Analysis of genome-wide DNA arrays reveals the genomic population structure and diversity in autochthonous Greek goat breeds.

Goats play an important role in the livestock sector in Greece. The national herd consists mainly of two indigenous breeds, the Eghoria and Skopelos. Here, we report the population structure and genomic profiles of these two native goat breeds using Illumina's Goat SNP50 BeadChip. Moreover, we present a panel of candidate markers acquired using different genetic models for breed discrimination. Quality control on the initial dataset resulted in 48,841 SNPs kept for downstream analysis. Principal component and admixture analyses were applied to assess population structure. The rate of inbreeding within breed was evaluated based on the distribution of runs of homozygosity in the genome and respective coefficients, the genomic relationship matrix, the patterns of linkage disequilibrium, and the historic effective population size. Results showed that both breeds exhibit high levels of genetic diversity. Level of inbreeding between the two breeds estimated by the Wright's fixation index FST was low (Fst = 0.04362), indicating the existence of a weak genetic differentiation between them. In addition, grouping of farms according to their geographical locations was observed. This study presents for the first time a genome-based analysis on the genetic structure of the two indigenous Greek goat breeds and identifies markers that can be potentially exploited in future selective breeding programs for traceability purposes, targeted genetic improvement schemes and conservation strategies.

Use of proteomics in the study of microbial diseases of small ruminants.

Objective of the paper is to review potential applications of proteomics methodologies in the study of microbial diseases of small ruminants. Proteomics has been employed for the elucidation of pathogenesis of various diseases, i.e., in the study of determinants of microbial agents and the study of host-pathogen interactions, as well as in improved disease diagnosis by the identification of biomarkers. Extensive uses of proteomics in sheep and goat diseases have been applied primarily in mastitis, in reproductive infections, in paratuberculosis, in respiratory infections and in scrapie. Mining deeper into the various proteomes and application of new methodological strategies in clinical studies will provide information about disease processes. Improvement of diagnostic techniques, development of vaccines against diseases and establishment of tools for optimum animal production are key-areas for targeted research.

Proteomics reveal rat hippocampal lateral asymmetry.

Brain laterality has been observed in animals and humans structurally, functionally, and behaviorally. MRI and CT scans have revealed pathological and normal brain asymmetry. A coarse assessment of rat or human brain fails to expose profound left/right differences, while a finer examination of its structure reveals an array of asymmetric features. This lateralization may be derived from evolutionary, genetic, developmental, epigenetic, and pathologic factors. However, brain structure and function is complex and macroscopic or microscopic asymmetries may be hard to discern from random fluctuations. This study concentrated on the hippocampus and we explored lateralization employing a molecular high-throughput approach. Using proteomic analysis based on a combined approach of 2-D PAGE and MS, we examined differential protein expression in the hippocampi (left vs. right) of young adult male rats. Initial proteomic analysis demonstrated quantitative differences of approximately eighty proteins between the right (RH) and left hippocampus (LH). These were primarily energy-, cell metabolism-, stress-inducible chaperone proteins and cytoskeleton- proteins. Analysis revealed higher abundance of metabolic enzymes related to cellular energy metabolism, in the RH than the LH. In contrast, higher concentrations of proteins which are located mainly in astrocytes were shown in the LH than the RH. Immunoblotting of brain-specific proteins, on single animal hippocampal lysates confirmed the expression of Dynamin-1, DRP2, synapsin-1 and others, to be higher in the RH than LH lysates. These findings demonstrate major laterality in the expression of protein molecules between the two hippocampi providing a fertile field for mapping studies relating molecular, neuroimaging and functional data. Undoubtedly, asymmetries found at the animal level are hard to extrapolate to humans; however, studies in animal models will increase our understanding of the developing and adult brain and the healthy and diseased brain.

10 years' experience in fragile X testing among mentally retarded individuals in Greece: a molecular and epidemiological approach.

Fragile X syndrome, the second most common genetic cause of mental retardation, is due to the expansion of a trinucleotide repeat (CGG)n within the first exon of the FMR-1 gene. Molecular genetic analysis provides accurate diagnosis and facilitates genetic counselling and prenatal testing. Screening for the fragile X mutation in a sample of 3,888 individuals in Greece is reported: 1,755 children with non-specific mental retardation, 1,733 parents and other family members and 400 normal individuals. Molecular analysis allowed for the identification and characterization of 52 fragile X families confirming the clinical diagnosis in 57 males and 4 females. Sixty-six female carriers (6 mentally retarded) and 4 normal transmitting males were also identified. Four severely retarded males and their mothers carried unmethylated premutations, while a moderately retarded girl had a deletion of approximately equal to 150 bp. Overall sizing of the CGG repeat produced an allele distribution of 6-58 CGG repeats (mean 28-30), similar to that in other Caucasian populations.

Two-way trafficking of Annexin V positive cells between mother and fetus: determination of apoptosis at delivery.

