Strong association of de novo copy number mutations with autism

We tested the hypothesis that de novo copy number variation (CNV) is associated with autism spectrum disorders (ASDs). We performed comparative genomic hybridization (CGH) on the genomic DNA of patients and unaffected subjects to detect copy number variants not present in their respective parents. Candidate genomic regions were validated by higher-resolution CGH, paternity testing, cytogenetics, fluorescence in situ hybridization, and microsatellite genotyping. Confirmed de novo CNVs were significantly associated with autism (P = 0.0005). Such CNVs were identified in 12 out of 118 (10%) of patients with sporadic autism, in 2 out of 77 (3%) of patients with an affected first-degree relative, and in 2 out of 196 (1%) of controls. Most de novo CNVs were smaller than microscopic resolution. Affected genomic regions were highly heterogeneous and included mutations of single genes. These findings establish de novo germline mutation as a more significant risk factor for ASD than previously recognized.     

A genomic regulatory network for development

Development of the body plan is controlled by large networks of regulatory genes. A gene regulatory network that controls the specification of endoderm and mesoderm in the sea urchin embryo is summarized here. The network was derived from large-scale perturbation analyses, in combination with computational methodologies, genomic data, cis-regulatory analysis, and molecular embryology. The network contains over 40 genes at present, and each node can be directly verified at the DNA sequence level by cis-regulatory analysis. Its architecture reveals specific and general aspects of development, such as how given cells generate their ordained fates in the embryo and why the process moves inexorably forward in developmental time.     

Tay-Sachs disease: prenatal diagnosis

Fifteen pregnant women with a 25 percent risk of delivering a child with Tay-Sachs disease were monitored by amniocentesis and hexosaminidase A assays of amniotic fluid, uncultured amniotic cells, and cultured amniotic cells. Tay-Sachs disease was diagnosed prenatally in six fetuses; the diagnosis was confirmed in one child after birth and in five fetuses after therapeutic abortion. Prenatal diagnosis indicated the absence of Tay-Sachs disease in nine other fetuses; this diagnosis was confirmed postnatally in six, three are still in utero.     

The mosquito genome--a breakthrough for public health

The Anopheles gambiae genome sequence will accelerate identification of new insect vector target genes leading to improved strategies for malaria control.     

Atmospheric deposition sampler intercomparison

Two wet/dry atmospheric deposition sampler types were compared for 1 yr. The resistance required to open each of ten collectors was determined. Additionally, the opening and closing history of each sampler was recorded using a microdatalogger with a resolution of 1 min. The frequency distribution of amount of time that a collector was open was used to evaluate the comparability of opening and closing of each collector. Weekly amounts of rainfall for each of the collectors was used to determine the efficiency of collection as compared to a Belfort 5–780 weighing rain gauge. The performance of a collector as determined by the efficiency of collection and also by the distribution of frequencies of times that a sampler was exposed to precipitation were statistically different for the different sampler configurations. Disclaimer. Publication, does not signify that the contents necessarily reflect the views and policies of Department of the Army and the US Military Academy, nor does mention of trade names or commerical products constitute endorsement or recommendation for use. Not subject to copyright restrictions, work of US Government.     

The stability of hydrogen ion and specific conductance in filtered wet-deposition samples stored at ambient temperatures

Separate experiments by the U.S. Geological Survey (USGS) and the Illinois State Water Survey Central Analytical Laboratory (CAL) independently assessed the stability of hydrogen ion and specific conductance in filtered wet-deposition samples stored at ambient temperatures. The USGS experiment represented a test of sample stability under a diverse range of conditions, whereas the CAL experiment was a controlled test of sample stability. In the experiment by the USGS, a statistically significant (α=0.05) relation between [H⁺] and time was found for the composited filtered, natural, wet-deposition solution when all reported values are included in the analysis. However, if two outlying pH values most likely representing measurement error are excluded from the analysis, the change in [H⁺] over time was not statistically significant. In the experiment by the CAL, randomly selected samples were reanalyzed between July 1984 and February 1991. The original analysis and reanalysis pairs revealed that [H⁺] differences, although very small, were statistically different from zero, whereas specific-conductance differences were not. Nevertheless, the results of the CAL reanalysis project indicate there appears to be no consistent, chemically significant degradation in sample integrity with regard to [H⁺] and specific conductance while samples are stored at room temperature at the CAL. Based on the results of the CAL and USGS studies, short-term (45–60 day) stability of [H⁺] and specific conductance in natural filtered wet-deposition samples that are shipped and stored unchilled at ambient temperatures was satisfactory.     

Quantification of Aluminum-Induced Changes in Wheat Root Architecture by X-ray Microcomputed Tomography

Root architectural traits are of fundamental importance for plant performance, especially under unfavorable soil conditions. This study examined the effect of aluminum (Al) toxicity in different growing media (nutrient solutions and soil) on root architecture of two wheat (Triticum aestivum L.) cultivars with different Al tolerances. Seedlings were grown in acidic and limed soil and in two contrasting nutrient solutions. Root systems of soil-grown plants were scanned using x-ray microcomputed tomography (µCT) while that of nutrient solution–grown plants were assesses using WinRhizo, 3 and 5 days after planting (DAP), respectively. Aluminum caused significant reduction of all examined root traits (number of seminal roots, root length, length of the longest seminal root, root surface area, and root volume). Growth in acidic soil caused significant reduction in root length, length of the longest seminal root, and root surface area at 5 DAP. Soil-grown plants produced a larger root system compared to plants grown in nutrient solutions. Aluminum toxicity–induced differences of root traits were also found between different nutrient solutions. Beside the well-known reduction of root length, Al toxicity had a profound effect on other root architectural traits. X-ray µCT has revealed root architectural changes under specific conditions of acidic, Al-toxic soil. Differences obtained in Al-induced effects on root architecture between different nutrient solutions as well as between different growing systems emphasize the need for further study of root architecture, especially under specific conditions of Al toxicity in acidic soils.     

Reciprocal recurrent selection applied to Coffea canephora Pierre

Summary Genetic parameters were estimated in trials planted in connection with a reciprocal recurrent selection programme applied to Coffea canephora in Côte d'Ivoire. Narrow sense heritability values, estimated from a breakdown of the analysis of variance, were high for architectural characters (0.22 to 0.78) and medium for tree vigour (0.13 to 0.40) and for bean weight (0.15 to 0.28). Calculated heritability values for the first two harvests were high (h²>0.7), but much lower for the following harvests (less than 0.2). Heritability estimates by parent-offspring regressions gave variable results, though they were often similar to those obtained by variance analysis, especially for bean weight. Phenotypic and genetic correlations between tree vigour traits and productivity were high. Bean weight was not correlated with vigour or production. Canopy diameter of 4 year-old trees was closely correlated with cumulated productivity from 2 to 5 years in the absence of development competition between trees, but the correlation was low if trees were in competition with each other. The consequences of the results for the choice of characters to be selected among intergroup hybrids or the parents of both populations are discussed.