Archive for the ‘Environment’ Category

Biotransformation of arsenic by algae

Thursday, March 26th, 2009

Laguna Verde Arsenic is the most common toxic substance in the environment, ranking first on the US Superfund list of hazardous substances. It is introduced to the environment primarily from geologic sources and is acted on biologically, creating an arsenic biogeocycle. Geothermal environments are well known for their elevated arsenic content and thus provide an excellent setting in which to study microbe–arsenic interactions. So far, studies aimed at identifying the organisms participating in these and other arsenic transformations have focused almost entirely on microorganisms belonging to the domains Archaea and Bacteria. In contrast, comparatively little attention has been paid to the Eukarya that inhabit these extreme environments, much less their potential contribution to biogeochemical cycles in these extreme habitats. Now it would appear that algae play a significant role in arsenic cycling in the geothermal environment as also found in a range of marine and freshwater environments. These observations indicate that arsenic methylation forms an important component of the global arsenic biogeocycle.

Biotransformation of arsenic by a Yellowstone thermoacidophilic eukaryotic alga. PNAS USA March 10, 2009
Arsenic is the most common toxic substance in the environment, ranking first on the Superfund list of hazardous substances. It is introduced primarily from geochemical sources and is acted on biologically, creating an arsenic biogeocycle. Geothermal environments are known for their elevated arsenic content and thus provide an excellent setting in which to study microbial redox transformations of arsenic. To date, most studies of microbial communities in geothermal environments have focused on Bacteria and Archaea, with little attention to eukaryotic microorganisms. Here, we show the potential of an extremophilic eukaryotic alga of the order Cyanidiales to influence arsenic cycling at elevated temperatures. Cyanidioschyzon sp. isolate 5508 oxidized arsenite [As(III)] to arsenate [As(V)], reduced As(V) to As(III), and methylated As(III) to form trimethylarsine oxide (TMAO) and dimethylarsenate [DMAs(V)]. Two arsenic methyltransferase genes, CmarsM7 and CmarsM8, were cloned from this organism and demonstrated to confer resistance to As(III) in an arsenite hypersensitive strain of Escherichia coli. The two recombinant CmArsMs were purified and shown to transform As(III) into monomethylarsenite, DMAs(V), TMAO, and trimethylarsine gas, with a Topt of 60–70°C. These studies illustrate the importance of eukaryotic microorganisms to the biogeochemical cycling of arsenic in geothermal systems, offer a molecular explanation for how these algae tolerate arsenic in their environment, and provide the characterization of algal methyltransferases.

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Comprehensive map of global malaria

Tuesday, March 24th, 2009

Malaria is one of the most common infectious diseases in the world and one of the greatest global public health problems. The Plasmodium falciparum parasite causes approximately 500 million cases each year and over one million deaths in sub-Saharan Africa. More than 40% of the world’s population is at risk of malaria. The parasite is transmitted to people through the bites of infected mosquitoes. These insects inject a life stage of the parasite called sporozoites, which invade human liver cells where they reproduce briefly. The liver cells then release merozoites (another life stage of the parasite), which invade red blood cells. Here, they multiply again before bursting out and infecting more red blood cells, causing fever and damaging vital organs. The infected red blood cells also release gametocytes, which infect mosquitoes when they take a blood meal. In the mosquito, the gametocytes multiply and develop into sporozoites, thus completing the parasite’s life cycle. Malaria can be prevented by controlling the mosquitoes that spread the parasite and by avoiding mosquito bites by sleeping under insecticide-treated bed nets. Effective treatment with antimalarial drugs also helps to decrease malaria transmission.

Malaria map

In 1998, the World Health Organization and several other international agencies launched Roll Back Malaria, a global partnership that aims to reduce the human and socioeconomic costs of malaria. Targets have been continually raised since this time and have culminated in the Roll Back Malaria Global Malaria Action Plan of 2008, where universal coverage of locally appropriate interventions is called for by 2010 and the long-term goal of malaria eradication again tabled for the international community. For malaria control and elimination initiatives to be effective, financial resources must be concentrated in regions where they will have the most impact, so it is essential to have up-to-date and accurate maps to guide effort and expenditure. In 2008, researchers of the Malaria Atlas Project constructed a map that stratified the world into three levels of malaria risk: no risk, unstable transmission risk (occasional focal outbreaks), and stable transmission risk (endemic areas where the disease is always present). Now, researchers extend this work by describing a new evidence-based method for generating continuous maps of P. falciparum endemicity within the area of stable malaria risk over the entire world’s surface. They then use this method to produce a P. falciparum endemicity map for 2007. Endemicity is important as it is a guide to the level of morbidity and mortality a population will suffer, as well as the intensity of the interventions that that will be required to bring the disease under control or additionally to interrupt transmission.

