Overview of Metagenomics for Marine Biodiversity Research

We are in the midst of the fastest growing revolution in molecular biology,perhaps in all of life science, and it appears to be speeding up. We still know very little about the vast diversity of micro-organisms, their metabolic pathways and microbial activity in natural environments. Modern genomic tools are providing deep access to natural microbial diversity and ecology. Interdisciplinary approaches will be required to fully understand microbial ecology by: (1) analysis of genomes, transcriptomes, proteomes and metabolomes and (2) analysis at various levels of individuals, populations, communities and ecosystems. Data gathered is not only theoretical. It holds the promise of practical applications in the control of infectious diseases, in the production of biotechnology goods and services and in environmentalremediation. It is an incredibly exciting time in science for the newer generation of scientists, “loaded” with opportunities. It is an excellent time to develop and apply tools to solve problems of local and global importance.We are in the midst of the fastest growing revolution in molecular biology,perhaps in all of life science, and it appears to be speeding up. We still know very little about the vast diversity of micro-organisms, their metabolic pathways and microbial activity in natural environments. Modern genomic tools are providing deep access to natural microbial diversity and ecology. Interdisciplinary approaches will be required to fully understand microbial ecology by: (1) analysis of genomes, transcriptomes, proteomes and metabolomes and (2) analysis at various levels of individuals, populations, communities and ecosystems. Data gathered is not only theoretical. It holds the promise of practical applications in the control of infectious diseases, in the production of biotechnology goods and services and in environmentalremediation. It is an incredibly exciting time in science for the newer generation of scientists, “loaded” with opportunities. It is an excellent time to develop and apply tools to solve problems of local and global importance

Denaturing Polyacrylamide Gel Electrophoresis

Thin polyacrylamide gels that contain a high concentration of urea as a denaturant are capable of resolving short (<500 nucleotides) single‐stranded fragments of DNA or RNA that differ in length by as little as one nucleotide. Such gels are uniquely suited for nucleic acid sequence analysis, which is required, for instance, for all footprinting protocols. Thicker gels are often used to purify oligonucleotides. This appendix describes the pouring, running, and processing of a typical sequencing gel, which is 40 cm long with a uniform thickness of 0.4 mm, containing 7 M urea and 4% to 8% acrylamide.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143785/1/cpnca03b.pd

Pendokumentasian Aplikasi Ragam Hias Budaya Bali, sebagai Upaya Konservasi Budaya Bangsa Khususnya pada Perancangan Interior

Various ornament of Indonesian people comes from the ethnic groups from all over the archipelago. As a tangible cultural ornament has a specific purpose and it does not change throughout the ages. Bali is one of the ethnic group in archipelago that has beautiful decorative art and one of the most popular tourism destination in Indonesia. Bali\u27s ornament generally seen as decorative carving on the column, window or even in door. The beauty of Bali is not only as an inspiration for their colors and sculpture but also the variety of forms that have been simplified in the ornament. Moreover, floral &amp; fauna forms are easy to apply as an interior element in modern buildings. Generally the value of these ornament has a specific purpose related to the cultural and social custom in Bali people. So that the application need to consider more about the purpose of the symbol of the ornament

Lack of an Interchromosomal Effect Associated with Spontaneous Recombination in Males of Drosophila Melanogaster

Author Institution: Department of Biological Sciences, Bowling Green State UniversityIt is shown that the frequency of spontaneous male recombination in two different lines of Drosophila melanogaster (OKI and T-007) are not subject to an interchromosomal effect. Second-chromosome male recombination in these lines was not affected by heterozygosity for the multiple third-chromosome inversions In(3LR)TM3 or In(3LR)Ubxm, which do affect recombination in females. It seems, therefore, that a large fraction of spontaneous recombination in males of D. melanogaster occurs by some mechanism other than that in females. We discuss the possibility that the mechanism is chromosome breakage and reunion, and that these breakage events may be caused by a microorganism

