A Virginia Bioinformatics Institute research team at Virginia Tech has identified an enormous superfamily of pathogen genes involved in the infection of plants. The Avh superfamily comprises genes found in the plant pathogens Phytophthora ramorum and Phytophthora sojae. The pathogen genes produce effector proteins that manipulate how plant cells work in such a way as to make the plant hosts more susceptible to infection. The results suggest that a single gene from a common ancestor of the both pathogen species has spawned hundreds of very different, fast-evolving genes that encode for these highly damaging effector proteins.P. sojae causes severe devastation in soybean crops and results in $1–2 million in annual losses for commercial farmers in the United States. P. ramorum, which causes sudden oak death, has attacked and killed tens of thousands of oak trees in California and Oregon. Both pathogens belong to the oomycete group of organisms that also includes the potato late blight pathogen responsible for the Irish potato famine. The scientists probed the recently published genome sequences of both organisms using bioinformatic tools that can look for specific amino acid sequences or motifs. Advanced searches of the genome sequences (BLAST and Hidden Markov Model) revealed that the P. sojae and P. ramorum genomes encode large numbers of effector proteins (374 from P. ramorum and 396 from P. sojae) that likely facilitate the infection of their host plants. Given that there are more than 80 species of Phytophthora pathogens, these findings imply that there are more than 30 000 members of this superfamily within the genus Phytophthora.

Proteins arising from the Avh superfamily have very different amino acid sequences but share two common motifs at one end of the protein (N-terminus). The readily identified RXLR and dEER motifs (single letter code for amino acids) are required for entry of the proteins into plant host cells. Similar motifs are also found in the effector proteins produced by the malarial parasite Plasmodium as it invades red blood cells. The team also detected some conserved amino acid motifs (W, Y and L) at the other end (C terminus) of some of the proteins that have been selected over years of evolution. These C-terminal motifs are usually arranged as a module that can be repeated up to eight times. The functions of these C-terminal motifs are being investigated further.

The Avh gene superfamily is one of the most rapidly evolving parts of the genome. Duplications of genes are common and presumably responsible for the rapid expansion of the family. The diversity and duplication of genes noted in the sequences are consistent with maximizing the number of effector genes in the pathogens while making it increasingly difficult for the host defense systems to recognize invading molecules, ideal features for effector proteins aimed at wreaking havoc on susceptible plant hosts. Professor Brett Tyler of the Virginia Bioinformatics Institute, the leader of the project, remarked: “The extraordinary speed with which the Avh genes are evolving suggests that these genes are key to the pathogens’ ability to outwit the defense systems of the plants.”

The research appears in the March 25 issue of The Proceedings of the National Academy of Sciences (vol. 105, no. 12, pp. 4874-4879, 2008)

According to researchers at Temple University an increase in the CD163+/CD16+ monocyte subset could be a biomarker for the progression of HIV disease.The researchers reported their findings, “CD163/CD16 Coexpression by Circulating Monocytes/Macrophages in HIV: Potential Biomarkers for HIV Infection and AIDS Progression,” in the March issue of AIDS Research and Human Retroviruses (www.liebertonline.com/aid).

A monocyte is a specific white blood cell, a part of the human body’s immune system that protects against blood-borne pathogens and moves quickly to sites of infection within the body’s tissues. As monocytes enter tissue, they undergo a series of changes to become macrophages.

The researchers were investigating alterations in this monocyte subset in patients with HIV infection. As part of this study, they examined a cohort of 18 patients from the Comprehensive HIV Program at Temple University Hospital, under the direction of Ellen Tedaldi, and seven individuals without HIV infection.

“At first, we were just looking at whether or not we saw alterations in this CD163+/CD16+ subset and whether it might be reflective of the amount of virus they have in circulation,” said Tracy Fischer-Smith, an associate scientist in Temple’s Neuroscience Department and the study’s lead author. “We did, indeed, find that patients with detectable virus had an increase of this monocyte subset that correlated with the amount of virus they had in their blood. We were surprised to find that patients with CD4+ T cell counts of less than 450 cells per microliter [200 or less per microliter is defined as AIDS], the increase of this monocyte subset correlates inversely with the number of T cells.”