The researchers identified nearly 8,000 surveys of P. falciparum parasite rates (Pf PR; the percentage of a population with parasites detectable in their blood) completed since 1985 that met predefined criteria for inclusion into a global database of PfPR data. They then used ‘‘model-based geostatistics’’ to build a world map of P. falciparum endemicity for 2007 that took into account where and, importantly, when and all these surveys were done. Predictions were comprehensive (for every area of stable transmission globally) and continuous (predicted as a endemicity value between 0% and 100%). The population at risk of three levels of malaria endemicity were identified to help summarize these findings: low endemicity, where PfPR is below 5% and where it should be technically feasible to eliminate malaria; intermediate endemicity where PfPR is between 5% and 40% and it should be theoretically possible to interrupt transmission with the universal coverage of bed nets; high endemicity is where PfPR is above 40% and suites of locally appropriate intervention will be needed to bring malaria under control. The global level of malaria endemicity is much reduced when compared with historical maps. Nevertheless, the resulting map indicates that in 2007 almost 60% of the 2.4 billion people at malaria risk were living in areas with a stable risk of P. falciparum transmission – 0.69 billion people in Central and South East Asia (CSE Asia), 0.66 billion in Africa, Yemen, and Saudi Arabia (Africaþ), and 0.04 billion in the Americas. The people of the Americas were all in the low endemicity class. Although most people exposed to stable risk in CSE Asia were also in the low endemicity class (88%), 11% were in the intermediate class, and 1% were in the high endemicity class. By contrast, high endemicity was most common and widespread in the Africaþ region (53%), but with significant numbers in the intermediate (30%), and low (17%) endemicity classes.

The accuracy of this new world map of P. falciparum endemicity depends on the assumptions made in its construction and critically on the accuracy of the data fed into it, but because of the statistical methods used to construct this map, it is possible to quantify the uncertainty in the results for all users. Thus, this map (which, together with the data used in its construction, will be freely available) represents an important new resource that clearly indicates areas where malaria control can be improved (for example, Africa) and other areas where malaria elimination may be technically possible. In addition, planned annual updates of the global P. falciparum endemicity map and the PfPR database by the Malaria Atlas Project will help public health experts to monitor the progress of the malaria control community towards international control and elimination targets.

A world malaria map: Plasmodium falciparum endemicity in 2007. 2009 PLoS Med 6(3): e1000048
Efficient allocation of resources to intervene against malaria requires a detailed understanding of the contemporary spatial distribution of malaria risk. It is exactly 40 y since the last global map of malaria endemicity was published. This paper describes the generation of a new world map of Plasmodium falciparum malaria endemicity for the year 2007. A total of 8,938 P. falciparum parasite rate (PfPR) surveys were identified using a variety of exhaustive search strategies. Of these, 7,953 passed strict data fidelity tests for inclusion into a global database of PfPR data, age-standardized to 2–10 y for endemicity mapping. A model based geostatistical procedure was used to create a continuous surface of malaria endemicity within previously defined stable spatial limits of P. falciparum transmission. These procedures were implemented within a Bayesian statistical framework so that the uncertainty of these predictions could be evaluated robustly. The uncertainty was expressed as the probability of predicting correctly one of three endemicity classes; previously stratified to be an informative guide for malaria control. Population at risk estimates, adjusted for the transmission modifying effects of urbanization in Africa, were then derived with reference to human population surfaces in 2007. Of the 1.38 billion people at risk of stable P. falciparum malaria, 0.69 billion were found in Central and South East Asia (CSE Asia), 0.66 billion in Africa, Yemen, and Saudi Arabia (Africaþ), and 0.04 billion in the Americas. All those exposed to stable risk in the Americas were in the lowest endemicity class. The vast majority (88%) of those living under stable risk in CSE Asia were also in this low endemicity class; a small remainder(11%) were in the intermediate endemicity class; and the remaining fraction (1%) in high endemicity areas. High endemicity was widespread in the Africaþ region, where 0.35 billion people are at this level of risk. Most of the rest live at intermediate risk (0.20 billion), with a smaller number (0.11 billion) at low stable risk. High levels of P. falciparum malaria endemicity are common in Africa. Uniformly low endemic levels are found in the Americas. Low endemicity is also widespread in CSE Asia, but pockets of intermediate and very rarely high transmission remain. There are therefore significant opportunities for malaria control in Africa and for malaria elimination elsewhere. This 2007 global P. falciparum malaria endemicity map is the first of a series with which it will be possible to monitor and evaluate the progress of this intervention process.