OBJECTIVES: The aim of this study was to quantitate apoptosis in maternal circulation and umbilical cord blood (UCB) at delivery. The proportion of fetal cells in maternal blood as well as that of maternal cells in UCB was also determined. MATERIAL AND METHODS: Three milliliters of peripheral blood was collected from nine women during labor. Five women delivered males and four delivered females. Immediately after delivery, 3 mL UCB was collected. Ten microliters was used to quantitate apoptosis by the ethidium bromide assay (EthBr) and from the remaining blood, Annexin V positive cells were isolated by MACS. RESULTS: The Median apoptosis rate in maternal samples was 25% (19-34) and in UCB 20% (16-28). Annexin V positive cells were present in all samples analyzed. As shown by Fluorescence in situ hybridization (FISH) in maternal samples, cells with an XY hybridization pattern were identified in cases with male newborns in a median concentration of 1.7% (1.6-2.1). On the corresponding UCB, a median of 1.2% (0.8-1.6) XX cells were detected. CONCLUSION: The study demonstrates the existence of a bidirectional transfer of fetal and maternal cells under apoptosis across the placenta and provides useful information regarding use of UCB for transplantation.

Identification of autosomal supernumerary chromosome markers (SMCs) by fluorescent in situ hybridization (FISH).

Supernumerary marker chromosomes (SMCs) are rare chromosomal abnormalities resulting in partial trisomy of specific genomic regions with characteristic phenotypic effects. Twenty six cases with autosomal SMCs are reported. Four were identified prenatally and 22 postnatally in children, aged from 8 days to 15 years, who were referred for genetic evaluation because of various congenital anomalies and developmental delay. In 22 of the 26 cases, the SMCs were de novo, in two they were familial and in another two a 11;22 reciprocal translocation was revealed in the mothers. In only one patient was the SMC present in a mosaic form. Sequential fluorescent in situ hybridization studies (FISH) using Whole Chromosome Paint (WCP) probes were performed in order to determine the chromosomal origin of the SMCs. Sixteen of them originated from chromosome 15, five were shown to be an isochromosome 18p and one was derived from chromosome 22, but did not contain the DiGeorge/ VCFS critical region. In two instances, the SMCs were derivatives of chromosome 13 and in two the SMCs resulted from a 11;22 maternal translocation and contained material from both chromosomes 11 and 22. Molecular investigation of two of the patients with an SMC[15] revealed three copies of the SNRPN gene, but the diagnosis of PW/AS due to possible imprinting was excluded in both patients by a methylation-specific PCR. FISH and molecular studies have greatly facilitated the characterization of marker chromosomes. As more SMCs are classified, better genetic counseling and risk evaluation can be achieved.

Impact of cytogenetic and molecular cytogenetic studies on hematologic malignancies.

Conventional cytogenetic analysis of chromosome abnormalities in hematologic malignancies is hampered by the low mitotic index and poor quality of metaphases. A range of techniques based on fluorescence in situ hybridization (FISH) has greatly enhanced the identification of non-random translocations and deletions, pinpointing regions which contain genes involved in leukemogenesis. One of the main advantages of FISH is its ability to use non-dividing interphase cells as DNA targets, enabling the screening of large numbers of cells and providing access to a variety of cells with different hematopoetic activity. Furthermore, multicolor FISH (SKY, M-FISH and CGH microarrays) combines the screening potential of cytogenetics with the accuracy of molecular genetics, allowing the visualization of the entire human genome in 24 different colors.

Detection of 22q11.2 deletion among 139 patients with Di George/Velocardiofacial syndrome features.

Cytogenetic and FISH analysis was performed in 139 patients to detect the pathognomonic of Di George/ Velocardiofacial syndrome (DGS/VFCS) deletion 22q11.2. An abnormal karyotype was revealed in 2/139 cases (47, XXY and 46, XX, 2p+). A deletion was found in 17/139 (12.2%) patients (14 males/ 3 females), inherited in 3 (2 maternal and 1 paternal). Patients with 22q11.2 deletion exhibited facial dysmorphic features (82%), congenital heart defects (70%), immunological problems (47%), multiple congenital anomalies (64%), hypocalcemia (47%), mental retardation/learning difficulties (35%), cleft palate/velopharyngeal insufficiency (23.5%), seizures/hypotonia (23%) and growth retardation (12%). Among 56/139 patients with detailed available clinical data, the 22q11.2 deletion was confirmed in all cases with hypocalcemia and in over half of the cases with multiple congenital anomalies, immunological problems and hypotonia/seizures (70%, 60% and 57%, respectively). Genetic reevaluation of 39 patients without the 22q11.2 deletion contributed to the classification of 14 (37%) under different syndromes, emphasizing the need for stricter referral criteria.

Conventional cytogenetics and fluorescence in situ hybridization in persistent cytopenias and myelodysplastic syndromes in childhood.

Accurate detection of the abnormal clone in children with persistent cytopenia (PC) may confirm the diagnosis of myelodysplastic syndrome (MDS) and determine prognosis and evolution of the disease. Bone marrow (BM) samples were obtained from 65 children, 11 of which were finally diagnosed as primary or secondary MDS. Ten to 20 G-banded metaphases were analyzed and FISH was performed using a-satellite probes for chromosomes 7 and 8. Conventional cytogenetic analysis (CCA) was successful in 40/65 samples, revealing clonal aberrations in 3 patients with MDS. FISH was successful in all cases, detecting monosomy 7 and trisomy 8 abnormal clones in 5 patients. Abnormalities were identified in 3/6 children with primary MDS and 3/5 with secondary MDS. None of the patients with PC of etiology other than MDS had a clonal abnormality in the BM. The results confirm the high incidence of chromosome abnormalities in childhood MDS and the sensitivity of FISH in detecting minor abnormal clones.