Hybrid de novo and haplotype-resolved genome assembly of Vechur cattle - elucidating genetic variation.

Cattle contribute to the nutritional needs and economy of a place. The performance and fitness of cattle depend on the response and adaptation to local climatic conditions. Genomic and genetic studies are important for advancing cattle breeding, and availability of relevant reference genomes is essential. In the present study, the genome of a Vechur calf was sequenced on both short-read Illumina and long-read Nanopore sequencing platforms. The hybrid de novo assembly approach was deployed to obtain an average contig length of 1.97 Mbp and an N50 of 4.94 Mbp. By using a short-read genome sequence of the corresponding sire and dam, a haplotype-resolved genome was also assembled. In comparison to the taurine reference genome, we found 28,982 autosomal structural variants and 16,926,990 SNVs, with 883,544 SNVs homozygous in the trio samples. Many of these SNPs have been reported to be associated with various QTLs including growth, milk yield, and milk fat content, which are crucial determinants of cattle production. Furthermore, population genotype data analysis indicated that the present sample belongs to an Indian cattle breed forming a unique cluster of Bos indicus. Subsequent FST analysis revealed differentiation of the Vechur cattle genome at multiple loci, especially those regions related to whole body growth and cell division, especially IGF1, HMGA2, RRM2, and CD68 loci, suggesting a possible role of these genes in its small stature and better disease resistance capabilities in comparison with the local crossbreeds. This provides an opportunity to select and engineer cattle breeds optimized for local conditions.

Genotypic Analysis of COL4A1 Gene in Diabetic Nephropathy and Type 2 Diabetes Mellitus Patients: A Comparative Genetic Study.

Diabetic nephropathy (DN) is specified by microalbuminuria, glomerular lesions, and renal fibrosis leading to end-stage renal disease. The pathophysiology of DN is multifactorial as a result of gene-environment interaction. Clinical studies suggested that gene mutations affect various pathways involved in DN, including extracellular matrix (ECM). During chronic hyperglycemia, collagen type-4-mediated ECM overproduction occurs, leading to renal fibrosis and DN development. In this study, COL4A1 gene variant rs605143 (G/A) was analyzed in diabetes and DN patients from the study population. We genotyped 386 study subjects, comprising 120 type 2 diabetes mellitus (T2DM) patients, 120 DN, and 146 healthy controls. All study subjects were analyzed for biochemical assays by commercially available kits and genotypic analysis by polymerase chain reaction-restriction fragment length polymorphism and confirmed by Sanger sequencing. Statistical analyses were done using SPSS and GraphPad. Anthroclinicopathological parameters showed a significant association between T2DM and DN. Genotype AA of COL4A1 gene variant rs605143 (G/A) showed a significant association with T2DM and DN compared with controls with 5.87- and 8.01-folds risk, respectively. Mutant allele A also significantly associated with T2DM and DN independently compared with healthy controls with 2.29- and 2.81-time risk in the study population. This study's findings suggested that COL4A1 gene variant rs605143 (G/A) can be used as predictive biomarkers for T2DM and DN independently. However, this gene variant needs to be analyzed in a large sample to explore the shared genetic association between T2DM and DN.

Cancer stem cell in prostate cancer progression, metastasis and therapy resistance.

Prostate cancer (PCa) is the most diagnosed malignancy in the men worldwide. Cancer stem cells (CSCs) are the sub-population of cells present in the tumor which possess unique properties of self-renewal and multilineage differentiation thus thought to be major cause of therapy resistance, disease relapse, and mortality in several malignancies including PCa. CSCs have also been shown positive for the common stem cells markers such as ALDH EZH2, OCT4, SOX2, c-MYC, Nanog etc. Therefore, isolation and characterization of CSCs specific markers which may discriminate CSCs and normal stem cells are critical to selectively eliminate CSCs. Rapid advances in the field offers a theoretical explanation for many of the enduring uncertainties encompassing the etiology and an optimism for the identification of new stem-cell targets, development of reliable and efficient therapies in the future. The emerging reports have also provided unprecedented insights into CSCs plasticity, quiescence, renewal, and therapeutic response. In this review, we discuss the identification of PCa stem cells, their unique properties, stemness-driving pathways, new diagnostics, and therapeutic interventions.

Assessment of geographical origin of virgin coconut oil using inductively coupled plasma mass spectrometry along with multivariate chemometrics.

