Archive for March, 2010

A New Type of Prion Disease

Monday, March 8th, 2010

BSE Prion diseases, also known as transmissible spongiform encephalopathies, are infectious fatal neurodegenerative diseases of humans and animals. A major feature of prion diseases is the refolding and aggregation of a normal host protein, prion protein (PrP), into a disease-associated form which may contribute to brain damage. In uninfected individuals, normal PrP is anchored to the outer cell membrane by a sugar-phosphate-lipid linker molecule. This report shows that prion infection of mice expressing PrP lacking the anchor can result in a new type of fatal neurodegenerative disease. The disease displays mechanisms of damage to brain cells and brain blood vessels found in Alzheimer’s disease and in familial amyloid brain diseases. In contrast, the typical sponge-like brain damage seen in prion diseases was not observed. These results suggest that presence or absence of PrP membrane anchoring can influence the type of neurodegeneration seen after prion infection. Understanding these interactiions could lead to new therapeutic approaches.

Fatal Transmissible Amyloid Encephalopathy: A New Type of Prion Disease Associated with Lack of Prion Protein Membrane Anchoring. 2010 PLoS Pathog 6(3): e1000800. doi:10.1371/journal.ppat.1000800

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Five Questions about Viruses and MicroRNAs

Friday, March 5th, 2010

miRNA MicroRNAs (miRNAs) are ~22-nt regulatory RNAs expressed by all multicellular eukaryotes. Humans encode >700 miRNAs and similar numbers are likely to exist in other mammalian species. Almost all cellular miRNAs are initially transcribed by RNA polymerase II (Pol II) as part of a long, capped, polyadenylated primary miRNA (pri-miRNA) precursor. The miRNA forms part of one arm of an RNA stem-loop that consists of an ~32-bp imperfect stem flanked by unstructured RNA sequences. This stem-loop is recognized by the nuclear RNase III enzyme Drosha, which cleaves the stem to liberate an ~60-nt pre-miRNA hairpin. The pre-miRNA is then transported to the cytoplasm where it is cleaved by a second RNase III enzyme, called Dicer, which removes the terminal loop to generate the miRNA duplex intermediate. One strand of this duplex is incorporated into the RNA-induced silencing complex (RISC), where it acts as a guide RNA to direct RISC to complementary mRNA species. Depending on the level of complementarity, RISC can either cleave bound mRNAs and/or inhibit their translation. Inhibition of mRNA translation generally requires full complementarity of the mRNA to nucleotides 2 through 7 or 8 from the miRNA 5′ end – the miRNA seed region. The primary, and possibly sole, function of mammalian miRNAs is therefore to act as specific post-transcriptional inhibitors of mRNA function.

  1. Do All Viruses Encode miRNAs? In general, we can divide mammalian viruses into three categories, i.e., the herpesviruses, which encode multiple viral miRNAs; other nuclear DNA viruses, which may encode one or two miRNAs; and the RNA viruses and cytoplasmic DNA viruses, which appear to lack any miRNAs.
  2. What Do Viral miRNAs Do? Virus miRNAs may serve two major functions. First, to inhibit the expression of cellular factors that play a role in cellular innate or adaptive antiviral immune responses. Second, to downregulate the expression of virus regulatory proteins.
  3. Are Virus miRNAs Conserved between Related Virus Species? No, but the miRNAs of individual viruses are conserved.
  4. Do Viruses Regulate miRNA Transcription, Processing, or Function? At present, there is no evidence indicating that viruses modify the cellular environment to selectively favor the processing and expression of viral miRNAs, although viral miRNAs may be expressed at such high levels that they have the potential to competitively inhibit cellular miRNA function.
  5. Can Viruses Use Cellular miRNAs to Promote Their Replication? At least one clear-cut example of a cellular miRNA that facilitates virus replication is known, activation of HCV replication by the liver-specific miRNA miR-122.

