In Silico Molecular Docking Analysis of α-Pinene: An Antioxidant and Anticancer Drug Obtained from Myrtus communis

Background: Testis-specific protein on Y chromosome (TSPY) is the output of a tandem gene cluster. TSPY expression has been observed in gonadoblastoma and numerous distinct kinds of germ cell tumors, such as carcinoma in situ/intratubular germ cell neoplasia, seminoma, and extragonadal intracranial germ cell tumors (GCT). Myrtus communis extract rich in α-pinene showed high antioxidant and anticancer activity against a TSPY. Methods: The molecular weight and theoretical isoelectric of the TSPY proteins were calculated, using the ExPASSY ProtParam tools. Some software like mega 6, BioEdit, NEB cutter (New England Biolabs), and CAP3 were used to analyze clustering and find restriction enzymes on the TSPY sequence. To evaluate the nucleotide diversity of all sequences, the number of diverse situations and Tajima’s and Watterson’s estimators of theta were assessed. Nucleotide polymorphism can be measured by several parameters, such as haplotypes diversity, nucleotide diversity, Theta using Dnasp software. To find interaction networks of protein-protein search tool for the retrieval of interacting genes/proteins (STRING) tools and to predict 3D structure, SWISS-MODEL was used; however, for docking protein-peptide based on interaction, Swiss Dock, Galaxy web, and CABS-dock software were employed. Results: We report a high (0.91) dN/dS index, positive Tajima's D, Fu, and Li’s tests, and a non-significant D test suggesting the occurrence of old modifications or a decrease of newborn mutations in the TSPY gene family. Interestingly, several hub proteins produced a strong chain or an operative module within their protein groups, such as nucleosome assembly protein (1NAP1L), RBMXL2, TBL1Y, and AMELY, which are all associated with the same cellular appliance elements and/or genetic uses. The docking of the TSPY target with α-pinene using docking revealed that the computationally-prognosticated lowest energy networks of TSPY are established by intermolecular hydrogen bonds and stacking interactions. Conclusions: The results of this study demonstrated that α-pinene interacts with the TSPY protein target and could be developed as a promising candidate for the new anticancer agent.

Molecular evidence indicates the existence of multiple lineages of Sperata species in Indian Rivers

Sperata seenghala (Giant river-catfish) and Sperata aor (Long-whiskered catfish) are commercially important freshwater catfishes of India, belongs to family Bagridae. Due to high nutritional significance and the low number of intramuscular bones, both fishes have considerable demand in South Asian countries. Both of the Sperata species are morphologically close and well adapted to the same habitat. In this study, we have assessed the level of genetic diversity and differentiation of S. seenghala and S. aor in the Ganga River based on the mitochondrial DNA (mtDNA) control region and compared with the other major Indian rivers. We found high haplotypes diversity for both the species in the Ganga. However, it was comparatively low for S. seenghala in Mahanadi and Brahmaputra populations. The phylogenetic and median-joining network strongly indicated the presence of two distinct maternal lineages of S. seenghala from the Ganga river. Interestingly, the genetic differentiation between S. seenghala of Ganga-Brahmaputra was much higher (~25.3%) than the S. seenghala and S. aor (~17%), whereas it was comparatively low between Ganges-Mahanadi (~8.0%). Our finding provided evidence that all the three rivers: Ganga, Mahanadi, and the Brahmaputra sustain a highly diverse and genetically distinct stock of giant river catfish; therefore, all populations should be considered as a different management unit for the protection of stocks. Our findings indicated that Brahmaputra lineages qualify the species level variations. This study can be further used as a reference database for proper lineage identification of S. seenghala and S. aor that could formulate the appropriate conservation and management plans.