Diversifying selection and host adaptation in two endosymbiont genomes

Background: The endosymbiont Wolbachia pipientis infects a broad range of arthropod and filarial nematode hosts. These diverse associations form an attractive model for understanding host: symbiont coevolution. Wolbachia's ubiquity and ability to dramatically alter host reproductive biology also form the foundation of research strategies aimed at controlling insect pests and vector-borne disease. The Wolbachia strains that infect nematodes are phylogenetically distinct, strictly vertically transmitted, and required by their hosts for growth and reproduction. Insects in contrast form more fluid associations with Wolbachia. In these taxa, host populations are most often polymorphic for infection, horizontal transmission occurs between distantly related hosts, and direct fitness effects on hosts are mild. Despite extensive interest in the Wolbachia system for many years, relatively little is known about the molecular mechanisms that mediate its varied interactions with different hosts. We have compared the genomes of the Wolbachia that infect Drosophila melanogaster, wMel and the nematode Brugia malayi, wBm to that of an outgroup Anaplasma marginale to identify genes that have experienced diversifying selection in the Wolbachia lineages. The goal of the study was to identify likely molecular mechanisms of the symbiosis and to understand the nature of the diverse association across different hosts. Results: The prevalence of selection was far greater in wMel than wBm. Genes contributing to DNA metabolism, cofactor biosynthesis, and secretion were positively selected in both lineages. In wMel there was a greater emphasis on DNA repair, cell division, protein stability, and cell envelope synthesis. Conclusion: Secretion pathways and outer surface protein encoding genes are highly affected by selection in keeping with host: parasite theory. If evidence of selection on various cofactor molecules reflects possible provisioning, then both insect as well as nematode Wolbachia may be providing substances to hosts. Selection on cell envelope synthesis, DNA replication and repair machinery, heat shock, and two component switching suggest strategies insect Wolbachia may employ to cope with diverse host and intra-host environments

Lipoprotein biosynthesis as a target for anti-Wolbachia treatment of filarial nematodes

<p>Abstract</p> <p>Background</p> <p>Lymphatic filariasis and onchocerciasis are debilitating diseases caused by filarial nematodes. Disease pathogenesis is induced by inflammatory responses following the death of the parasite. <it>Wolbachia </it>endosymbionts of filariae are potent inducers of innate and adaptive inflammation and bacterial lipoproteins have been identified as the ligands that bind toll-like receptors (TLR) 2 and TLR6. Lipoproteins are important structural and functional components of bacteria and therefore enzymes involved in <it>Wolbachia </it>lipoprotein biosynthesis are potential chemotherapeutic targets.</p> <p>Results</p> <p>Globomycin, a signal peptidase II (LspA) inhibitor, has activity against Gram-negative bacteria and a putative <it>lspA </it>gene has been identified from the <it>Wolbachia </it>genome of <it>Brugia malayi </it>(<it>w</it>Bm). The amino acids required for function are strictly conserved and functionality was verified by complementation tests in a temperature-sensitive <it>Escherichia coli lspA </it>mutant. Also, transformation of wild type <it>E. coli </it>with <it>Wolbachia lspA </it>conferred significant globomycin resistance. A cell-based screen has been developed utilizing a <it>Wolbachia</it>-containing <it>Aedes albopictus </it>cell line to assay novel compounds active against <it>Wolbachia</it>. Globomycin was screened using this assay, which resulted in a dose-dependent reduction in <it>Wolbachia </it>load. Furthermore, globomycin was also effective in reducing the motility and viability of adult <it>B. malayi in vitro</it>.</p> <p>Conclusions</p> <p>These studies validate lipoprotein biosynthesis as a target in an organism for which no genetic tools are available. Further studies to evaluate drugs targeting this pathway are underway as part of the A-WOL drug discovery and development program.</p

Tasting Phenylthiocarbamide (PTC): A New Integrative Genetics Lab with an Old Flavor

First reported in the early 1930s, variation in the ability to taste phenylthiocarbamide (PTC) has since become one of the most widely studied of all human genetic traits. Guo and Reed (2001) provide an excellent review of work on this polymorphism prior to the identification and sequencing of the PTC gene by Kim et al. (2003), and Wooding (2006) provides a stimulating historical review of the role various scientists have played in the study of PTC taste sensitivity and the importance of these studies in relation to natural selection. Identification of the PTC gene and a number of subsequent publications (Wooding et al., 2004; Kim et al., 2005; Wooding et al., 2006) have provided the basis for a new, integrative laboratory investigation of PTC taste sensitivity. This genetics laboratory culminates in the use of the polymerase chain reaction (PCR) and restriction endonuclease digestion to determine the PTC genotype of each student. But “getting there is half the fun” and, in this case, “getting there” requires students to use not only their knowledge of molecular techniques in genetics but also their knowledge of Mendelian genetics, population genetics, probability, and pedigree analysis. The other “half the fun” in this case is that in determining their PTC phenotypes and genotypes, students are learning something about themselves

