R. Scott Winters

THERMAL EFFECTS ON THE ENERGETICS OF LIZARD EMBRYOS: IMPLICATIONS FOR HATCHLING PHENOTYPES

In many ectotherms, incubation temperature has profound effects on the timing of hatching and size of hatchlings, but the mechanisms underlying these effects are poorly understood. We studied the energetics of embryonic development and growth in the lizard Sceloporus undulatus. Eggs were incubated at six constant temperatures, ranging from 288 to 388C, and embryonic metabolism, incubation period, and body size at hatching were determined. The duration of embryonic development decreased significantly from 55 da t 28 8 to 40 da t 32 8C but did not differ significantly between 328 and 348C. Embryos incubated at temperatures above 348C did not survive to hatching. Metabolic rate at specific stages of development (percentage of total incubation period) did not differ among embryos incubated at 288 ,3 0 8, and 348C. As a result, the total amount of energy expended during the incubation period at 288C (2.0 kJ) was greater than that at 308-348C (1.7-1.8 kJ). However, the difference in energy expenditure did not affect body size at hatching; neither snout-vent length nor body mass varied significantly with incubation temperature, and both were the same as those of hatchlings collected in the field. Thus, there was no apparent trade-off between hatching date and body size of lizards at hatching. In a natural population in New Jersey, USA, we quantified soil temperatures at potential nesting sites and studied the thermoregulatory behavior of gravid females to examine the possible consequences of female behavior for hatchling phenotypes. In females and at potential nest sites, embryos would experience temperatures that resulted in high mortality in the laboratory experiment ( .328C). Gravid females had a field body temperature of 33.98C (95% CI 5 0.88C) and selected a body temperature of 33.38C (95% CI 5 1.08C) when placed in thermal gradients in the laboratory. Soil temperatures rose above 328C for several hours each day. Embryos must be able to survive intermittent exposure to tem- peratures that were lethal under conditions of chronic exposure in the laboratory. Selection of relatively high body temperatures by gravid females, coupled with tolerance of acute exposure to relatively high soil temperatures, would reduce the incubation period without a concomitant reduction in body size at hatching.

Simple Algorithms for Complex Relation Extraction with Applications to Biomedical IE

A complex relation is any n-ary relation in which some of the arguments may be be unspecified. We present here a simple two-stage method for extracting complex relations between named entities in text. The first stage creates a graph from pairs of entities that are likely to be related, and the second stage scores maximal cliques in that graph as potential complex relation instances. We evaluate the new method against a standard baseline for extracting genomic variation relations from biomedical text.

Genetic analysis of 14 families with Schnyder crystalline corneal dystrophy reveals clues to UBIAD1 protein function

Schnyder crystalline corneal dystrophy (SCCD) is a rare autosomal dominant disease characterized by progressive corneal opacification resulting from abnormal deposition of cholesterol and phospholipids. Recently, six different mutations on the UBIAD1 gene on chromosome 1p36 were found to result in SCCD. The purpose of this article is to further characterize the mutation spectrum of SCCD and identify structural and functional consequences for UBIAD1 protein activity. DNA sequencing was performed on samples from 36 individuals from 14 SCCD families. One affected individual was African American and SCCD has not been previously reported in this ethnic group. We identified UBIAD1 mutations in all 14 families which had 30 affected and 6 unaffected individuals. Eight different UBIAD1 mutations, 5 novel (L121F, D118G, and S171P in exon 1, G186R and D236E in exon 2) were identified. In four families with DNA samples from both affected and unaffected individuals, the D118G, G186R, T175I, and G177R mutations cosegregated with SCCD. In combination with our previous report, we have identified the genetic mutation in UBIAD1 in 20 unrelated families with 10 (including 5 reported here), having the N102S mutation. The results suggest that N102S may be a mutation hot spot because the affected families were unrelated including Caucasian and Asian individuals. There was no genotype phenotype correlation except for the T175I mutation which demonstrated prominent diffuse corneal haze, typically without corneal crystals. Protein analysis revealed structural and functional implications of SCCD mutations which may affect UBIAD1 function, ligand binding and interaction with binding partners, like apo E.

