Identification of β Casein Genotypes in Indian Gir and Crossbred Exotic Cows from Mumbai Dairy Farms

Background: Collective evidence of polymorphic β-casein and associated health problems has led to the concern about milk consumption and cow breeding policies worldwide. This association has also engrossed the interest of dairy scientist and industry in evaluation of β casein genotype distribution. With increasing proportion of exotic and crossbred cows in India it is worth while to screen cattle for A1A2 β casein and enhance indigenous cow breeds. Methods: The present study intended to identify β casein genotypes in pure Indian Gir cows and crossbred Holstein and jersey cows from three local dairy farms. We analysed β casein genotypes by PCR-RFLP method in total 95 cows during the period of 2017-2019. Result: All the indigenous Gir cows had fixed A2 allele whereas crossbred Jersey and Holstein Frisian both had A1A2 as the most common genotype (frequency: 0.473 and 0.6 respectively) followed by A2A2 (Frequency 0.368 and 0.333 respectively) and A1A1 (Frequency 0.158 and 0.066 respectively). The results show that in this study group Gir, a native Indian breed has fixed A2 β casein variant whereas crossbred Jersey and Holstein Frisian have A1A2 as a most common genotype. Screening of cattle for â casein genotypes is vital to monitor the frequency of A1 beta casein in native Indian cow breeds.

GA genotype of the Arg280His polymorphism on the XRCC1 gene: Genetic susceptibility genotype in differentiated thyroid carcinomas?

Differentiated thyroid carcinomas (DTC) are the most common form of endocrine malignancies. The role of genetic variations in the development of papillary thyroid carcinoma (PTC) is approximately 60.0-70.0%. The X-ray repair cross-complementing group 1 (XRCC1) protein has an important role in DNA repair mechanisms and genomic polymorphisms of XRCC1 gene affect the function of the protein. In the present case-control study, we aimed to compare the genotype frequency distributions of XRCC1 single nucleotide polymorphisms (SNPs) in terms of the presence of other risk factors (Hashimoto’s thyroiditis, smoking, obesity, radiation exposure) in patients with thyroid nodules who had fine-needle aspiration biopsy (FNAB) and/or thyroid surgery due to thyroid cancer. The genotype frequency distributions of three common XRCC1 SNPs (Arg194Trp, Arg399Gln, Arg280His) were compared to those with DTC (n = 228), benign thyroid nodules (BTN, n = 100) and healthy controls (n = 93) in terms of certain pre defined risk factors such as the presence of Hashimoto’s thyroiditis, smoking, obesity, a family history of thyroid cancer and radiation exposure. The frequency of the GA genotype of Arg280His in DTC cases was found to be higher than in those with BTN and the healthy control group (p <0.001). The DTC group had the lowest frequency of AA genotype of Arg280His (35.5%, p <0.001). Among those with a family history of thyroid cancer, 78.9% had a GA genotype and 21.1% had the AA genotype of Arg280His (p = 0.004). The Arg280His GA genotype was more common in DTC than in cancer-free controls. The GA genotype frequency was also high in DTC cases with a family history of thyroid cancer.

sxtA4+ and sxtA4- Genotypes Occur Together within Natural Pyrodinium bahamense Sub-Populations from the Western Atlantic

