The Genome of Setaria digitata: A Cattle Nematode Closely Related to Human Filarial Parasites.

Here we present the draft genome sequence of Setaria digitata, a parasitic nematode affecting cattle. Due to its similarity to Wuchereria bancrofti, the parasitic nematode that causes lymphatic filariasis in humans, S. digitata has been used as a model organism at the genomic level to find drug targets which can be used for the development of novel drugs and/or vaccines for human filariasis. Setaria digitata causes cerebrospinal nematodiasis in goats, sheep, and horses posing a serious threat to livestock in developing countries. The genome sequence of S. digitata will assist in finding candidate genes to use as drug targets in both S. digitata and W. bancrofti. The assembled draft genome is ∼90 Mb long and contains 8,974 genomic scaffolds with a G+C content of 31.73%.

A study of genetic polymorphisms in mitochondrial DNA hypervariable regions I and II of the five major ethnic groups and Vedda population in Sri Lanka.

Diversity of the hypervariable regions (HV) I and II of the mitochondrial genome was studied in maternally unrelated Sri Lankans (N=202) from six ethnic groups (i.e.: Sinhalese, Sri Lankan Tamil, Muslim, Malay, Indian Tamil and Vedda). DNA was extracted from blood and buccal swabs and HVI and HVII regions were PCR amplified and sequenced. Resulting sequences were aligned and edited between 16024-16365 and 73-340 regions and compared with revised Cambridge reference sequences (rCRS). One hundred and thirty-five unique haplotypes and 22 shared haplotypes were observed. A total of 145 polymorphic sites and 158 polymorphisms were observed. Hypervariable region I showed a higher polymorphic variation than hypervariable region II. Nucleotide diversities were quite low and similar for all ethnicities apart from a slightly higher value for Indian Tamils and a much lower value for the Vedda population compared to the other groups. When the total population was considered South Asian (Indian) haplogroups were predominant, but there were differences in the distribution of phylo-geographical haplogroups between ethnic groups. Sinhalese, Sri Lankan Tamil and Vedda populations had a considerable presence of West Eurasian haplogroups. About 2/3rd of the Vedda population comprised of macro-haplogroup N or its subclades R and U, whereas macro-haplogroup M was predominant in all other populations. The Vedda population clustered separately from other groups and Sri Lankan Tamils showed a closer genetic affiliation to Sinhalese than to Indian Tamils. Thus this study provides useful information for forensic analysis and anthropological studies of Sri Lankans.

Association of cord blood leptin, soluble leptin receptor, insulin-like growth factor-I and insulin-like growth factor-binding protein-1 on birth indices in healthy full-term newborns.

BACKGROUND: Leptin and insulin-like growth factor-I (IGF-I) promote fetal growth. Their availability is modulated by soluble leptin receptor (SLR) and insulin-like growth factor-binding proteins (IGFBP). Studies that accounted for SLR levels when investigating the association of leptin, IGF-I and IGFBPs on birth indices are scarce. METHODS: Cord blood leptin, SLR, IGF-I, IGFBP-1 and their association with birth indices were studied in term newborns (n = 110; males = 60). Data were compared between males and females using the Mann-Whitney U test/unpaired Student's t test as appropriate. Univariate correlations and multiple regression analyses were performed to identify variables significantly influencing birth indices. RESULTS: Birth indices were comparable between male and female newborns. Females had a significantly lower SLR (p = 0.0142), a higher leptin/Ponderal index (p = 0.033) and a higher free leptin index (leptin/SLR) (p = 0.0081). Leptin and male gender positively and IGFBP-1 negatively influenced birth weight (p = 0.0005, p = 0.02, and p = 0.005, respectively) and head circumference (p = 0.0052, p = 0.0098, and p = 0.0183, respectively) when accounted for other variables. When tested in a different multiple regression model, the free leptin index positively influenced crown-heel length (p = 0.0016) in addition to birth weight (p < 0.0001) and head circumference (p = 0.0016). CONCLUSIONS: In healthy full-term pregnancies, cord blood leptin and IGFBP-1 exert independent and opposing effects on fetal growth.

Novel sequence variants and common recurrent polymorphisms of BRCA2 in Sri Lankan breast cancer patients and a family with BRCA1 mutations.

We previously reported BRCA1 mutations and sequence variants in Sri Lankan breast cancer patients. Mutations and sequence variants of the BRCA2 gene were studied in 149 study participants from the same cohort. There were 55 familial and 54 sporadic breast cancer patients, 20 at-risk individuals and 20 healthy controls. Direct sequencing (exon 11) and sequencing of abnormal bands after screening with single-strand conformation polymorphism (remaining exons) were used to detect mutations and sequence variants. Twenty-three sequence variants were found in the BRCA2 gene. Two novel pathogenic frame-shift additions resulting in a premature stop codon (c.2403 insA/exon 11, c.2667 insT/exon 11) were identified. Possibly pathogenic two novel missense mutations (c.1191 A>C/exon 10, c.5695 A>C/exon 11) one novel intronic variant (IVS15-21 insTT), four novel silent mutations (c.969 C>T/exon 9, c.1353 C>T/exon 10, c.2766 A>C/exon 11 and c.7452 A>G/exon 14) and one novel missense mutation (c.971 C>G/exon 9) were observed. One previously reported possibly pathogenic intronic variant (IVS81 G>C) and several previously reported silent mutations, missense mutations, and one 5' UTR polymorphism were detected. Pathogenic and possibly pathogenic mutations were more frequent in the BRCA2 gene among Sri Lankan familial breast cancer patients when compared to our previous findings for the BRCA1 gene.

Novel sequence variants and a high frequency of recurrent polymorphisms in BRCA1 gene in Sri Lankan breast cancer patients and at risk individuals.