Fischer-Smith said this finding suggests that as the monocyte cells are increasing, these patients are losing CD4+ T cells, which are critical for the maintenance of immunological competence.

“This may actually provide an earlier window into what is happening with HIV-infected patients where we might be able to see that immune impairment is taking place before we see a dramatic loss of CD4+ T cells,” she said.

“It looks like, based on these correlations, that this particular cell type may be involved in immune impairment and the progression of HIV,” said Jay Rappaport, professor of neuroscience and neurovirology, who oversaw the study. “Is it a good prognostic indicator” If you have a lot of these monocytes, does it mean you are going to progress into AIDS faster” “Right now, all we know is what the correlations are,” he said.

Rappaport added that he believes the CD163+/CD16+ monocyte subset is the first biomarker that correlates with viral load and CD4+ count. “The fact that it actually correlates with both, we think, might make it a key cell type in the pathogenesis of AIDS.” Fischer-Smith said the researchers plan to expand this study by following a cohort of patients longitudinally to see if their findings really can provide doctors with an early warning system and help to design better therapeutic strategies.

“When you are just looking at a single time-point, you don’t know how changes in this monocyte subset might occur over time, and how these changes might relate to the viral load and T cell number in individual patients,” she said. “That is why we want to investigate this further with a longitudinal study of HIV patients.”

The study was supported by the National Institute of Neurological Disorders and Strokes (NINDS) and the National Institute on Drug Abuse (NIDA)

BIRMINGHAM, Ala. – A significant drop in abnormal Pap test results happened after girls and women were given a vaccine to prevent cervical cancer, according to a researcher at the University of Alabama at Birmingham (UAB).The findings show the vaccine, named GARDASIL, appears to prevent the development of cell changes that lead to cervical disease, the researcher said.

In testing GARDASIL reduced abnormal Pap test results by 43 percent compared to women not given the vaccine. The 43 percent reduction was for tests that found pre-cancerous changes called high-grade squamous intraepithelial lesions (HSIL) more than three years after women were given the vaccine.

GARDASIL reduced other abnormal Pap results, including milder pre-malignant cell changes, by 16 to 35 percent compared to women not given the vaccine.

While the findings are not definitive that GARDASIL prevents cancer, they do signal the vaccine will spare thousands of women a diagnosis of cell abnormality or malignant changes that may lead to more tests and possibly surgery, said Warner Huh, M.D., associate professor in the UAB Division of Gynecologic Oncology and the doctor chosen to present the data.

“Clearly the vaccine’s benefits include something that can be appreciated by women and daughters fairly quickly,” Huh said. “This is a positive first sign, and it will take many more years to know definitively if the vaccine prevents cancer.”

The findings were presented March 10 at the annual meeting of the Society of Gynecological Oncologists held in Tampa.

The results are a compilation of three separate trials involving more than 18,000 women, ages 16 to 26, in the United States, Europe and Asia. All test subjects had normal Pap smear readings at the start of the trial.

In addition to the drop in unwanted Pap results, the study found invasive procedures like cervical biopsies were performed up to 42 percent less in GARDASIL recipients compared to women not given the vaccine, Huh said.

GARDASIL is approved to fight the human papilloma virus (HPV) strains believed to cause 70 percent of cervical cancers and more than 90 percent of genital warts.

For many unvaccinated women HPV infections clear up naturally without causing any cervical problems, as do many pre-malignant lesions. In other cases, HPV prompts cell changes that can gradually put women at greater risk of cervical cancer.

Nearly 25 million U.S. women between the ages of 14 and 59 are infected with HPV, and the annual cost of screening and treating cervical abnormalities is about $4 billion, according to a statement from the Society of Gynecologic Oncologists. “Dr. Huh’s study concludes that the trials covered in this paper indicate an overall benefit of vaccination,” the society’s statement said.

Human Papillomavirus is the virus responsible for most cases of cervical cancer has a serious weakness which may provide hope for new treatments for the disease.Human Papillomavirus (HPV), a virus which causes several types of cancer but is particularly associated with cervical cancer, has developed clever ways of hiding in the body, but researchers at the University of Leeds have found that its ability to trick the body’s first line of defence leaves it vulnerable to attack from a second defence system.

When viruses enter cells, they produce proteins to assist their growth and replication, and the body’s immune system is programmed to recognise and attack these non-native proteins.

