Novel extraction of high quality genomic DNA from frozen bovine blood samples by using detergent method

ELANE rs17223045C/T and rs3761007G/A variants: Protective factors against COVID-19

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for causing coronavirus disease 2019 (COVID-19). The development and severity of this infectious disease is influenced by a combination of environmental and genetic factors. Angiotensin-converting enzyme 2 (ACE2) facilitates SARS-CoV-2 entry into human cells, with transmembrane serine protease 2 (TMPRSS2) playing a crucial role in S protein priming. Other proteases, such as cathepsin L and elastase, neutrophil-expressed (ELANE), have the capability to prime the S protein and contribute to SARS-CoV-2 infection. ELANE variants have not been previously examined in COVID-19 patients. We aimed to assess the association of single nucleotide variants (SNVs) within ELANE with COVID-19 and biochemical markers. The study included 319 SARS-CoV-2-infected patients and 288 controls. Genotyping of ELANE rs17216663C/T (Pro257Leu), rs17223045C/T (As1n30Asn), and rs3761007G/A was conducted using a 5'-nuclease allelic discrimination assay (TaqMan assay). Our findings indicate that ELANE rs17223045C/T (C vs T: odds ratio [OR] 0.08, P = 0.005, and CC vs CT: OR 0.08, P = 0.005) and rs3761007G/A (G vs A: OR 0.38, P = 0.009, and GG vs GA: OR 0.40, P = 0.008) confer protection against COVID-19. However, these variants were not associated with biochemical markers. In conclusion, our data suggests that ELANE rs17223045C/T and rs3761007G/A SNVs may play a protective role against COVID-19.

Elucidation of the Anticancer Mechanism of Durian Fruit (Durio zibethinus) Pulp Extract in Human Leukemia (HL-60) Cancer Cells

Durian (Durio zibethinus L.) grows widely in Southeast Asia. The pulp of the durian fruit contains carbohydrates, proteins, lipids, fibers, various vitamins, minerals, and fatty acids. This study was carried out to elucidate the anticancer mechanism of action of the methanolic extract of the fruit of Durio zibethinus (D. zibethinus) on human leukemia (HL-60) cells. The methanolic extract of D. zibethinus fruits exhibited its anticancer effect on HL-60 cells by inducing DNA damage and apoptosis. The DNA damage was confirmed by comet and DNA fragmentation assays. The methanolic extract of D. zibethinus fruits has been shown to cause cell cycle arrest in HL-60 cells during the S phase and G2/M phase. Additionally, the methanolic extract caused induction of the apoptotic pathway in the HL-60 cell line. This was confirmed by increased expression in pro-apoptotic proteins, viz., Bax protein expression, and a substantial reduction (p < 0.001) in anti-apoptotic proteins, viz., Bcl-2 and Bcl-xL expressions. Therefore, this study confirms that the methanolic extract of D. zibethinus exerts its anticancer effects on the HL-60 cell line, causing cell cycle arrest and induction of apoptosis by an intrinsic mechanism.

Slaughterhouse and poultry wastes: management practices, feedstocks for renewable energy production, and recovery of value added products

The slaughterhouse and poultry industry is possibly one of the fastest-growing sectors driven by the increasing demand in food availability. Subsequently, the wastes produced from the slaughterhouse and poultry industry are in huge quantities, which could be a promising resource for the recovery of value added products, and bioenergy production to minimize the dependence on fossil fuels. Furthermore, the wastes from slaughterhouses and poultry are a hub of pathogens that is capable of infecting humans and animals. This demands the emerging need for an effective and safe disposal method to reduce the spread of diseases following animal slaughtering. In light of that, the state of the production of slaughterhouse and poultry wastes was presented at first. Following this, the impact of solid waste exposure in terms of air, water, and soil pollution and the associated health challenges due to improper solid waste management practices were presented to highlight the importance of the topic. Secondly, the potency of these solid wastes and the various waste-to-energy technologies that have been employed for effective management and resource utilization of wastes generated from slaughterhouses and poultry were reviewed in detail. Finally, this review also highlights the opportunities and challenges associated with effective solid waste management, future requirements for the development of effective technologies for the recovery of value added products (like keratin, fibreboards), and biofuel production.