An entity tagger for recognizing acquired genomic variations in cancer literature

VTag is an application for identifying the type, genomic location and genomic state-change of acquired genomic aberrations described in text. The application uses a machine learning technique called conditional random fields. VTag was tested with 345 training and 200 evaluation documents pertaining to cancer genetics. Our experiments resulted in 0.8541 precision, 0.7870 recall and 0.8192 F-measure on the evaluation set.

me-PCR: a refined ultrafast algorithm for identifying sequence-defined genomic elements

We have adapted the originally described electronic PCR (e-PCR) algorithm to perform string searches more accurately and much more rapidly than previously possible. Our implementation [multithreaded e-PCR (me-PCR)] runs sufficiently fast to allow even desktop machines to query quickly large genomes with very large genomic element sets. In addition, me-PCR is multithreaded, interprets all IUPAC nucleotide symbols, allows searches with elements specified by long sequences (such as SNPs), accepts ranges in the expected PCR size input field, requires substantially less memory for analysis of large sequences and corrects a number of minor flaws causing misreporting of hits in exceptional cases. Thus, me-PCR provides increased annotation capabilities for complex genomes to non-expert laboratories.

Genetic analysis of 14 families with Schnyder crystalline corneal dystrophy reveals clues to UBIAD1 protein function (American Journal of Medical Genetics Part A 146A, (271-283))

Schnyder crystalline corneal dystrophy (SCCD) is a rare autosomal dominant disease characterized by progressive corneal opacification resulting from abnormal deposition of cholesterol and phospholipids. Recently, six different mutations on the UBIAD1 gene on chromosome 1p36 were found to result in SCCD. The purpose of this article is to further characterize the mutation spectrum of SCCD and identify structural and functional consequences for UBIAD1 protein activity. DNA sequencing was performed on samples from 36 individuals from 14 SCCD families. One affected individual was African American and SCCD has not been previously reported in this ethnic group. We identified UBIAD1 mutations in all 14 families which had 30 affected and 6 unaffected individuals. Eight different UBIAD1 mutations, 5 novel (L121F, D118G, and S171P in exon 1, G186R and D236E in exon 2) were identified. In four families with DNA samples from both affected and unaffected individuals, the D118G, G186R, T175I, and G177R mutations cosegregated with SCCD. In combination with our previous report, we have identified the genetic mutation in UBIAD1 in 20 unrelated families with 10 (including 5 reported here), having the N102S mutation. The results suggest that N102S may be a mutation hot spot because the affected families were unrelated including Caucasian and Asian individuals. There was no genotype phenotype correlation except for the T175I mutation which demonstrated prominent diffuse corneal haze, typically without corneal crystals. Protein analysis revealed structural and functional implications of SCCD mutations which may affect UBIAD1 function, ligand binding and interaction with binding partners, like apo E.

From a Monk in His Garden

Gregor Mendel: Planting the Seeds of Genetics. developed by the Field Museum, the Vereinigung zur Förderung der Genomforschung in Vienna, Austria, and the Mendel Museum in Brno, Czech Republic. The Field Museum, Chicago, through 1 April 2007. www.fieldmuseum.org/mendel/ This relatively small exhibition uses artifacts from Mendels life to place his work in context and interactive displays to help explain genetics.

GENETICS: From a Monk in His Garden

Gregor Mendel: Planting the Seeds of Genetics. developed by the Field Museum, the Vereinigung zur Förderung der Genomforschung in Vienna, Austria, and the Mendel Museum in Brno, Czech Republic. The Field Museum, Chicago, through 1 April 2007. www.fieldmuseum.org/mendel/ This relatively small exhibition uses artifacts from Mendels life to place his work in context and interactive displays to help explain genetics.