Professor Eric Blair of the University’s Faculty of Biological Sciences and Dr Graham Cook from the Leeds Institute for Molecular Medicine have been specifically looking at one of the proteins produced by HPV, called E7, and have discovered that it suppresses markers on the cell surface, making infected cells much less visible to T cells, one of the body’s key defence systems.

“T cells can normally tell when there are molecules in the body that shouldn’t be there and activate an immune response,” says Professor Blair. “But HPV uses the E7 protein to hide from them. We’ve always known the virus has clever ways of defending itself, but we now know how one of its main defence mechanism works.”

However, in a twist that offers hope for the development of potential new therapies for cervical cancer, Professor Blair and Dr Cook have also discovered that this subterfuge may be the virus’s downfall.

Cells without surface protein markers are targeted by another of the body’s white blood cell armoury, Natural Killer cells - cellular assassins, which when activated, release specialised enzymes into target cells to kill them.

“Despite the body’s valiant efforts to ward off the virus, women are still contracting this awful disease, so there are clearly other mechanisms at work. We need to look at the role of the other components of the virus, to see if they prevent the Natural Killer cells from attacking,” says Professor Blair. “For example, we’ve started examining the contribution of the virus protein E6, which we believe works in partnership with E7. The recent introduction of a vaccine against HPV is an important development in the fight against cervical cancer. However, it may take many years for the vaccine to reduce the number of cases of this cancer and other approaches to eliminating tumour cells need to be discovered.”

This research was funded by Yorkshire Cancer Research, the charity’s Chief Executive, Elaine King commented: “Human Papillomavirus is extremely complex with many mechanisms affecting how it operates. However, through this research we have discovered how the E7 protein works, which is a huge step forward, and will hopefully help us to develop effective ways to combat Human Papillomavirus in the future.”

Viruses and bacterial viruses (known as phages) are among the most abundant life forms on the planet. Two papers published recently in Nature, March 2 and 12, 2008, analyse the geographical distribution of viral communities in modern organosedimentary structures (sedimentary features, built by the interaction of organisms and their environment) known as microbialites, the living analogues of the oldest fossils on Earth, and come up with some surprising nuggets of information.Microbialites first appeared in the geological record, 3.5 billion years ago, and for more than 2 billion years they are the main evidence of life on Earth. A team of scientists from US and Singapore used a comparative metagenomics approach to show that phages associated with such structures are very different not only from each other but also from those found in any other ecosystem so far. The team’s findings indicate that modern microbialites are endemic remnants of ancient ecosystems.

Dr Ruan Yijun, Senior Group Leader at the Genome Institute of Singapore (GIS), said, “Using DNA sequencing technology, we were able to identify unknown viruses in various environments relevant to human health. This collaboration is the first ever large-scale effort to analyse biodiversity and biogeography of viruses in the environments around humans.”

“We have been interested in this kind of analysis since the SARS (severe acute respiratory syndrome) outbreak in 2002,” added Dr Ruan. “In pursuit of this interest, we established a virus discovery programme at GIS, resulting in the discovery of abundant viruses in the human gut (PLoS Biology, 2006) and different variants of dengue viruses. Now, with more viral metagenomic data accumulated, we are able to summarise the biodiversity and biogeography on a global scale.”

Microbialites are organosedimentary structures accreted by sediment trapping, binding and in situ precipitation due to the growth and metabolic activities of microorganisms.

Stromatolites and thrombolites are morphological types of microbialites classified by their internal mesostructure: layered and clotted, respectively.

###

Notes to the Editor:

Research publication:

The research findings described in the press release can be found in the March 2, 2008 issue of Nature under the title “Biodiversity and biogeography of phages in modern stromatolites and thrombolites”; and the March 12, 2008 issue of Nature under the title “Functional metagenomic profiling of nine biomes”.