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Badgers to be given anti-TB jabs

Sunday, March 22nd, 2009

Badgers in the wild will be vaccinated against bovine tuberculosis for the first time next year
BBC News

Bacterial sensors of oxygen

Tuesday, March 17th, 2009

Oxygen Many bacteria are facultative anaerobes, that is, they can grow in the presence or absence of O2. In contrast to anaerobic respiration or fermentation, O2 and aerobic respiration confer enormous energetic benefits on facultative bacteria by allowing the complete oxidation of a growth substrate and the concomitant conservation of much larger amounts of energy. Moreover, some energetically expensive processes such as nitrogen fixation are inhibited by O2. Furthermore, hypoxic conditions are a signal to adopt a different “lifestyle” for some bacteria such as the dormant state of Mycobacterium tuberculosis associated with latent TB infections. The ability to adapt to changes in O2 availability by expressing different groups of genes is controlled at the level of transcription by O2-sensing regulatory proteins.

Bacterial sensors of oxygen. Curr Opin Microbiol. Feb 24 2009
The concentration of molecular oxygen (O2) began to increase in the Earth’s atmosphere approximately two billion years ago. Its presence posed a threat to anaerobes but also offered opportunities for improved energy conservation via aerobic respiration. The ability to sense environmental O2 thus became, and remains, important for many bacteria, both for protection and switching between anaerobic and aerobic respiration. Utilizing an iron–sulfur cluster as the sensor of O2 exploits the ability of O2 to oxidize the iron–sulfur cluster, ultimately resulting in cluster disassembly. When utilizing heme as the sensor, the capacity of O2 to form a reversible Fe–O2 bond or alternatively the oxidation of the heme iron atom itself is used to detect O2 and switch regulators between active and inactive forms.

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New vector for Chagas disease

Tuesday, March 10th, 2009

Triatoma dimidiata Chagas disease is considered the largest parasitic disease burden in Latin America with a cost of the loss of 667,000 Disability Adjusted Life Years in 2002. Trypanosoma cruzi, the parasite that causes Chagas disease, infects approximately 9.8 million people in the Americas with 200,000 new Chagas cases annually. Most transmission occurs by contamination with the parasite-containing faeces of triatomine insect vectors (“kissing bugs”). There is no vaccine available and treatment shows limited effectiveness, comes with troublesome side effects, and is out of reach of most people in endemic countries. Therefore, as with most parasitic infections, control of transmission by the vectors is the control strategy of choice.

Pesticide spraying has effectively halted transmission in most of southern South America, especially where the bugs live exclusively inside houses. In Mesoamerica, bugs living in the forest readily reinfest treated houses. In addition, one of the main species of insect that transmits Chagas in Mesoamerica, Triatoma dimidiata, although it looks similar in different localities, may consist of genetically distinct populations, even different species, which differ in how efficiently they transmit the parasite: characteristics which confound control efforts. Nuclear and mitochondrial DNA were analyzed to characterize different populations of T. dimidiata from Mexico and Central America. Both the nuclear and mitochondrial DNA show that there is a very distinct population of T. dimidiata, perhaps even a different species, that lives in very close proximity with other T. dimidiata in Mexico and Guatemala. The nuclear DNA divides the remaining T. dimidiata into three additional genetically distinct groups. However, the mitochondrial DNA does not distinguish these additional groups. This study helps inform control efforts by showing where genetically distinct populations of T. dimidiata occur.

Since 1997, the Central America Initiative for the Control of Chagas disease has shown dramatically different results following insecticide spraying in houses, e.g. in Nicaragua, the bugs did not return; in stark contrast to rapid reinfestation in Jutiapa, Guatemala. It is important to understand how much of the differences in epidemiology and control outcomes are due to distinct taxa of T. dimidiata. The area of Peten, Guatemala has not been included in the control program since most are forest populations. Deforestation and increasing encroachment of human populations in the area means that T. dimidiata could become domesticated in this region. It is critical to realize that there are at least two distinct T. dimidiata populations in this area (and in Mexico and Belize) as control measures are designed. For effective control it will be imperative to understand the mechanisms maintaining this reproductive isolation and the epidemiological importance of distinct taxa.

