended to decrease after 3 consecutive sorghum crops. Soil pH was generally highest under sorghum and lowest under lablab. Soil after sorghum had higher bulk density and penetrometer resistance compared with the effect of legumes but these differences were comparatively small. Saturated hydraulic conductivity of the soil was much higher on the soil surface than at 10 cm. On the surface, soil hydraulic conductivity (saturated) values were generally lower following siratro and higher after sorghum than the other species. At 10 cm depth, soil hydraulic conductivity (saturated) was generally lower in sorghum and, to a lesser extent, in mungbean plots reflecting the significantly lower density of macropores under these crops. It was concluded that although all legumes generally enhanced the chemical and physical properties of the cracking clay, perennial legumes such as siratro would have a greater beneficial effect in the longer term than annual legumes.

Legume and opportunity cropping systems in central Queensland. 1. Legume growth, nitrogen fixation, and water use

An experiment, established on a cracking clay (Vertisol) at Emerald, central Queensland, studied the dry matter (DM) production, nitrogen (N) fixation, and water use of several potential ley-legume species over 4 seasons (1994–1997). Four ley legumes (siratro, Macroptilium atropurpureum cv. Siratro; lucerne, Medicago sativa cv. Trifecta; lablab, Lablab purpureus cv. Highworth; and desmanthus, Desmanthus virgatus cv. Marc) were compared with a pulse (mungbean, Vigna radiata cv. Satin), and grain sorghum (Sorghum bicolor) was included as a non-legume control. Overall, the annual legumes lablab (17.5 t/ha) and mungbean (13.4 t/ha) and the perennial siratro (16.2 t/ha) accumulated more DM than the perennials lucerne (9.6 t/ha) and desmanthus (7.1 t/ha). Lucerne produced little DM in its first year, but in later years had similar production to siratro and lablab. Desmanthus produced >4 t/ha of DM in the first year but barely survived during later seasons. Annual legumes grew faster and exhausted soil water more rapidly than the perennials. The perennials were able to extract more water from the soil than the annual legumes and sorghum, but were inefficient at converting small to moderate rainfall events (25–50 mm) into DM production. During the fallow following the growth of lablab and mungbean, nitrate-N in soil increased and was always greater at the time of re-sowing than for the perennial legumes and sorghum. Initially, the 2 annual legumes derived a high proportion (50% to >70%) of their above-ground N from fixation (%Ndfa) but this declined as the experiment progressed to low values (<13%) in the third and fourth years, reflecting increased supply of nitrate from the soil. In contrast, %Ndfa peaked at 72% for siratro and >90% for lucerne, and remained high (25–50%) throughout the experiment. N fixation rates were strongly negatively correlated with soil nitrate. Over the 4 years, siratro fixed 161 kg N/ha, lucerne 120, lablab 119, mungbean 78, and desmanthus 19 based on above-ground biomass. Mungbean had a net negative N balance (–80 kg N/ha) due to N exported in grain.

Applying nitrogen to grain sorghum in central Queensland: residual value and effect of fallowing and tillage practice

In the northern cereal belt of Australia, farmers are reluctant to apply nitrogen (N) fertilizers because of a perception that if N is added to the soil and no crop is subsequently planted due to lack of rain, the N is 'lost'. An experiment was conducted on a cracking clay soil over three seasons to compare the response of grain sorghum to N applied to the current crop v. N applied the previous season which was then either planted or left fallow (to simulate a missed planting opportunity). Recovery of 15~-labelled fertilizer by the crop and that remaining in the soil were simultaneously determined in microplots. The effect of tillage practice [zero (ZT) and conventional (CT)] was also examined. Sorghum grain yield responded to fresh applications of N in 1993 and 1993194 but not 1992, reflecting the importance of timing of rainfall rather than the total amount received within the season. Applications of N to the current crop always improved yield more than equivalent amounts of N applied to the previous crop. Grain yields of plots that were previously fallowed (fallow-sorghum rotation) were higher than the combined yields of sorghum-sorghum rotations, although fallowing was an inefficient means of accumulating both water and mineral N. Recovery of applied 1 5 ~ by sorghum varied from 48% in 1992 to 36% in 1993 but was not related to the overall N responsiveness of the crop. Sorghum recovered a similar proportion of 1 5 ~ from plots which had been fertilized and then fallowed the previous year compared to fresh applications to the current crop, despite the fallow plots having less 1 5 ~ in them due to losses from the previous season. Losses of 1 5 ~ from the soil/plant system varied markedly with year and appeared to be related to the pattern of rainfall occurring and its possible effect on denitrification. Tillage practice did not affect grain yields or PAWC, had minimal effect on the amount of mineral N present, and little influence on the fertilizer N requirements of sorghum per se. This study suggests that there is only a small residual value to subsequent sorghum crops of fertilizer N if added initially to a successful crop. However, if N is applied pre-plant and the crop is not planted, for example due to lack of planting rain, a large proportion of this N can remain available to the following crop depending on the nature of the subsequent rainfall.