Nematode-Bacterium Symbioses—Cooperation and Conflict Revealed in the “Omics” Age

Nematodes are ubiquitous organisms that have a significant global impact on ecosystems, economies, agriculture, and human health. The applied importance of nematodes and the experimental tractability of many species have promoted their use as models in various research areas, including developmental biology, evolutionary biology, ecology, and animal-bacterium interactions. Nematodes are particularly well suited for the investigation of host associations with bacteria because all nematodes have interacted with bacteria during their evolutionary history and engage in a variety of association types. Interactions between nematodes and bacteria can be positive (mutualistic) or negative (pathogenic/parasitic) and may be transient or stably maintained (symbiotic). Furthermore, since many mechanistic aspects of nematode-bacterium interactions are conserved, their study can provide broader insights into other types of associations, including those relevant to human diseases. Recently, genome-scale studies have been applied to diverse nematode-bacterial interactions and have helped reveal mechanisms of communication and exchange between the associated partners. In addition to providing specific information about the system under investigation, these studies also have helped inform our understanding of genome evolution, mutualism, and innate immunity. In this review we discuss the importance and diversity of nematodes, “omics”' studies in nematode-bacterial systems, and the wider implications of the findings

Absence of the Filarial Endosymbiont Wolbachia in Seal Heartworm (Acanthocheilonema spirocauda) but Evidence of Ancient Lateral Gene Transfer

The symbiotic relationship of Wolbachia spp. was first observed in insects and subsequently in many parasitic filarial nematodes. This bacterium is believed to provide metabolic and developmental assistance to filarial parasitic nematodes, although the exact nature of this relationship remains to be fully elucidated. While Wolbachia is present in most filarial nematodes in the familyOnchocercidae, it is absent in several disparate species such as the human parasite Loa loa. All tested members of the genusAcanthocheilonema, such as Acanthocheilonema viteae, have been shown to lack Wolbachia. Consistent with this, we show thatWolbachia is absent from the seal heartworm (Acanthocheilonema spirocauda), but lateral gene transfer (LGT) of DNA sequences between Wolbachia and A. spirocauda has occurred, indicating a past evolutionary association. Seal heartworm is an important pathogen of phocid seals and understanding its basic biology is essential for conservation of the host. The findings presented here may allow for the development of future treatments or diagnostics for the disease and also aid in clarification of the complicated nematode–Wolbachia relationship

Phenotypic and Molecular Analysis of the Effect of 20-hydroxyecdysone on the Human Filarial Parasite Brugia malayi

A homologue of the ecdysone receptor has been identified and shown to be responsive to 20- hydroxyecdysone in Brugia malayi. However, the role of this master regulator of insect development has not been delineated in filarial nematodes. Gravid adult female B. malayi cultured in the presence of 20-hydroxyecdysone produced significantly more microfilariae and abortive immature progeny than control worms, implicating the ecdysone receptor in regulation of embryogenesis and microfilarial development. Transcriptome analyses identified 30 genes whose expression was significantly up-regulated in 20-hydroxyecdysone-treated parasites compared with untreated controls. Of these, 18% were identified to be regulating transcription. A comparative proteomic analysis revealed 932 proteins to be present in greater amounts in extracts of 20- hydroxyecdysone-treated adult females than in extracts prepared from worms cultured in the absence of the hormone. Of the proteins exhibiting a greater than two-fold difference in the 20- hydroxyecdysone-treated versus untreated parasite extracts, 16% were involved in transcriptional regulation. RNA interference (RNAi) phenotype analysis of Caenorhabditis elegans orthologs revealed that phenotypes involved in developmental processes associated with embryogenesis were significantly over-represented in the transcripts and proteins that were up-regulated by exposure to 20-hydroxyecdysone. Taken together, the transcriptomic, proteomic and phenotypic data suggest that the filarial ecdysone receptor may play a role analogous to that in insects, where it serves as a regulator of egg development