Two Distinct Triatoma dimidiata (Latreille, 1811) Taxa Are Found in Sympatry in Guatemala and Mexico. PLoS Negl Trop Dis 3(3): e393
Approximately 10 million people are infected with Trypanosoma cruzi, the causative agent of Chagas disease, which remains the most serious parasitic disease in the Americas. Most people are infected via triatomine vectors. Transmission has been largely halted in South America in areas with predominantly domestic vectors. However, one of the main Chagas vectors in Mesoamerica, Triatoma dimidiata, poses special challenges to control due to its diversity across its large geographic range (from Mexico into northern South America), and peridomestic and sylvatic populations that repopulate houses following pesticide treatment. Recent evidence suggests T. dimidiata may be a complex of species, perhaps including cryptic species; taxonomic ambiguity which confounds control. The nuclear sequence of the internal transcribed spacer 2 (ITS2) of the ribosomal DNA and the mitochondrial cytochrome b (mt cyt b) gene were used to analyze the taxonomy of T. dimidiata from southern Mexico throughout Central America. ITS2 sequence divides T. dimidiata into four taxa. The first three are found mostly localized to specific geographic regions with some overlap: (1) southern Mexico and Guatemala (Group 2); (2) Guatemala, Honduras, El Salvador, Nicaragua, and Costa Rica (Group 1A); (3) and Panama (Group 1B). We extend ITS2 Group 1A south into Costa Rica, Group 2 into southern Guatemala and show the first information on isolates in Belize, identifying Groups 2 and 3 in that country. The fourth group (Group 3), a potential cryptic species, is dispersed across parts of Mexico, Guatemala, and Belize. We show it exists in sympatry with other groups in Peten, Guatemala, and Yucatan, Mexico. Mitochondrial cyt b data supports this putative cryptic species in sympatry with others. However, unlike the clear distinction of the remaining groups by ITS2, the remaining groups are not separated by mt cyt b. This work contributes to an understanding of the taxonomy and population subdivision of T. dimidiata, essential for designing effective control strategies.

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Saturday Cinema: Hunting the next killer virus

Saturday, February 7th, 2009

Joe DeRisi talks about amazing new ways to diagnose viruses (and treat the illnesses they cause) using DNA. His work may help us understand malaria, SARS, avian flu – and the 60 percent of everyday viral infections that go undiagnosed.

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Microbial survival in challenging environments

Friday, February 6th, 2009

Hydrothermal vent Extreme environments, such as deep-sea hydrothermal vents 2,500 meters below the ocean surface, support large macrofaunal communities via microbially mediated carbon fixation processes using chemicals (chemoautotrophy) rather than light (photoautotrophy). Photosynthesis cannot occur in this dark environment, where hot, toxic fluids oozing from below the seafloor combine with cold seawater at very high pressures.

Nautilia profundicola, distantly related to the pathogenic Helicobacter and Campylobacter species, contains a number of genes and pathways predicted to be important in DNA repair, environmental sensing, and metabolism, which are novel to either its subdivision or to all microbes. The study combined genome analysis with physiological and ecological observations to investigate the importance of one gene in N. profundicola. Previous studies found the gene only in microorganisms growing in temperatures greater than 80oC, but N. profundicola thrives best at much lower temperatures.

The genes and deduced metabolic pathways include several hydrogen uptake and release systems as well as a novel predicted nitrogen assimilation pathway. One gene involved in DNA repair, reverse gyrase, was thought to be a hallmark protein in hyperthermophiles, which are microbes that grow above 80oC. The gene’s presence in N. profundicola suggests that it might play a role in the bacterium’s ability to survive rapid and frequent temperature fluctuations in its environment. The researchers also uncovered further adaptations to the vent environment, including genes necessary for growth and sensing environmental conditions, and a new route for nitrate assimilation related to how other bacteria use ammonia as an energy source. These results help to explain how microbes survive near deep-sea hydrothermal vents, where conditions are thought to resemble those found on early Earth, as described in the study. Improved understanding of microbes living in these conditions may aid our understanding of how life evolved here.