Saxitoxin (STX) is a secondary metabolite and potent neurotoxin produced by several genera of harmful algal bloom (HAB) marine dinoflagellates. The basis for variability in STX production within natural bloom populations is undefined as both toxic and non-toxic strains (of the same species) have been isolated from the same geographic locations. Pyrodinium bahamense is a STX-producing bioluminescent dinoflagellate that blooms along the east coast of Florida as well as the bioluminescent bays in Puerto Rico (PR), though no toxicity reports exist for PR populations. The core genes in the dinoflagellate STX biosynthetic pathway have been identified, and the sxtA4 gene is essential for toxin production. Using sxtA4 as a molecular proxy for the genetic capacity of STX production, we examined sxtA4+ and sxtA4- genotype frequency at the single cell level in P. bahamense populations from different locations in the Indian River Lagoon (IRL), FL, and Mosquito Bay (MB), a bioluminescent bay in PR. Multiplex PCR was performed on individual cells with Pyrodinium-specific primers targeting the 18S rRNA gene and sxtA4. The results reveal that within discrete natural populations of P. bahamense, both sxtA4+ and sxtA4- genotypes occur, and the sxtA4+ genotype dominates. In the IRL, the frequency of the sxtA4+ genotype ranged from ca. 80–100%. In MB, sxtA4+ genotype frequency ranged from ca 40–66%. To assess the extent of sxtA4 variation within individual cells, sxtA4 amplicons from single cells representative of the different sampling sites were cloned and sequenced. Overall, two variants were consistently obtained, one of which is likely a pseudogene based on alignment with cDNA sequences. These are the first data demonstrating the existence of both genotypes in natural P. bahamense sub-populations, as well as sxtA4 presence in P. bahamense from PR. These results provide insights on underlying genetic factors influencing the potential for toxin variability among natural sub-populations of HAB species and highlight the need to study the genetic diversity within HAB sub-populations at a fine level in order to identify the molecular mechanisms driving HAB evolution.

Adrenal-permissive HSD3B1 genetic inheritance and risk of estrogen-driven postmenopausal breast cancer.

10503 Background: Genetic factors that contribute to endogenous estrogen synthesis and postmenopausal breast cancer risk are unknown. We set out to test the hypothesis that homozygous inheritance of the common 1245A→C missense-encoding polymorphism in HSD3B1, which is common (8-10%) in White populations, functionally adrenal permissive and increases synthesis of the aromatase substrate, androstenedione, is associated with postmenopausal estrogen receptor-positive breast cancer. Methods: A prospective single institution study of postmenopausal estrogen receptor-driven breast cancer for determination of HSD3B1 genotype, circulating steroid concentrations, and adrenal-permissive genotype frequency compared with the genotype frequency in the general population and in estrogen receptor-negative breast cancer. Validation was performed in 2 breast cancer genomic studies with estrogen receptor documentation. The primary outcome is the adrenal-permissive genotype frequency in postmenopausal estrogen receptor-positive breast cancer and the general population. Genotype comparisons were also done with postmenopausal estrogen receptor-negative breast cancer and the association with circulating adrenal androgen concentrations determined. Results: The prospective and validation studies had 199 and 1628 women, respectively. The adrenal-permissive genotype frequency in postmenopausal White women with estrogen-driven breast cancer in the prospective cohort was 17.5% (21/120) compared with 9.6% (429/4451) in the general population [p = 0.0077]. The adrenal-permissive genotype frequency for estrogen-driven postmenopausal breast cancer was validated using the Cambridge and TCGA genomic datasets together: 14.4% (56/389) compared with 6.0% (9/149) for estrogen receptor-negative breast cancer (p = 0.007) and the general population (p = 0.005). Circulating androstenedione concentration was significantly higher for women with the adrenal-permissive genotype compared with the other genotypes (p = 0.03). Conclusions: The adrenal-permissive genotype is associated with estrogen-driven postmenopausal breast cancer. These findings link genetic inheritance of endogenous estrogen exposure to estrogen-driven breast cancer and have broad implications for risk stratification, prevention, potential biomarkers for hormonal therapy response and possibly other clinical outcomes related to estrogen physiology in postmenopausal women.

Genetic Study of Phenylthiocarbamide (PTC) Taste Sensitivity In Population of The Osing in Kemiren Village-Banyuwangi

The ability to taste phenylthiocarbamide (PTC), is autosomal trait inherited in a simple Mendelian recessive pattern. The frequency of Taster and non-Taster allele is varies in different populations. The purpose of the research is to investigate the prevalence, gene frequency and genotype frequency of taster (T) and non taster (ts of Osing population in Kemiren-Banyuwangi. PTC serial dilution method was used to assess the PTC Taster and non-Taster phenotypes. The Hardy–Weinberg method was used to determine allele frequencies. The total of samples were 227 people, male were 117 and female were 110 with age range of 15–30 years were randomly selected. The result showed that the Osing population as Taster were 210 (92,52%) and non Taster were 17samples (7,48%) . The allele frecuency of Taster (T) was 0,73 and non Taster (t) was 0,27 respectively. The genotype frequency of dominant Taster (TT) was 0,54, heterozygosity Taster (Tt) was 0,39, and genotype of non Taster (tt) was 0,07.