BACKGROUND: Breast Cancer is the most commonly diagnosed cancer among Sri Lankan women. Germline mutations in the susceptibility genes BRCA1 and BRCA2 in hereditary breast/ovarian cancer, though low in prevalence, are highly penetrant and show geographical variations. There have been only a few reports from Asia on mutations in BRCA1/2 genes and none from Sri Lanka. METHODS: A total of 130 patients with (N = 66) and without (N = 64) a family history of breast cancer, 70 unaffected individuals with a family history of breast cancer and 40 control subjects were analysed for BRCA1 mutations. All but exon 11 were screened by single strand conformation analysis (SSCP) and heteroduplex analysis. PCR products which showed abnormal patterns in SSCP were sequenced. Exon 11 was directly sequenced. RESULTS: Nineteen sequence variants were found in BRCA1 gene. Two novel deleterious frame-shift mutations; c.3086delT/exon11 (in one patient) and c.5404delG/exon21 (in one patient and two of her family members) were identified. A possibly pathogenic novel missense mutation (c.856T>G/exon 11) and three novel intronic variants (IVS7+36C>T, IVS7+41C>T, IVS7+49del15) were characterised. Ten previously reported common polymorphisms and three previously reported intronic variants were also observed. CONCLUSION: After screening of 66 patients with family history and 64 sporadic breast cancer patients, 2 deleterious mutations (c.3086delT and c.5404delG) in two families were identified and two more possibly pathogenic mutations (c.856T>G and IVS17-2A>T) in two families were identified. DATA BASE: BRCA1--Gene Bank: Accession # U14680 Version # 14680.1.

Effect of leptin on prolactin and insulin-like growth factor-I secretion by cultured rat endometrial stromal cells.

OBJECTIVE: To study the possible effect of leptin on PRL and insulin-like growth factor (IGF)-I secretion from rat endometrial stromal cells. DESIGN: The effect of recombinant murine leptin on the secretion of PRL and IGF-I by cultured rat endometrial cells was investigated. SETTING: Academic institutions. ANIMAL(S): Laboratory bred virgin female rats aged 3-4 months. INTERVENTION(S): Endometrial stromal cell (ESC) cultures in the fourth passage stimulated with 1-1,000 ng/mL of leptin for 24 hours and with 1 ng/mL leptin for 24-72 hours. MAIN OUTCOME MEASURE(S): Measurement of PRL and IGF-I levels in the conditioned media by enzyme immunoassay. RESULT(S): Endometrial stromal cells grown in vitro secreted both PRL and IGF-I into the medium and the concentrations significantly increased with passage of time even in the absence of leptin. The increase in PRL was seen mainly at 72 hours and in IGF-I at 24 and 72 hours. Presence of leptin in the culture medium (1-1,000 ng/mL) further enhanced PRL secretion in a dose-dependent manner and this effect was seen with all leptin doses used. Leptin also increased PRL secretion in a time-dependent manner and the increase was seen at 24, 48, and 72 hours. Leptin did not significantly affect IGF-I secretion either in a dose- or a time-dependent manner. CONCLUSION(S): Biological effects of leptin on the rat endometrium include dose- and time-dependent stimulatory effects on stromal cell PRL secretion.

Serum leptin and lactational amenorrhea in well-nourished and undernourished lactating women.

OBJECTIVE: To ascertain the possible role of leptin in the resumption of postpartum menstruation in lactating women with differing nutritional statuses. DESIGN: Analysis of data and blood samples collected during a previous prospective study. SETTING: Healthy volunteers in an academic research environment. PATIENT(S): Undernourished (body mass index [BMI]< or =19 kg/m(2)) and well-nourished (BMI> or =26 kg/m(2)) lactating women who resumed regular menstruation before 24 weeks and at or after 24 weeks postpartum. INTERVENTION(S): Venous blood samples at four-weekly intervals and other clinical data collected until resumption of regular menstruation. MAIN OUTCOME MEASURE(S): Serum leptin concentrations. RESULT(S): Leptin concentrations were significantly higher in the well-nourished than in the undernourished women, irrespective of the time of resumption of menstruation. Time of resumption of menstruation did not significantly affect leptin levels within well-nourished and undernourished groups. Leptin significantly correlated with BMI (r = 0.78). The BMI (r = -0.53), but not leptin, was significantly and negatively correlated with the duration of lactational amenorrhea. CONCLUSION(S): Leptin is unlikely to be a major determinant of early resumption of regular menstruation in well-nourished women.

Development of a DNA probe and a PCR based diagnostic assay for Rhizoctonia solani using a repetitive DNA sequence cloned from a Sri Lankan isolate.

Rhizoctonia solani is a destructive fungal pathogen of many economically important plants all over the world and the causative organism of sheath blight of rice in many tropical countries including Sri Lanka. A repetitive sequence from the genome of R. solani was cloned and characterized with a view to develop a DNA probe and a PCR diagnostic assay for detection of the fungus. The cloned sequence was 1550 bp long and appeared to be interspersed throughout the genome. The cloned sequence hybridized only to R. solani DNA and was sensitive enough to detect 100 pg of R. solani genomic DNA. PCR primers were designed from the cloned sequence and it was possible to develop a PCR assay for the specific detection of the fungal DNA with 10 pg sensitivity.

Genetic variation in Corynespora cassiicola: a possible relationship between host origin and virulence.

Genetic variation of 42 isolates of Corynespora cassiicola, a destructive fungal pathogen of many economically important crop plants including rubber, was investigated using RAPD-PCR analysis. Five genetic groups were identified using RAPD-PCR profiles generated by eight random primers. Results indicate that there is a significant genetic variation among C. cassiicola isolates collected from different host plants. These results should facilitate the development of rubber clones with enhanced resistance against all genetic groups of C. cassiicola.