Analysis of the evolutionarily conserved repeat motifs in the genome of the highly endangered central Indian swamp deer Cervus duvauceli branderi

Icariin protects cerebral neural cells from ischemia‑reperfusion injury in an in vitro model by lowering ROS production and intracellular calcium concentration

Ischemia is one of the major causes of stroke. The present study investigated the protection of cultured neural cells by icariin (ICA) against ischemia-reperfusion (I/R) injury and possible mechanisms underlying the protection. Neural cells were isolated from neonatal rats and cultured in vitro. The cells were subjected to oxygen-glucose deprivation and reoxygenation (OGD-R) as an I/R mimic to generate I/R injury, and were post-OGD-R treated with ICA. Following the treatments, cell viability, apoptosis, reactive oxygen species (ROS), lactate dehydrogenase (LDH), superoxide dismutase (SOD) and Ca²⁺ concentration were assessed using Cell Counting Kit-8 assay, flow cytometry, CyQUANT™ LDH Cytotoxicity Assay, H₂DCFDA and SOD colorimetric activity kit. After OGD-R, considerable I/R injury was observed in the neural cells, as indicated by reduced cell viability, increased apoptosis and increased production of ROS and LDH (P<0.05). Cellular Ca²⁺ concentration was also increased, while SOD activity remained unchanged. Post-OGD-R ICA treatments increased cell viability up to 87.1% (P<0.05) and reduced apoptosis as low as 6.6% (P<0.05) in a concentration-dependent manner. The treatments also resulted in fewer ROS (P<0.05), lower extracellular LDH content (440.5 vs. 230.3 U/l; P<0.05) and reduced Ca²⁺ increase (P<0.05). These data suggest that ICA protects the neural cells from I/R injury in an in vitro model through antioxidation activity and maintaining cellular Ca²⁺ homeostasis. This function may be explored as a potential therapeutic strategy for ischemia-related diseases after further in vivo studies.

Forensic Epigenetic Analysis: The Path Ahead

Unlike DNA fingerprinting, which scores for differences in the genome that are phenotype neutral, epigenetic variations are gaining importance in forensic investigations. Methylation of DNA has a broad range of effects on the lifestyle, health status, and physical appearance of individuals. DNA methylation profiling of forensic samples is useful in determination of the cell or tissue type of the DNA source and also for estimation of age. The quality and quantity of the biosample available from the crime scene limits the possible number of DNA methylation tests and the selection of the technology that can be used. Several techniques have been used for DNA methylation analysis for epigenetic investigations of forensic biological samples. However, novel techniques are needed for multiplex analysis of epigenetic markers as the techniques that are currently available require a large amount of high-quality DNA and are also limited in their multiplexing capacities that are often insufficient to fully resolve a forensic query of interest.

Genetic characterization of wild swamp deer populations: ex situ conservation and forensics implications

Swamp deer (Rucervus duvaucelii) is an endemic, Scheduled I species under the Wildlife (Protection) Act 1972, India. According to variations in antler size, it has been classified into three subspecies, namely Western (R. duvaucelii duvaucelii), Central (R. duvaucelii branderi), and Eastern (R. duvaucelii ranjitsinhii). For planning effective ex situ and in situ conservation of a wide-ranging species in different bioclimatic regions and in wildlife forensic, the use of genetic characterization in defining morpho/ecotypes has been suggested because of the geographic clines and reproductive isolation. In spite of these morphotypes, very little is known about the genetic characteristics of the three subspecies, hence no strict subspecies-based breeding plan for retaining the evolutionary characteristics in captive populations for subsequent re-introduction is available except for a few studies. We describe the genetic characteristics of these three subspecies using cytochrome b of the mtDNA genome (400 bp). The DNA sequence data indicated 11 variable sites within the three subspecies. Two paraphyletic clades, namely the Central India and Western-Eastern populations were found, whereas the Western and Eastern populations are monophyletic with a bootstrap value of 69% within the clade. We suggest the need of sorting these three subspecies using different molecular mtDNA markers in zoos for captive breeding purposes so as to retain the genetic diversity of the separate geographic clines and to use a subspecies-specific fixed-state nucleotide to assess the extent of poaching to avoid any population demography stochastically in India.

A complete phylogeny of the whales, dolphins and even-toed hoofed mammals (Cetartiodactyla)

Despite the biological and economic importance of the Cetartiodactyla, the phylogeny of this clade remains controversial. Using the supertree approach of matrix representation with parsimony, we present the first phylogeny to include all 290 extant species of the Cetacea (whales and dolphins) and Artiodactyla (even-toed hoofed mammals). At the family-level, the supertree is fully resolved. For example, the relationships among the Ruminantia appear as (((Cervidae, Moschidae) Bovidae) (Giraffidae, Antilocapridae) Tragulidae). However, due to either lack of phylogenetic study or contradictory information, polytomies occur within the clades Sus, Muntiacus, Cervus, Delphinidae, Ziphiidae and Bovidae. Complete species-level phylogenies are necessary for both illustrating and analysing biological, geographical and ecological patterns in an evolutionary framework. The present species-level tree of the Cetartiodactyla provides the first opportunity to examine comparative hypotheses across entirely aquatic and terrestrial species within a single mammalian order.