Genetic diversity of Ongole Grade, Aceh, and Sumbawa cattle based on polymorphism on ND-5 fragment mitochondrial DNA using PCR-RFLP technique

Sutarno, Zahrah S, Astirin OP, Herawati E, Setyawan AD. 2019. Genetic diversity of Ongole Grade, Aceh, and Sumbawa cattle based on polymorphism on ND-5 fragment mitochondrial DNA using PCR-RFLP technique. Biodiversitas 20: 783-788. Genetic diversity is the basis of livestock breeding because it can be used as an initial improvement in livestock quality through artificial selection. This study aims to determine polymorphism in ND-5 fragment of mitochondrial DNA in Ongole Grade, Aceh, and Sumbawa cattle and their genetic diversity. The total DNA from the blood of the local cattle was extracted using the Wizard genomic DNA purification system from Promega and amplified using the PCR technique. The PCR product was then digested with HindIII enzyme using the RFLP technique to detect polymorphism. The genetic diversity of the Ongole Grade, Aceh, and Sumbawa cattle was analyzed using the formula from Nei and its genetic relationship was evaluated with the 2.02i NTSYSpc version program. Our findings showed there were polymorphisms in the ND-5 fragment of mitochondrial DNA. Digestion with HindIII restriction enzyme produces two types of haplotypes. Haplotype B is a 453 bp-sized DNA fragment that is not truncated by the HindIII enzyme, and haplotype A is a DNA fragment cut by HindIII enzyme into two with fragments of 336 bp and 117 bp. Polymorphism was found in Ongole Grade cattle, but not in Sumbawa and Aceh cattle. Haplotypes diversity in ND-5 fragments of mitochondrial DNA of Ongole Grade was 0.6250 while Sumbawa and Aceh cattle displayed no diversity of haplotypes. The genetic relationship shows that Sumbawa cattle belonged to the same cluster with Ongole Grade but separated from Aceh cattle.

A New Sequence Change in the Hs2-Lcr (G→A − 10.677) and Gg-Globin Gene Promoter Region (T→C − 157 and a 4 Bp Deletion − 222 to − 225) in Sickle Cell Anemia Patients with Fetal Hemoglobin Level and bS-Globin Gene Haplotypes Diversity.

The sickle cell anemia has a very high prevalence in Bahia, a state of Brazil. The HbF levels and bS-globin gene haplotypes of 125 sickle cell anemia patients were investigated and the Gγ and Aγ gene promoter and HS2-LCR regions of ten patients were selected for DNA sequence. The study was approved by the Oswaldo Cruz Research Foundation’s human research ethics committee. The bS- globin gene haplotypes were investigated using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) techniques; the HbF levels were estimated by high performance liquid chromatography (HPLC). The Gg and Ag-globin gene promoter and HS2-LCR regions were sequenced in an automatic sequencer. The distribution of bS- globin gene haplotypes showed 64 (51.2%) patients with genotype CAR/Ben; 36 (28.8%) Ben/Ben; 18 (14.4%) CAR/CAR; two (1.6%) CAR/Aty; two (1.6%) Ben/Cam; one (0.8%) Car/Cam; one (0.8%) CAR/Arab-India and one (0.8%) Sen/Aty. Among these patients, four CAR/CAR had HbF ≥10.0%; three Ben/Ben had HbF ≤ 5.0%; 11 CAR/Ben had HbF ≥15.0% and 18 had HbF ≤ 5.0%; two Cam/Ben patients had HbF levels ≥15.0%. Ten individuals presenting HbF and bS-globin gene haplotypes diversity were selected to sequence the Gg and Ag-globin gene promoter and HS2-LCR regions. The HS2-LCR sequence analyses demonstrated a G→A change (−10.677) (GeneBank DQ873522) in five sickle cell anemia patients with Ben haplotype and high HbF levels (Table 1); the CAR/Ben and Ben/Ben patients with low HbF levels did not have this sequence variation; among the small patient group investigated, there were two CAR/CAR patients with high HbF levels without this substitution. The Gg gene promoter sequence analyses showed a T→C substitution (−157) (GeneBank DQ873521) among all patients and a 4 bp deletion (−222 to −225) (GeneBank DQ873519) related to Cam haplotype (Figure 1). The HS2-LCR sequence change reported here is located in the proximity to a binding site of the GATA-1 and a ubiquitous trans-acting factor and can constitute a motif associated to the Ben chromosome and may play an important role in g-globin gene transcription regulation. The polymorphic site on Gg-globin gene promoter region can be a common sequence characteristic among the Brazilian sickle cell anemia patients. The results described here suggest new polymorphisms in the HS2-LCR and Gg gene promoter and confirms the genotypic heterogeneity among Brazilian sickle cell anemia patients, justifying further studies to investigate its correlation with HbF synthesis and clinical profile in sickle cell anemia patients. Figure Figure