Adaptations to Submarine Hydrothermal Environments Exemplified by the Genome of Nautilia profundicola. 2009 PLoS Genet 5(2): e1000362
Submarine hydrothermal vents are model systems for the Archaean Earth environment, and some sites maintain conditions that may have favored the formation and evolution of cellular life. Vents are typified by rapid fluctuations in temperature and redox potential that impose a strong selective pressure on resident microbial communities. Nautilia profundicola strain Am-H is a moderately thermophilic, deeply-branching Epsilonproteobacterium found free-living at hydrothermal vents and is a member of the microbial mass on the dorsal surface of vent polychaete, Alvinella pompejana. Analysis of the 1.7-Mbp genome of N. profundicola uncovered adaptations to the vent environment – some unique and some shared with other Epsilonproteobacterial genomes. The major findings included: (1) a diverse suite of hydrogenases coupled to a relatively simple electron transport chain, (2) numerous stress response systems, (3) a novel predicted nitrate assimilation pathway with hydroxylamine as a key intermediate, and (4) a gene (rgy) encoding the hallmark protein for hyperthermophilic growth, reverse gyrase. Additional experiments indicated that expression of rgy in strain Am-H was induced over 100-fold with a 20oC increase above the optimal growth temperature of this bacterium and that closely related rgy genes are present and expressed in bacterial communities residing in geographically distinct thermophilic environments. N. profundicola, therefore, is a model Epsilonproteobacterium that contains all the genes necessary for life in the extreme conditions widely believed to reflect those in the Archaean biosphere – anaerobic, sulfur, H2- and CO2-rich, with fluctuating redox potentials and temperatures. In addition, reverse gyrase appears to be an important and common adaptation for mesophiles and moderate thermophiles that inhabit ecological niches characterized by rapid and frequent temperature fluctuations and, as such, can no longer be considered a unique feature of hyperthermophiles.

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Saturday Cinema: Earth’s mass extinctions – are bacteria to blame?

Saturday, January 31st, 2009

Asteroid strikes get all the coverage, but “Medea Hypothesis” author Peter Ward argues that most of Earth’s mass extinctions were caused by lowly bacteria. The culprit, a poison called hydrogen sulfide, may have an interesting application in medicine.

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Pathogenic soil bacterium is influenced by land management

Tuesday, January 20th, 2009

Burkholderia pseudomallei Melioidosis is a severe disease affecting humans and animals in the tropics. It is caused by the bacterium Burkholderia pseudomallei, which lives in tropical soil and especially occurs in southeast Asia and northern Australia. Despite the recognition that melioidosis is an emerging infectious disease, little is known about the habitat of B. pseudomallei in the environment.

Researchers from Menzies School of Health Research in Darwin, Australia have found that the soil bacterium Burkholderia pseudomallei, which causes the emerging infectious disease melioidosis in humans and animals, is associated with land management changes such as livestock husbandry or residential gardening. They performed a survey in the Darwin area in tropical Australia, screening 809 soil samples for the presence of these bacteria using molecular methods. The study sheds light on the environmental occurrence of this bacterium in the soil.

B. pseudomallei lives in tropical soil and is endemic in southeast Asia and northern Australia, where it can be a common cause of fatal community-acquired bacterial pneumonia. In predisposed hosts such as those with diabetes, it can also lead to systemic sepsis, with mortality rates over 50 percent. Through a large survey in the tropical Darwin area of Australia, the authors found that environmental factors describing the habitat of these bacteria differed between environmentally undisturbed and disturbed sites. At undisturbed sites, B. pseudomallei was primarily found in close proximity to streams and in grass- and roots-rich areas. In disturbed soil, B. pseudomallei was associated with the presence of animals, farming or irrigation. Highest B. pseudomallei counts were retrieved from paddocks, pens and kennels holding livestock and dogs. This study contributes to the elucidation of the habitat of B. pseudomallei in northern Australia. It also raises concerns that B. pseudomallei may spread due to changes in land management.

These findings raise concerns that B. pseudomallei may spread due to the influence of land management changes. This would increase the risk of human and livestock exposure to these potentially deadly bacteria which are transmitted by contact with contaminated soil or surface water through cuts in the skin or inhalation. In-depth analysis of the influence of anthropogenic factors upon B. pseudomallei and further studies in other endemic areas are needed to confirm the results of this study.

Landscape Changes Influence the Occurrence of the Melioidosis Bacterium Burkholderia pseudomallei in Soil in Northern Australia. PLoS Negl Trop Dis 3(1): e364

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