Development of a DNA marker by minisatellite associated sequence amplification (MASA) from the endangered Indian rhino (Rhinoceros unicornis)

Rhinoceroses are highly endangered species and their protection warrants immediate remedial measures. Development of DNA markers is envisaged to complement global efforts of the conservation of these extant animals. Minisatellite associated sequence amplification (MASA) of DNA from Indian rhinoceros (Rhinoceros unicornis) and three sub-species of South African black rhinoceros (Diceros bicornis) was carried out using a primer based on consensus sequence of the minisatellite repeat locus 33.15. Several bands in the range of 3.0 kilobases (kb) to 650 base pairs (bp) were identified that were useful for successful differentiation of R. unicornis from D. bicornis. Of these fragments, a 688 bp one, unique to R. unicornis was cloned and sequenced (Accession No. AF-296689). The band patterns uncovered by MASA and the species-specific hybridisation of pSG5 may be utilised as a tool for differentiating the R. unicornis genome from that of D. bicornis. This approach may also be adopted for the development of DNA-based genetic marker(s) useful for identification of other endangered species.

Detection of species of graft in xenotransplants using arbitrary primed polymerase chain reaction

Because of a shortage in the availability of human organs, xenografts have been attempted in humans with cardiac, renal, and hepatic failure, despite limited success. Use of xenografts, however, is regulated under law in various countries. In xenotransplant cases related to violation of transplantation law, determination of species of the source of tissue and organ(s) becomes highly essential. Random amplified polymorphic DNA (RAPD) protocols using six sets of arbitrary short-sequenced primers have been standardized for verifying claims of porcine cardiac and renal grafts in human transplantation cases. Six arbitrary primers used were found to generate unique amplicon patterns at 36 degrees C annealing temperature. Among the selected primers, a single primer set having the sequence 5'- GGTGCGGGAA -3' is found to be the most informative in discerning porcine tissue contamination in humans. The patterns obtained were consistent for a particular genome. The grafted organs in the studied case were analyzed to be of porcine origin.

PCR-detected genome polymorphism in malignant cell growth

In this chapter, we analyze the problem of genetic polymorphism in tumorigenesis, which determines basic capacities of tumors. The study of genome polymorphism with modified PCR methods allows the detection of various forms of polymorphism in tumor cells. This method has made it possible to determine association of DNA polymorphism with conditions of oncogenes, antioncogenes, and genes of apoptosis and with their allelic states. A special type of nonspecific DNA polymorphism that resulted from an increase in the mutation number in the cancer cell genome was discovered. This phenomenon was called the microsatellite mutator phenotype. Because the type of DNA polymorphism correlates with various biological capacities of malignant tumors and has an important prognostic significance, the analysis of DNA polymorphism in benign and malignant tumors of different histogenesis will play an important role both in theoretical studies of cancer and in oncological practice. A modified B1-PCR was used to study the genome polymorphism in the mouse tumor cells. The gain of the band 470 bp and the loss of the band 600 bp were revealed in the hepatoma cell line MH-22a as compared with liver cells of C3HA mice. The differentiation of teratocarcinoma EC F9 cells to endoderm-like cells was not accompanied by any changes in the B1-AF DNA fingerprint.

Characterization of a species-specific repetitive DNA from a highly endangered wild animal, Rhinoceros unicornis, and assessment of genetic polymorphism by microsatellite associated sequence amplification (MASA)

We have cloned and sequenced a 906bp EcoRI repeat DNA fraction from Rhinoceros unicornis genome. The contig pSS(R)2 is AT rich with 340 A (37.53%), 187 C (20.64%), 173 G (19.09%) and 206 T (22.74%). The sequence contains MALT box, NF-E1, Poly-A signal, lariat consensus sequences, TATA box, translational initiation sequences and several stop codons. Translation of the contig showed seven different types of protein motifs, among which, EGF-like domain cysteine pattern signatures and Bowman-Birk serine protease inhibitor family signatures were prominent. The presence of eukaryotic transcriptional elements, protein signatures and analysis of subset sequences in the 5' region from 1 to 165nt indicating coding potential (test code value=0.97) suggest possible regulatory and/or functional role(s) of these sequences in the rhino genome. Translation of the complementary strand from 906 to 706nt and 190 to 2nt showed proteins of more than 7kDa rich in non-polar residues. This suggests that pSS(R)2 is either a part of, or adjacent to, a functional gene. The contig contains mostly non-consecutive simple repeat units from 2 to 17nt with varying frequencies, of which four base motifs were found to be predominant. Zoo-blot hybridization revealed that pSS(R)2 sequences are unique to R. unicornis genome because they do not cross-hybridize, even with the genomic DNA of South African black rhino Diceros bicornis. Southern blot analysis of R. unicornis genomic DNA with pSS(R)2 and other synthetic oligo probes revealed a high level of genetic homogeneity, which was also substantiated by microsatellite associated sequence amplification (MASA). Owing to its uniqueness, the pSS(R)2 probe has a potential application in the area of conservation biology for unequivocal identification of horn or other body tissues of R. unicornis. The evolutionary aspect of this repeat fraction in the context of comparative genome analysis is discussed.