Minimum population size,genetic diversity,and social structure of the Asian elephant in Cat Tien National Park and its adjoining areas,Vietnam, based on molecular genetic analyses

Vietnam’s elephant population that has suffered severe declines during the past three decades is now believed to number 60–80 individuals in the wild. Cat Tien National Park is thought to be one of the key areas for the recovery of Vietnam’s elephants. We carried out a molecular genetic study of elephants in Cat Tien National Park and its adjoining areas with the objectives of estimating minimum population size, assessing genetic diversity, and obtaining insights into social organization. We obtained a minimum population size of 11 elephants based on a combination of unique nuclear microsatellite genotypes and mitochondrial haplotypes. While mitochondrial diversity based on a 600-base pair segment was high in this small sample of individuals, the six microsatellite loci examined showed low diversity and the signature of a recent population bottleneck. Along with nuclear genetic depauperation of Cat Tien’s elephants, we also report disruption of normal social organization, with different matrilines having coalesced into a single social group because of anthropogenic disturbance. The results emphasize the critical condition of this elephant population and the need for urgent conservation measures if this population is to be saved.     

Meprin A and meprin α generate biologically functional IL-1β from pro-IL-1β

The present study demonstrates that both oligomeric metalloendopeptidase meprin A purified from kidney cortex and recombinant meprin α are capable of generating biologically active IL-1β from its precursor pro-IL-1β. Amino-acid sequencing analysis reveals that meprin A and meprin α cleave pro-IL-1β at the His¹¹⁵-Asp¹¹⁶ bond, which is one amino acid N-terminal to the caspase-1 cleavage site and five amino acids C-terminal to the meprin β site. The biological activity of the pro-IL-1β cleaved product produced by meprin A, determined by proliferative response of helper T-cells, was 3-fold higher to that of the IL-1β product produced by meprin β or caspase-1. In a mouse model of sepsis induced by cecal ligation puncture that results in elevated levels of serum IL-1β, meprin inhibitor actinonin significantly reduces levels of serum IL-1β. Meprin A and meprin α may therefore play a critical role in the production of active IL-1β during inflammation and tissue injury.     

Quantitative PCR for Genetic Markers of Human Fecal Pollution

Assessment of health risk and fecal bacterial loads associated with human fecal pollution requires reliable host-specific analytical methods and a rapid quantification approach. We report the development of quantitative PCR assays for quantification of two recently described human-specific genetic markers targeting Bacteroidales-like cell surface-associated genes. Each assay exhibited a range of quantification from 10 to 1 × 10⁶ copies of target DNA. For each assay, internal amplification controls were developed to detect the presence or absence of amplification inhibitors. The assays predominantly detected human fecal specimens and exhibited specificity levels greater than 97% when tested against 265 fecal DNA extracts from 22 different animal species. The abundance of each human-specific genetic marker in primary effluent wastewater samples collected from 20 geographically distinct locations was measured and compared to quantities estimated by real-time PCR assays specific for rRNA gene sequences from total Bacteroidales and enterococcal fecal microorganisms. Assay performances combined with the prevalence of DNA targets in sewage samples provide experimental evidence supporting the potential application of these quantitative methods for monitoring fecal pollution in ambient environmental waters.Waterborne diseases that originate from human fecal pollution remain a significant public health issue. As a result, a large number of methods have been developed to detect and quantify human fecal pollution (10, 12, 18, 20). The majority of these methods are based on real-time quantitative PCR (qPCR) assays designed to estimate the concentrations of 16S rRNA gene sequences from various subpopulations within the order Bacteroidales. This bacterial order constitutes a large proportion of the normal gut microbiota of most animals, including humans (3, 15, 27). Bacterial 16S rRNA genes are useful as markers because they have relatively low mutation rates (7) and are typically present in multiple operons, increasing template DNA levels available for detection (2, 11, 17, 29). While several studies have demonstrated the value of Bacteroides 16S rRNA gene-based qPCR assays, currently available assays cannot discriminate between several animal sources closely associated with humans, including cats, dogs, and/or swine (10, 12, 18, 20). Alternative qPCR assays targeting genes directly involved in host-specific interactions may be capable of increased discrimination of fecal pollution sources (22, 23) and are needed to complement existing qPCR-based approaches used to identify sources of human fecal pollution.A recent metagenomic survey of a human fecal bacterial community using genome fragment enrichment has led to the identification of hundreds of candidate human fecal bacterium-specific DNA sequences (23). PCR assays targeting two gene sequences encoding a hypothetical protein potentially involved in remodeling of bacterial surface polysaccharides and lipopolysaccharides (assay 19) and a putative RNA polymerase extracytoplasmic function sigma factor (assay 22) from Bacteroidales-like microorganisms exhibited a high level of specificity (100%) for human fecal material (23). However, it remained to be determined whether these reported chromosomal DNA sequences are abundant and uniform enough within human populations to be detected once diluted in the environment. On the basis of these considerations, the next steps toward the application of these gene sequences for water quality monitoring applications were to design qPCR assays for their detection and then to use these assays to evaluate the overall abundance and distribution of these sequences in human populations relative to those of rRNA gene sequences from different currently recognized fecal indicator bacterial groups.Here, we report the development of two qPCR assays for quantification of the human-specific DNA sequences targeted by previously reported PCR assays 19 and 22 (23). Method performance characteristics, including specificity, range of quantification (ROQ), limit of quantification, amplification efficiency, and analytical precision, were defined for each assay. An internal amplification control (IAC) was designed to monitor for the presence of inhibitors commonly associated with environmental sampling that can confound DNA target copy number estimations. Finally, the abundance of each DNA target in primary effluent wastewater samples representative of 20 geographically distinct human populations was measured by qPCR analysis. In addition, the abundances of these human-specific DNA genes in wastewater were compared to those of rRNA genes of Bacteroidales and enterococci, two general fecal indicator bacterial groups that have been widely used for water quality testing.     