Statistical Tests and Algorithms

In this chapter statistical tests are performed in R, including the χ‎2 tests; testing can be started if allele and genotype frequency data match the reader’s expectations. Writing and running algorithms are introduced as functions, specifically working through building an Expectation Maximization function. The function is then used to estimate and update the reader’s inferences of allele frequencies from observed and expected genotypes.

BCL-2 (-938C>A), BAX (-248G>A), and HER2 Ile655Val Polymorphisms and Breast Cancer Risk in Indian Population

Breast cancer is the most common carcinoma in women worldwide. The present case-control study was aimed to examine the association of BCL-2 (-938C> A), BAX (-248G > A), and HER2 (I655V i.e. A > G) polymorphisms with breast cancer risk in Indian population. This study enrolled 117 breast cancer cases and 104 controls. BCL-2 (-938C > A), BAX (-248G > A), and HER2 Ile655Val polymorphisms were screened by PCR-RFLP method. There was no significance difference in the allelic and genotype frequency of the BCL-2 (-938C > A) and BAX (-248G > A) polymorphisms between cases and controls. In relation to HER2 Ile655Val polymorphism, the statistical analysis of observed genotypic frequencies showed significant association ( p -0.0059). Compared to Ile/Ile (A/A) genotype, frequency of Ile/Val (A/G) genotype was significantly higher among cases than in control group and observed to increase the breast cancer risk (OR, 2.43; 95%CI, 1.32–4.46; p -0.004). The frequency of Val (G) allele was significantly higher in cases as compared to controls (6.83% vs 2.88%, resp.). Compared to Ile (A) allele, significant increase in the risk of breast cancer was observed with Val (G) allele (OR, 2.21; 95% CI, 1.35–3.63; p -0.0016). We observed significant association between HER2 Ile655Val polymorphism and breast cancer risk under the dominant (OR = 2.52; 95% CI: 1.41–4.51; p -0.001) and codominant (OR, 2.24; 95% CI: 1.23–4.09; p-0.008) model. In our study, BCL-2 (-938C > A) and BAX (-248G > A) polymorphism were not found to be associated with breast cancer risk. This present study for the first time shows significant association of HER2 Ile655Val polymorphism with risk of breast cancer in Indian population. Therefore, we suggest that each population need to evaluate its own genetic profile for breast cancer risk that may be helpful for better understanding the racial and geographic differences reported for breast cancer incidence and mortality.

The ACE and ACTN3 polymorphisms in female soccer athletes

Objects We investigated the association of ACE I/D and ACTN3 R577X polymorphisms with the performance of Chinese elite female soccer athletes for the first time. Material and methods The genotype distributions of ACE I/D and ACTN3 R577X in the athlete group and the control group of Chinese females were evaluated via PCR and compared. VO2max value was tested as per standard protocol. Results Regarding the distribution of ACE polymorphisms, the genotype frequency was indifferent between the athletes (II 40 %, ID 46.7 %, DD 13.3 %) and the controls (II 42 %, ID 48 %, DD 10 %). No difference in the I/D allele frequency was observed between the athlete group and the control group. Regarding the distribution of ACTN3 polymorphisms, the genotype frequency was significantly different between the athletes (XX 0 %, XR 53.3 %, RR 46.7 %) and the controls (XX 16 %, XR 44 %, RR 40 %). The allele frequency was observed no different between the athlete and the control group. The ACE ID and ACTN3 RR genotype combination was associated with higher VO2max values among defenders than among other players. According to VO2max values,The ACE and ACTN3 genotype combinations (II/ID/DD + RR/XR) significantly differed between the athletes and the controls (p < 0.05). Conclusion These results suggested that the Chinese elite female soccer athletes were more likely to harbor the I allele and the R allele and that the combination of ACE II/ID and ACTN3 RR/XR was a synergetic determinant of the athletic performance of females in soccer.