Responses to nitrogen, phosphorus and irrigation by grain sorghum on cracking clay soils in central Queensland

The yield and dry matter (DM) responses to nitrogen (N), phosphorus (P) and irrigation in sorghum hybrids E57 and Goldfinger were measured near Emerald, Queensland, on a cracking clay soil (Ug 5.12) deficient in N and P. A raingrown experiment received factorial combinations of 0, 25, 50 and 75 kg N/ha as urea, and 0, 10, 20 and 40 kg P/ha as superphosphate. An irrigated experiment received the same rates of superphosphate in conjunction with 0, 50, 100 and 150 kg N/ha and irrigation applied at 80 mm deficit. Plants were sampled on days 20 (floral initiation), 41 (early booting), 55-57 (anthesis) and 142 (grain harvest). Factors affecting yields on a soil type fairly representative of a large area of the cultivated soils of the Central Highlands were, in decreasing order of importance, N, water and P. Goldfinger initially produced higher DM yields than E57, but E57 produced higher grain yields. Mean grain yields for the 2 hybrids from control plots were 1150 kg/ha (raingrown) and 1190 kg/ha (irrigated). Under raingrown conditions, a grain yield asymptote (1600 kg/ha) was reached with 50 kg N/ha, but rates higher than 150 kg N/ha (2700 kg/ha) would be required to achieve maximum yields under irrigation. Responses to P were smaller, with rates of 10-20 kg P/ha (raingrown) producing maximum yields for both hybrids. Phosphorus rates greater than 40 kg/ha would be required to achieve maximum yields under irrigation. Apparent recovery of fertiliser P was significantly (P<0.05) lower at the highest P rate of 40 kg/ha at anthesis in the raingrown experiment. All other P recoveries either at anthesis or in the grain were not significantly (P>0.05) different. Phosphorus recoveries between the raingrown and irrigated experiments showed little difference. Nitrogen, however, showed much higher apparent recoveries in the irrigated experiment, with no significant (P>0.05) differences between N treatments. A month after harvest the only plots on the raingrown site with an increase in soil nitrate were the 75 kg N/ha treatments; residual values from all other treatments were low.

Low effectiveness of Duchess rock phosphate on pastures in northern Queensland

Rock phosphate from Duchess, northeastern Australia, and superphosphate were compared as phosphorus (P) sources for pasture in glasshouse and field experiments in northern Queensland. Duchess rock phosphate was an inferior source of P for pastures, compared with superphosphate. The yield response to rock phosphate, however, varied between soils. On strongly acidic soils with high P sorption capacity, rock phosphate increased yield and bicarbonate-extractable P in the soil. On near neutral soils of low P sorption capacity, rock phosphate had little effect on yield. When the rate of rock phosphate was expressed as citrate-soluble P, its performance improved relative to superphosphate. Rates of coarse Duchess rock phosphate need to be at least 10 times those of superphosphate to produce a similar effect on pasture growth. In a glasshouse experiment, the fine rock phosphate was 1.6 times more effective than the coarse material.

Electrophysiologic behavior modification of frontal EMG in cerebral-palsied children

Four cerebral-palsied children participated in the following ABAB design: speech and motor pre-electrophysiologic behavior modification (EMB) evaluation; frontal EMG EMB, six weeks; speech and motor post-EBM evaluation; six weeks no training; speech and motor reevaluation; EMG EBM, four weeks; speech and motor evaluation. Auditory and visual feedback of frontal EMG was monitored by cumulative integration of frontal EMG voltage. The children were shaped by setting a cumulative voltage threshold (CVT). If the child's cumulative integrated frontal EMG voltage fell below the CVT at the end of each 60-sec epoch, a reward was automatically dispensed from a Universal Feeder. Frontal EMG decreased significantly over the initial twelve trials. Correspondingly, improvement was noted for the children in speech and motor skills. Follow-up six weeks later showed increased frontal EMG voltage and deterioration of speech and motor function. Reinstitution of frontal EMG EBM produced reacquisition of low frontal EMG and some recovery of speech and motor function. Collectively, these results indicate that frontal EMG EBM shows promise as an additional treatment modality in the habilitation of cerebral palsy children with spasticity.

Frontal EMG-biofeedback training of athetoid cerebral palsy patients: a report of six cases

Six athetoid cerebral palsy patients participated in the following: speech and motor prebiofeedback training evaluation; frontal EMG biofeedback training, 6 wk; speech and motor postbiofeedback training evaluation. Frontal pretraining levels for the subjects averaged 28.9 muV p-p. Subjects' feedback consisted of an auditory signal (clicks) varying proportionately with frontal EMG activity. A visual meter display of the integrated EMG was also provided. Self-regulation of frontal EMG was evident for all subjects within session 1. Throughout all sessions, EMG levels of 2-4 mu V were often attained. Trend analysis of EMG acquisition curves showed significant reduction in frontal tension across sessions for all but one subject. Frontal posttraining levels averaged 13.0 muV p-p. Parents or subjects, or both, reported subtle improvements in various speech and motor functions, a finding confirmed by objective postbiofeedback training evaluation. Only the 2 most severely impaired subjects, JA and DS, failed to improve significantly on the speech measures. All subjects improved significantly on those measures that tapped fine and gross motor skills. Collectively, these results indicate that EMG biofeedback training shows promise as an additional treatment modality in the habilitation of cerebral palsy patients.