Recently, Virgin coconut oil (VCO) has emerged as one of the most favorable edible oils because of its application in cooking, frying as well as additive used in food, pharmaceuticals, and cosmetic goods. These qualities have established VCO in high consumer demand and there is a great need of establishing a reliable method for the identification of its geographical origin. Through this present study, for the first time, it has been established that Inductively Coupled Plasma-Mass-Spectrometry (ICP-MS) combined with multivariate chemometrics can be used for the identification of the geographical origin of the VCO samples of various provinces. Principal Component Analysis (PCA), and Linear Discriminant Analysis (LDA) were able to differentiate and classify the VCO samples of different geographical origins. Further, calibration models (Principal Component Regression and Partial Least Square Regression) were developed on the calibration dataset of the elemental concentration obtained from the ICP-MS analysis. An external dataset was used to develop the prediction model to predict the geographical origin of an unknown sample. Both PCR and PLS-R models were successfully able to predict the geographical origin with a high R2 value (0.999) and low RMSEP value 0.074 and 0.075% v/v of prediction respectively. In conclusion, ICP-MS combined with regression modelling can be used as an excellent tool for the identification of the geographical origin of the VCO samples of various provinces. This whole technique is the most suitable as it has high sensitivity as well as provides easy multi-metal analysis for a single sample of edible oil.

Rapid and non-destructive approach for the detection of fried mustard oil adulteration in pure mustard oil via ATR-FTIR spectroscopy-chemometrics.

Attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy integrated with chemometrics was effectively applied for the rapid detection and accurate quantification of fried mustard oil (FMO) adulteration in pure mustard oil (PMO). PMO was adulterated with FMO in the range of 0.5-50% v/v. Principal component analysis (PCA) elucidated the studied adulteration using two components with an explained variance of 97%. The linear discriminant analysis (LDA) was adopted to classify the adulterated PMO samples with FMO. LDA model showed 100% accuracy initially, as well as when cross-validated. To enhance the overall quality of models, characteristic spectral regions were optimized, and principal component regression (PCR) and partial least square regression (PLS-R) models were constructed with high accuracy and precision. PLS-R model for the 2nd derivative of the optimized spectral region 1260-1080 cm-1 showed best results for prediction sample sets in terms of high R2 and residual predictive deviation (RPD) value of 0.999 and 31.91 with low root mean square error (RMSE) and relative prediction error (RE %) of 0.53% v/v and 3.37% respectively. Thus, the suggested method can detect up to 0.5% v/v of adulterated FMO in PMO in a short time interval.

Does 'activating' nuts affect nutrient bioavailability?

Claims in the lay literature suggest soaking nuts enhances mineral bioavailability. Research on legumes and grains indicate soaking reduces phytate levels, however, there is no evidence to support or refute these claims for nuts. We assessed the effects of different soaking regimes on phytate and mineral concentrations of whole and chopped almonds, hazelnuts, peanuts, and walnuts. The treatments were: 1. Raw; 2. soaked for 12 h in salt solution; 3. soaked for 4 h in salt solution; 4. soaked for 12 h in water. Phytate concentrations were analysed using high-performance liquid chromatography (HPLC) and minerals by inductively coupled plasma mass spectrometry (ICP-MS). Differences in phytate concentrations between treated and untreated nuts were small, ranging from -12% to +10%. Overall, soaking resulted in lower mineral concentrations, especially for chopped nuts, and did not improve phytate:mineral molar ratios. This research does not support claims that 'activating' nuts results in greater nutrient bioavailability.

The effects of 'activating' almonds on consumer acceptance and gastrointestinal tolerance.

PURPOSE: Recommendations to soak nuts prior to consumption to reduce phytate concentrations and improve gastrointestinal tolerance have received much attention in the popular press. This is despite no supporting scientific evidence for the practice. There is also a lack of information about how soaking nuts might affect consumer acceptability. This study primarily assessed the effects of soaking almonds on consumer acceptance and secondly assessed effects on gastrointestinal tolerance. METHODS: In this 8-week randomised crossover trial, 76 participants were allocated in balanced order to receive 30 g/day of four different preparations of almonds for 12 days: whole unsoaked, whole soaked, sliced unsoaked, and sliced soaked. Ratings of overall liking, desire to consume, and likelihood of future consumption, and severity of gastrointestinal symptoms were measured daily on visual analogue scales. The phytate concentrations were measured in all four nut types using high-performance liquid chromatography. RESULTS: Mean acceptance ratings of all nut types were above the neutral point indicating they were acceptable. However, sliced soaked almonds were rated significantly lower overall for all three acceptance scales compared to the other treatments (all P ≤ 0.003). The sliced unsoaked almonds were rated lower than both whole nut treatments (all P ≤ 0.006), while there were no significant differences between the two whole nut treatments (all P ≥ 0.511). Gastrointestinal symptoms were minimal, but flatulence was rated significantly higher for all time points combined for soaked whole nuts compared to unsoaked whole nuts (P = 0.005). Compared to the whole unsoaked nuts (mean [SD] 531 [9] mg/100 g), phytate concentration was higher for the whole soaked almonds (563 [38] mg/100 g, P = 0.016), with no evidence of a difference for the sliced soaked almonds (548 [27] mg/100 g, P = 0.197) and no difference between the soaked forms (P = 0.262). CONCLUSIONS: This research supports previous results suggesting nuts, including different forms, are an acceptable food. They are also well tolerated gastrointestinally, but soaking does not improve gastrointestinal tolerance or acceptance as claimed in the lay literature.