Authors for March 2 paper:

Christelle Desnues1, Beltran Rodriguez-Brito1,2, Steve Rayhawk1,2, Scott Kelley1,3, Tuong Tran1, Matthew Haynes1, Hong Liu1, Mike Furlan1, Linda Wegley1, Betty Chau1, Yijun Ruan4, Dana Hall1, Florent E. Angly1, Robert A. Edwards1,2,3,5, Linlin Li1, Rebecca Vega Thurber1, R. Pamela Reid6, Janet Siefert7, Valeria Souza8, David L. Valentine9, Brandon K. Swan9, Mya Breitbart10 & Forest Rohwer1,3

1. Department of Biology,
2. Computational Sciences Research Center,
3. Center for Microbial Sciences, San Diego State University, San Diego, California 92182, USA.
4. Genome Institute of Singapore, Singapore 138672, Singapore.
5. Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA.
6. Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida 33149, USA.
7. Department of Statistics, Rice University, Houston, Texas 77251, USA.
8. Departamento de Ecologı´a Evolutiva, Instituto de Ecologı´a, Universidad Nacional Auto´noma de Me´xico AP 70-275 Coyoaca´n, 04510 Mexico D.F., Mexico.
9. Department of Earth Science, University of California Santa Barbara, Santa Barbara, California 93106, USA.
10. College of Marine Science, University of South Florida, St Petersburg, Florida 33701, USA.

Authors for March 12 paper:

Elizabeth A. Dinsdale1,5*, Robert A. Edwards1,2,3,6*, Dana Hall1, Florent Angly1,4, Mya Breitbart7, Jennifer M. Brulc8, Mike Furlan1, Christelle Desnues1{, Matthew Haynes1, Linlin Li1, Lauren McDaniel7, Mary Ann Moran10, Karen E. Nelson11, Christina Nilsson12, Robert Olson6, John Paul7, Beltran Rodriguez Brito1,4, Yijun Ruan12, Brandon K. Swan13, Rick Stevens6, David L. Valentine13, Rebecca Vega Thurber1, Linda Wegley1, Bryan A. White8,9 & Forest Rohwer1,2

1 Department of Biology,
2 Center for Microbial Sciences,
3 Department of Computer Sciences, and
4 Computational Science Research Centre, San Diego State University, San Diego, California 92182, USA.
5 School of Biological Sciences, Flinders University, Adelaide, South Australia 5042, Australia.
6 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA.
7 University of South Florida, College of Marine Science, 140 7th Avenue South, St Petersburg, Florida 33701, USA.
8 Department of Animal Sciences, and
9 The Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, USA.
10 Department of Marine Sciences, University of Georgia, Athens, 30602 Georgia, USA.
11 The J. Craig Venter Institute, 9712 Medical Center Drive, Rockville, Maryland 20850, USA.
12 Genome Institute of Singapore, 60 Biopolis Street, 02-01, Genome, Singapore 138672, Singapore.
13 Department of Earth Science, University of California Santa Barbara, Santa Barbara, California 93106, USA.
{ Present address: Unite des Rickettsies, CNRS-UMR 6020, Faculte de medecine, 13385 Marseille, France.

About the Genome Institute of Singapore
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The Genome Institute of Singapore (GIS) is a member of the Agency for Science, Technology and Research (A*STAR). It is a national initiative with a global vision that seeks to use genomic sciences to improve public health and public prosperity. Established in 2001 as a centre for genomic discovery, the GIS will pursue the integration of technology, genetics and biology towards the goal of individualized medicine. The key research areas at the GIS include Systems Biology, Stem Cell & Developmental Biology, Cancer Biology & Pharmacology, Human Genetics, Infectious Diseases, Genomic Technologies, and Computational & Mathematical Biology. The genomics infrastructure at the GIS is utilized to train new scientific talent, to function as a bridge for academic and industrial research, and to explore scientific questions of high impact.

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The Agency for Science, Technology and Research, or A*STAR, is Singapore’s lead agency for fostering world-class scientific research and talent for a vibrant knowledge-based Singapore. A*STAR actively nurtures public sector research and development in Biomedical Sciences, Physical Sciences and Engineering, with a particular focus on fields essential to Singapore’s manufacturing industry and new growth industries. It oversees 14 research institutes and supports extramural research with the universities, hospital research centres and other local and international partners. At the heart of this knowledge intensive work is human capital. Top local and international scientific talent drive knowledge creation at A*STAR research institutes. The Agency also sends scholars for undergraduate, graduate and post-doctoral training in the best universities, a reflection of the high priority A*STAR places on nurturing the next generation of scientific talent.

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