Five Questions about Viruses and MicroRNAs. PLoS Pathog 6(2): e1000787. doi:10.1371/journal.ppat.1000787

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PLoS: A Primer on Metagenomics

Thursday, March 4th, 2010

Metagenomics Metagenomics is a discipline that enables the genomic study of uncultured microorganisms. Faster, cheaper sequencing technologies and the ability to sequence uncultured microbes sampled directly from their habitats are expanding and transforming our view of the microbial world. Distilling meaningful information from the millions of new genomic sequences presents a serious challenge to bioinformaticians. In cultured microbes, the genomic data come from a single clone, making sequence assembly and annotation tractable. In metagenomics, the data come from heterogeneous microbial communities, sometimes containing more than 10,000 species, with the sequence data being noisy and partial. From sampling, to assembly, to gene calling and function prediction, bioinformatics faces new demands in interpreting voluminous, noisy, and often partial sequence data. Although metagenomics is a relative newcomer to science, the past few years have seen an explosion in computational methods applied to metagenomic-based research. It is therefore not within the scope of this article to provide an exhaustive review. Rather, we provide here a concise yet comprehensive introduction to the current computational requirements presented by metagenomics, and review the recent progress made. We also note whether there is software that implements any of the methods presented here, and briefly review its utility. Nevertheless, it would be useful if readers of this article would avail themselves of the comment section provided by this journal, and relate their own experiences. Finally, the last section of this article provides a few representative studies illustrating different facets of recent scientific discoveries made using metagenomics.

A Primer on Metagenomics. 2010 PLoS Comput Biol 6(2): e1000667. doi:10.1371/journal.pcbi.1000667

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Bt protein effective against parasitic roundworms

Wednesday, March 3rd, 2010

Bt A soil bacterium protein used to kill insects on organic crops has been shown to be a highly effective treatment for intestinal parasitic roundworms. These parasites, which include hookworms and whipworms, infect about two billion people in underdeveloped tropical regions and are cumulatively one of the leading causes of debilitation worldwide. Scientists report that a crystal protein known as Cry5B produced by Bt (Bacillus thuringiensis) is highly effective at a single dose at curing mammals of intestinal roundworm infections.

The researchers showed that Bt crystal proteins, used as insecticides for over five decades and known to be non-toxic to vertebrates, kill roundworms. Parasitic roundworms are considered by public-health officials to have a combined debilitating impact on human populations that is comparable to, or in some estimates greater than, that of malaria or tuberculosis. Intestinal roundworm diseases are among the most important causes of disease burden in school-aged children worldwide, leading to stunted growth, retarded cognitive and mental development and malnutrition. Children with these parasites are more likely to be trapped in poverty because they cannot physically work or think their way out of their condition. The parasites also have a significant burden on pregnant women and working adults.

Despite the large impact of these parasites on the developing world, few drugs have been developed to effectively combat their infection in human populations. Only one drug, albendazole, is now widely used in administering single-dose treatments to large populations. But because of the enormous numbers of people that need to be treated repeatedly, the development of resistance to albendazole is a serious threat and is already suspected in three studies in Sri Lanka, Ethiopia and Uganda. Furthermore, albendazole is a far from ideal drug, having poor impact on whipworms and less than ideal incomplete impact on hookworms. The latest drug to be developed is tribendimidine, which clinically has similar efficacy as albendazole. But the Bt Cry5B protein is three times better than tribendimidine. Comparisons from the literature with the other anti-worm drugs against this same mouse parasite, Heligmosomoides bakeri, indicate that Cry5B is anywhere from 4 times to 10,000 times more effective than various other anti-worm drugs. Most of the Cry5B is degraded in the stomach, so if the protein can be protected from stomach degradation, it is likely to be an even more powerful drug against parasites. These results pave the way to developing Cry5B as a safe and superior drug against roundworms that can rid a terrible class of parasites from hundreds of millions of children and adults around the world.