Molecular characterization of coat color gene in Sahiwal versus Karan Fries bovine

Background

Melanocortin-1-receptor gene (MC1R) plays a significant role in signaling cascade of melanin production. In cattle, the coat colors, such as red and black, are an outcome of eumelanin and pheomelanin pigments, respectively. The coat colors have become critical factors in the animal selection process. This study is therefore aimed at the molecular characterization of reddish-brown coat-colored Sahiwal cattle in comparison to the black and white-colored Karan Fries.

Results

The Sequence length of the MC1R gene was 954 base pairs in Sahiwal cattle. The sequences were examined and submitted to GenBank Acc.No. MG373575 to MG373605. Alignment of both (Sahiwal and Karan Fries) protein sequences by applying ClustalO multiple sequence alignment programs revealed 99.8–96.8% sequence similarity within the bovine. MC1R gene phylogenetic studies were analyzed by MEGA X. The gene MC1R tree, protein confines, and hereditary difference of cattle were derived from Ensemble Asia Cow Genome Browser 97. One unique single-nucleotide polymorphism (c.844C>A) (SNP) was distinguished. Single amino acid changes were detected in the seventh transmembrane structural helix region, with SNP at p.281 T>N of MC1R gene in Karan Fries cattle.

Conclusions

In this current research, we first distinguished the genomic sequence of the MC1R gene regions that showed evidence of coat variation between Indian indigenous Sahiwal cattle breed correlated with crossbreed Karan Fries. These variations were found in the Melanocortin 1 receptor coding regions of the diverse SNPs. The conclusions of this research provide new insights into understanding the coat color variation in crossbreed compared to the Indian Sahiwal cattle.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s43141-021-00117-2.

DNA Extraction with TRIzol Reagent Using a Silica Column

TRIzol is a monophasic solution of phenol and guanidine isothiocyanate used for the extraction of RNA, DNA and proteins from tissues or cells. However, few studies have described its application to DNA extraction due to its time-consuming procedure. We present a TRIzol-modified method of extracting DNA from tissues using the TRIzol reagent and a silica column, which requires only one-third of the time required for the classic extraction procedure. Spectrophotometric analysis showed that the 260/280 and 260/230 nm optical density ratio of the DNA extracted using the TRIzol-modified method is ideal and equal to that obtained by the classic method and commercial DNAiso methods. The DNA extracted by the TRIzol-modified method had the same performance in a restriction enzyme digestion and quantitative PCR as that extracted using the classic method. Using the TRIzol-modified method saves time, simplifies the DNA extraction procedure, and facilitates various molecular biology assays.

Identification and sequence characterization of melanocortin 1 receptor gene (MC1R) in Bos indicus versus (Bos taurus X Bos indicus)

Melanocortin 1 receptor (MC1R) plays a vital role in melanogenesis and determines coat color of mammals. Polymorphic variants in MC1R, causing coat color variation, were described in few mammals; however, such studies were not done in cattle. The objective of the study was to explore the association of MC1R gene polymorphism within Tharparkar (Bos indicus) and Karan Fries (B. indicus X Bos taurus) cattle. Genomic DNA isolated from blood samples of Tharparkar breed by modified Phenol: Chloroform; Isoamyl alcohol method. Using genomic DNA as template for PCR, MC1R gene was amplified and sequenced. The sequences were analyzed and submitted to Genbank with Acc.No MG373615-MG373644. Comparison of sequence alignment with other bovine species using ClustalW revealed 99-96% similarity. MC1R gene phylogenetic analyses were analyzed using MEGA X. The MC1R gene tree, protein domains and genetic variation of cattle were retrieved from Ensemble Asia Cattle Genome Browser. Eight single nucleotide polymorphisms (SNPs) (c.296T > C, c.583T > C, c.663C > T, c.830T > C, c.853G > A, c.880G > A, c.906C > G, c.927C > T) in CDS reveal high genetic variability. Subsequent to amino acid changes p.L99P, p.F195L, p.F277S, p.A285T and p.D293N, p.R302S, respectively found in seven-transmembrane. Mutations appeared in MC1R of B. taurus with white and black coat color as compared to B. indicus with white coat.