IDENTIFYING GENETIC VARIANTS AND CHARACTERIZING THEIR ROLE IN CLUBFOOT

Clubfoot is a common, complex birth defect affecting 4,000 newborns in the United States and 135,000 world-wide each year. The clubfoot deformity is characterized by inward and rigid downward displacement of one or both feet, along with persistent calf muscle hypoplasia. Despite strong evidence for a genetic liability, there is a limited understanding of the genetic and environmental factors contributing to the etiology of clubfoot. The studies described in this dissertation were performed to identify variants and/or genes associated with clubfoot. Genome-wide linkage scan performed on ten multiplex clubfoot families identified seven new chromosomal regions that provide new areas to search for clubfoot genes. Troponin C (TNNC2) the strongest candidate gene, located in 20q12-q13.11, is involved in muscle contraction. Exon sequencing of TNNC2 did not identify any novel coding variants. Interrogation of fifteen muscle contraction genes found strong associations with SNPs located in potential regulatory regions of TPM1 (rs4075583 and rs3805965), TPM2 (rs2025126 and rs2145925) and TNNC2 (rs383112 and rs437122). In previous studies, a strong association was found with rs3801776 located in the basal promoter of HOXA9, a gene also involved in muscle development and patterning. Altogether, this data suggests that SNPs located in potential regulatory regions of genes involved in muscle development and function could alter transcription factor binding leading to changes in gene expression. Functional analysis of 3801776/HOXA9, rs2025126/TPM2 and rs2145925/TPM2 showed altered protein binding, which significantly influenced promoter activity. Although the ancestral allele (G) of rs4075583/TPM1 creates a DNA-protein complex, it did not affect TPM1 promoter activity. However and importantly, in the context of a haplotype, rs4075583/G significantly decreased TPM1 promoter activity. These results suggest dysregulation of multiple skeletal muscle genes, TPM1, TPM2, TNNC2 and HOXA9, working in concert may contribute to clubfoot. However, specific allelic combinations involving these four regulatory SNPs did not confer a significantly higher risk for clubfoot. Other combinations of these variants are being evaluated. Moreover, these variants may interact with yet to be discovered variants in other genes to confer a higher clubfoot risk. Collectively, we show novel evidence for the role of skeletal muscle genes in clubfoot indicating that there are multiple genetic factors contributing to this complex birth defect.

Determinación de la actividad de la óxido nítrico sintetasa endotelial y del factor NF-kB, en la piel del paciente con pseudoangiomatosis eruptiva : informe preliminar

La pseudoangiomatosis eruptiva se caracteriza por la aparición brusca de múltiples pápulas eritematosas, asintomáticas, rodeadas de un halo blanquecino, con remisión espontánea. Histológicamente se observa dilatación vascular con escaso infiltrado inflamatorio. Su etiología permanece incierta a pesar de ser relacionada con virus o picaduras de insectos. Basados en el compromiso vascular, el objetivo del trabajo fue investigar la actividad de la enzima endotelial oxido nítrico sintetasa (eNOS) y la expresión del factor NF-kB por inmunohistoquimica en un intento de esclarecer su patogenia. Material y métodos: Se estudiaron diez pacientes con diagnóstico clínico de pseudoangiomatosis eruptiva (PAE) que presentaron la dermatosis en forma epidémica. Se realizaron biopsias teñidas con Hematoxilina-Eosina y Tricrómico de Masson. Se efectuó estudio virológico de los pacientes Nª 4, 9 y 10 mediante determinaciones serológicas para echovirus, enterovirus, citomegalovirus, parvovirus B19 y hepatitis A, B y C. En cinco pacientes se obtuvo material para determinación de eNOS y NF-kB. Resultados: Todos los pacientes, 5 hombres y 5 mujeres presentaron pápulas eritematosas rodeadas por un halo blanquecino, especialmente en las extremidades, alrededor de las rodillas. Histológicamente mostraron vasos dilatados y células endoteliales prominentes con un infiltrado discreto perivascular. Todos los estudios serológicos fueron negativos. La actividad de eNOS fue significativamente menor comparada con la piel normal (p= 0,002) y la expresión de NF- ĸB fue fuertemente positiva en los vasos de la dermis papilar y reticular. Conclusiones: Todos los pacientes fueron afectados en verano, por lo que la picadura del mosquito debe ser considerada como un factor etiológico. La baja expresión de eNOS está relacionada con la vasodilatación y la expresión aumentada de NF-ĸB confirma que el proceso es de tipo inflamatorio.