Bacillus thuringiensis Cry5B Protein Is Highly Efficacious as a Single-Dose Therapy against an Intestinal Roundworm Infection in Mice. PLoS Negl Trop Dis 4(3): e614. doi:10.1371/journal.pntd.0000614

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Hepatitis Delta Virus Replication

Tuesday, March 2nd, 2010

Hepatitis delta virus (HDV) was first discovered in 1977 among a group of patients infected with hepatitis B virus (HBV). Subsequent studies revealed that HDV is a replication-defective virus which requires a helper virus, HBV, to supply the hepatitis B surface antigen (HBsAg) for virion assembly and infectivity. Being a human pathogen, HDV infection may lead to progressive chronic liver disease and occasional fulminant hepatitis in patients coinfected or superinfected with HBV. In recent years, the incidence of new HDV infections has significantly declined in some parts of the world due to HBV vaccination. However, investigation of the HDV replication cycle has raised many issues which molecular biologists are interested in.

HDV

Unlike other RNA satellite viruses which rely on the RNA-dependent RNA polymerase (RdRp) provided by the coexisting helper virus for genome replication, the dependence of HDV on HBV is limited to the supply of HBsAg for the production of HDV viral particle. Similar to plant viroids which do not encode RdRp, HDV undergoes robust RNA replication autonomously once inside the cells. Thus, it is certain that HDV and plant viroids have to replicate their RNA genome using a cellular enzyme(s). Unlike plant viroids which do not encode any protein, HDV encodes a protein, hepatitis delta antigen (HDAg), which is intimately involved in its RNA replication. In addition, HDV RNA not only has to replicate itself but also needs to transcribe a subgenomic mRNA species coding for HDAg. The transcription of the HDAg-encoding mRNA has all of the hallmarks of the cellular mRNA transcription except for the nature of the template (DNA versus RNA). Therefore, distinct from plant viroids, HDV represents a hybrid of the conventional DNA-dependent transcription and the unique RNA-dependent RNA synthesis in the absence of an RdRP. To coordinate with this sophisticated and unique RNA amplification process in mammalian cells, HDAg plays important regulatory roles which will be reviewed herein. Additionally, the nature of the enzyme involved in HDV RNA replication will also be addressed.

This review article examines the HDV RNA replication cycle, with emphasis on the function of HDAg in modulating RNA replication and the nature of the enzyme involved:

Hepatitis Delta Virus RNA Replication. Viruses 2009, 1(3), 818-831 doi:10.3390/v1030818

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The Biology of Viroid-Host Interactions

Monday, March 1st, 2010

Viroid With an amazingly small genome size (250–400 nt) and simple structure, viroids are giants in terms of functional versatility in the world of RNA. Without encoding proteins to provide specific functions and without being protected in a protein or membrane shell, these single-stranded, circular RNAs can triumph over the cellular RNA degradation machineries and further enlist host-encoded factors for replicating themselves in specific subcellular compartments and trafficking throughout a plant. They can also cause devastating plant diseases.

Viroids are single-stranded, circular, and noncoding RNAs that infect plants. They replicate in the nucleus or chloroplast and then traffic cell-to-cell through plasmodesmata and long distance through the phloem to establish systemic infection. They also cause diseases in certain hosts. All functions are mediated directly by the viroid RNA genome or genome-derived RNAs. This review summarizes recent advances in the understanding of viroid structures and cellular factors enabling these functions, emphasizing conceptual developments, major knowledge gaps, and future directions. Newly emerging experimental systems and research tools are discussed that are expected to enable significant progress in a number of key areas. It highlights examples of groundbreaking contributions of viroid research to the development of new biological principles and offer perspectives on using viroid models to continue advancing some frontiers of life science.

The Biology of Viroid-Host Interactions. 2009 Annual Review of Phytopathology 47: 105-131 doi: 10.1146/annurev-phyto-080508-081927

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