Enzymatic labeling of nucleic acids

Enzymatic labeling of nucleic acids is a fundamental tool in molecular biology with virtually every aspect of nucleic acid hybridization technique involving the use of labeled probes. Different methods for enzymatic labeling of DNA, RNA and oligonucleotide probes are available today. In this review, we will describe both radioactive and nonradioactive labeling methods, yet the choice of system for labeling the probe depends on the application under study.     

Suproxide dismutase in human testis preparations

A protein fraction from human testis was structurally investigated. The main component of the fraction reported to contain inhibin-like activity was purified and analyzed by tryptic digestion. The peptides obtained identified the protein as an enzyme, superoxide dismutase, previously known to be present in seminal plasma. The results show that superoxide dismutase is a major enzyme, also of testicular material. They further demonstrate the importance of using pure fractions, and controls such as checks with structural analysis or synthetic peptides, in the work of elucidating the nature of inhibin and other hormonal peptides.     

Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome

Natural selection leaves its footprints on protein-coding sequences by modulating their silent and replacement evolutionary rates. In highly expressed genes in invertebrates, these footprints are seen in the higher codon usage bias and lower synonymous divergence. In mammals, the highly expressed genes have a shorter gene length in the genome and the breadth of expression is known to constrain the rate of protein evolution. Here we have examined how the rates of evolution of proteins encoded by the vertebrate genomes are modulated by the amount (intensity) of gene expression. To understand how natural selection operates on proteins that appear to have arisen in earlier and later phases of animal evolution, we have contrasted patterns of mouse proteins that have homologs in invertebrate and protist genomes (Precambrian genes) with those that do not have such detectable homologs (vertebrate-specific genes). We find that the intensity of gene expression relates inversely to the rate of protein sequence evolution on a genomic scale. The most highly expressed genes actually show the lowest total number of substitutions per polypeptide, consistent with cumulative effects of purifying selection on individual amino acid replacements. Precambrian genes exhibit a more pronounced difference in protein evolutionary rates (up to three times) between the genes with high and low expression levels as compared to the vertebrate-specific genes, which appears to be due to the narrower breadth of expression of the vertebrate-specific genes. These results provide insights into the differential relationship and effect of the increasing complexity of animal body form on evolutionary rates of proteins.     

DNA staining in agarose and polyacrylamide gels by methyl green

ABSTRACT

Methyl green (MG) is an inexpensive, nonproprietary, traditional histological stain for cell nuclei. When bound to DNA and upon excitation with orange-red light, it fluoresces brightly in the far red region. We compared MG with ethidium bromide (EtBr), the conventional stain for DNA in gels, and Serva DNA stain G? (SDsG), a proprietary stain marketed as a safer alternative to EtBr for staining of electrophoresed DNA bands in agarose and polyacrylamide gels. DNA-MG fluorescence was recorded and 2.4 μg/ml MG produced crisp images of electrophoresed DNA after incubation for 10 min. Stain solutions were stable and detection limits for faint bands as well as relative densitometric quantitation were equivalent to EtBr. MG, EtBr and SDsG cost 0.0192, 0.024 and 157.5 US cents/test, respectively. MG is an effective stain for visualizing DNA in agarose and polyacrylamide gels. Its major advantages including low cost, comparable quality of staining, storage at room temperature, photo-resistance and low mutagenic profile outweigh its disadvantages such as staining of tracking dye and requirement for a gel documentation system with a red filter.