Geochemistry of serpentinized peridotites from ODP Holes 207-1272A and 207-1274A

Despite the key importance of altered oceanic mantle as a repository and carrier of light elements (B, Li, and Be) to depth, its inventory of these elements has hardly been explored and quantified. In order to constrain the systematics and budget of these elements we have studied samples of highly serpentinized (>50%) spinel harzburgite drilled at the Mid-Atlantic Ridge (Fifteen-Twenty Fracture zone, ODP Leg 209, Sites 1272A and 1274A). In-situ analysis by secondary ion mass spectrometry reveals that the B, Li and Be contents of mantle minerals (olivine, orthopyroxene, and clinopyroxene) remain unchanged during serpentinization. B and Li abundances largely correspond to those of unaltered mantle minerals whereas Be is close to the detection limit. The Li contents of clinopyroxene are slightly higher (0.44-2.8 µg/g) compared to unaltered mantle clinopyroxene, and olivine and clinopyroxene show an inverse Li partitioning compared to literature data. These findings along with textural observations and major element composition obtained from microprobe analysis suggest reaction of the peridotites with a mafic silicate melt before serpentinization. Serpentine minerals are enriched in B (most values between 10 and 100 µg/g), depleted in Li (most values below 1 µg/g) compared to the primary phases, with considerable variation within and between samples. Be is at the detection limit. Analysis of whole rock samples by prompt gamma activation shows that serpentinization tends to increase B (10.4-65.0 µg/g), H2O and Cl contents and to lower Li contents (0.07-3.37 µg/g) of peridotites, implying that-contrary to alteration of oceanic crust-B is fractionated from Li and that the B and Li inventory should depend essentially on rock-water ratios. Based on our results and on literature data, we calculate the inventory of B and Li contained in the oceanic lithosphere, and its partitioning between crust and mantle as a function of plate characteristics. We model four cases, an ODP Leg 209-type lithosphere with almost no igneous crust, and a Semail-type lithosphere with a thick igneous crust, both at 1 and 75 Ma, respectively. The results show that the Li contents of the oceanic lithosphere are highly variable (17-307 kg in a column of 1 m * 1 m * thickness of the lithosphere (kg/col)). They are controlled by the primary mantle phases and by altered crust, whereas the B contents (25-904 kg/col) depend entirely on serpentinization. In all cases, large quantities of B reside in the uppermost part of the plate and could hence be easily liberated during slab dehydration. The most prominent input of Li into subduction zones is to be expected from Semail-type lithosphere because most of the Li is stored at shallow levels in the plate. Subducting an ODP Leg 209-type lithosphere would mean only very little Li contribution from the slab. Serpentinized mantle thus plays an important role in B recycling in subduction zones, but it is of lesser importance for Li.

An integrated biostratigraphy (conodonts and foraminifers) and chronostratigraphy (paleomagnetic reversals, magnetic susceptibility, elemental chemistry, carbon isotopes and geochronology) for the Permian-Triassic strata of Guandao section

The chronostratigraphy of Guandao section has served as the foundation for numerous studies of the end-Permian extinction and biotic recovery in south China. Guandao section is continuous from the Permian-Triassic boundary to the Upper Triassic.Conodonts enable broad delineation of stage and substage boundaries and calibration of foraminifer biostratigraphy as follows. Changhsingian- Griesbachian: first Hindeodus parvus, and first appearance of foraminifers Postcladella kalhori and Earlandia sp. Griesbachian-Dienerian: first Neospathodus dieneri, and last appearance of foraminifer P. grandis. Dienerian-Smithian: first Novispathodus waageni and late Dienerian first appearance of foraminifer Hoyenella ex gr. sinensis. Smithian-Spathian: first Nv? crassatus and last appearance of foraminifers Arenovidalina n. sp. and Glomospirella cf. vulgaris. Spathian-Aegean: first Chiosella timorensis and first appearance of foraminifer Meandrospira dinarica. Aegean-Bithynian: first Nicoraella germanica and first appearance of foraminifer Pilammina densa. Bithynian-Pelsonian: after last Neogondolella regalis, prior to first Paragondolella bulgarica and first appearance of foraminifer Aulotortus eotriasicus. Pelsonian-Illyrian: first Pg. excelsa and last appearance of foraminifers Meandrospira ? deformata and Pilamminella grandis. Illyrian-Fassanian: first Budurovignathus truempyi, and first appearance of foraminifers Abriolina mediterranea and Paleolituonella meridionalis. Fassanian-Longobardian: first Bv. mungoensis and last appearance of foraminifer A. mediterranea. Longobardian-Cordevolian: first Quadralella polygnathiformis and last appearance of foraminifers Turriglomina mesotriasica and Endotriadella wirzi. The section contains primary magnetic signature with frequent reversals occurring around the Permian-Triassic, Olenekian-Anisian, and Anisian-Ladinian boundaries. Predominantly normal polarity occurs in the lower Smithian, Bithynian, and Longobardian-Cordevolian. Predominantly reversed polarity occurs in the upper Griesbachian, Induan-Olenekian, Pelsonian and lower Illyrian. Reversals match well with the GPTS. Large amplitude carbon isotope excursions, attaining values as low as -2.9 per mil d13C and high as +5.7 per mil d13C, characterize the Lower Triassic and basal Anisian. Values stabilize around +2 per mil d13C through the Anisian to Carnian. Similar signatures have been reported globally. Magnetic susceptibility and synthetic gamma ray logs show large fluctuations in the Lower Triassic and an overall decline in magnitude of fluctuation through the Middle and Upper Triassic. The largest spikes in magnetic susceptibility and gamma ray, indicating greater terrestrial lithogenic flux, correspond to positive d13C excursions. Several volcanic ash horizons occur in the Lower Triassic and Olenekian-Anisian boundary. High resolution U-Pb analysis of zircons provide a robust age of 247.2 Ma for the Olenekian-Anisian boundary.

Population genetic and dispersal modeling data for Bathymodiolus mussels from the Mid-Atlantic Ridge

The zip folder comprises a text file and a gzipped tar archive. 1) The text file contains individual genotype data for 90 SNPs, 9 microsatellites and the mitochondrial ND4 gene that were determined in deep-sea hydrothermal vent mussels from the Mid-Atlantic Ridge (genus Bathymodiolus). Mussel specimens are grouped according to the population (pop)/location from which they have been sampled (first column). The remaining columns contain the respective allele/haplotype codes for the different genetic loci (names in the header line). The data file is in CONVERT format and can be directly transformed into different input files for population genetic statistics. 2) The tar archive contains NetCDF files with larval dispersal probabilities for simulated annual larval releases between 1998 and 2007. For each simulated vent location (Menez Gwen, Lucky Strike, Rainbow, Vent 1-10) two NetCDF files are given, one for an assumed pelagic larval duration of 1 year and the other one for an assumed pelagic larval duration of 6 months (6m).