Genetic variation and population structure in Jamunapari goats using microsatellites, mitochondrial DNA, and milk protein genes.

Jamunapari, a dairy goat breed of India, has been gradually declining in numbers in its home tract over the years. We have analysed genetic variation and population history in Jamunapari goats based on 17 microsatellite loci, 2 milk protein loci, mitochondrial hypervariable region I (HVRI) sequencing, and three Y-chromosomal gene sequencing. We used the mitochondrial DNA (mtDNA) mismatch distribution, microsatellite data, and bottleneck tests to infer the population history and demography. The mean number of alleles per locus was 9.0 indicating that the allelic variation was high in all the loci and the mean heterozygosity was 0.769 at nuclear loci. Although the population size is smaller than 8,000 individuals, the amount of variability both in terms of allelic richness and gene diversity was high in all the microsatellite loci except ILST 005. The gene diversity and effective number of alleles at milk protein loci were higher than the 10 other Indian goat breeds that they were compared to. Mismatch analysis was carried out and the analysis revealed that the population curve was unimodal indicating the expansion of population. The genetic diversity of Y-chromosome genes was low in the present study. The observed mean M ratio in the population was above the critical significance value (Mc) and close to one indicating that it has maintained a slowly changing population size. The mode-shift test did not detect any distortion of allele frequency and the heterozygosity excess method showed that there was no significant departure from mutation-drift equilibrium detected in the population. However, the effects of genetic bottlenecks were observed in some loci due to decreased heterozygosity and lower level of M ratio. There were two observed genetic subdivisions in the population supporting the observations of farmers in different areas. This base line information on genetic diversity, bottleneck analysis, and mismatch analysis was obtained to assist the conservation decision and management of the breed.

Molecular screening of unculturable bacteria present in men with reproductive failure.

Objective: To determine the presence of unculturable bacteria using polymerase chain reaction (PCR) in infertile men with pyosperrmia. Design: Perspective clinical study. Setting: The study took place at the Department of Reproductive Medicine, Owaisi Hospital and Research Center; In vitro Fertilization Unit, Mahavir Hospital and Research Center; Center for Cellular and Molecular Biology; and Bharat Biotech Foundation, Hyderabad, India. Patients: A total of 68 infertile men and 15 donors, all with no symptoms of genito-urinary tract infections and sterile semen cultures were included in the study. Interventions: None. Main outcome measures: Screening bacteria using routine bacterial cultures and PCR based screening with universal eubacterial primers. Results: The statistical analysis of all the semen parameters in asthenazoospermic, azoospermic, ceyptazoospermic, severe oligospermic and mild oligospermic patients were found to be significant compared with the controls. All the groups were found to be significant compared with the controls (P < 0.05) except for volume and pus cells in the cryptozoospermia group. The Student's t-test also was significant for the seminal parameters before and after treatment of 68 selected individuals with pyospermia and sterile cultures. A total of 44.11% (30/68) samples were collected from the negative culture of pyospermic infertile men have shown the presence of bacteria on amplification using PCR with universal eubacterial primers. The DNA was purified and sequenced. The sequences were checked for homology using DNASTAR and Ribosomal DataBase Project II. A total of 90% of the samples have shown the nearest evolutionary relation to Pantoea P102 (AF394539) and 10% of samples have shown close relation with Burkholderia cepacia (AF042161). Conclusion: The routine bacteriological cultures were unable to detect certain bacterial species particularly with members of enterobacteriaceae family (Pantoea species). Polymerase chain reaction, when used for screening bacteria, can detect the unculturable form of bacteria in infertile men. No amplification for bacterial DNA was obtained in control samples (fertile men with sterile semen cultures.) (Reprod Med Biol 2004; 3: 77- 84).