Carratala A.,University of Barcelona |
Rusinol M.,University of Barcelona |
Hundesa A.,University of Barcelona |
Rodriguez-Manzano J.,University of Barcelona |
And 5 more authors.
Applied and Environmental Microbiology | Year: 2012
Poultry farming may introduce pathogens into the environment and food chains. High concentrations of chicken/turkey parvoviruses were detected in chicken stools and slaughterhouse and downstream urban wastewaters by applying new PCR-based specific detection and quantification techniques. Our results confirm that chicken/turkey parvoviruses may be useful viral indicators of poultry fecal contamination. © 2012, American Society for Microbiology.
News Article | December 10, 2015
As a junior in college around the turn of the century, Qi Zhang wanted to know how proteins worked. He wanted to see them work. He wanted to see how these ingenious little engines folded to perform a function vital to human health. So, of course, he created software – a computer program that could model how these tiny enzymes morphed their structure to affect change in the body. To some people, that step from wanting to know something to creating a way to know it might seem like too large a leap. But that’s how Qi Zhang’s mind has always worked. Biochemistry, to him, is a world of movement in need of further exploration. Ever since he was a boy growing up in eastern China, he has been intrigued with how things are built and how they move. Now, as an assistant professor of biochemistry and biophysics at the UNC School of Medicine, Qi Zhang, Ph.D., is creating new ways to explore how the tiniest things that make us human change and move. At the heart of his research is the fundamental question: how do tiny pieces of genetic code called microRNA (miRNA) keep us healthy and sometimes cause disease. For his work, Zhang earned a UNC School of Medicine Jefferson-Pilot Fellowship in Academic Medicine, which includes a $20,000 prize to support his scholarly endeavors. We sat down with Dr. Zhang for a Five Questions feature to discuss his love of science and math, his creation of novel technologies to study microRNA, his coming to UNC, and the importance of his research in understanding human health and disease. How did you become interested in science and biochemistry in particular? I was not only interested in science as a kid, but also technology, engineering, and math. I was a real STEM kid. I liked to build things that move. I’d make model cars, airplanes, and boats. I’d buy little pieces and follow instructions (and sometime not) to put them together and make sure the things would move like they were supposed to. It was quite an expensive hobby and these projects took a lot of time. I was 10. When I wanted to buy a computer for gaming, my parents – who were far from rich – said they couldn’t afford that. But when I said I wanted to build things, they were very supportive because they loved putting things together, too! Eventually, I really wanted to know how all these pieces moved and the secrets (science and math) behind them. This is when I got into chemistry, which is a field that combines science, math, and movement. Chemistry is all about dynamics; you mix things that are moving around, and something else is created. Ultimately, I realized that the human body is indeed an amazing stage where exciting chemistry happens; proteins, RNAs, and DNAs are constantly moving, communicating, and at the same time, new proteins, RNAs, and DNAs are being created. I wanted to know why and how. You began as a chemistry student at Fudan University in China and then a graduate student at the University of Michigan. Why did you decide to come to the United States? In the early 2000s, the Human Genome Project was booming, and biology was booming. I realized that biological processes are basically chemistry, a more complicated world of chemistry. Studying the chemistry of biology – biochemistry – seemed like fun, something I’d like to pursue. In my third year, I decided to do research. This is when I wrote my own computer programs to see how proteins folded. Proteins are made from various building blocks called amino acids; they start as random things and turn into unique shapes. I wanted to watch these proteins fold. But in China at the time, there wasn’t much technology available to do this. The most accessible technology was computer models, but there was no software available to make them. So I had to write my own software, which the principal investigator in the lab was happy to let me do. I did two years of this pretty much by myself, and it allowed me to create models and “watch” how proteins became folded molecules. But writing my own software to accomplish this was the most I could do in China. I didn’t have access to any other technologies to help me validate what I was doing. I graduated in 2001 and realized I had to go to the United States, a place full of state-of-the-art technologies that could help me create images of proteins folding. The University of Michigan was at the center of using nuclear magnetic resonance (NMR) spectroscopy to study how biomolecules function and how proteins fold to change their structures. When I arrived, I saw that this young professor, Hashim Al-Hashimi, who had just arrived in Ann Arbor, wasn’t doing normal protein work. He worked on RNA –chains of building blocks with ribonucleic acids, which are very similar to DNA. This was not long after the Science paper on the human genome project was published. We could finally see the entire human genome, and there looked to be all this genetic material that didn’t do anything. It was called junk DNA. Well, it turns out it isn’t junk at all. They turn into RNA. So, Hashim was this young guy winning awards who thought that RNA was the future. And I thought he was right. Only about 1.5 percent of the genome codes for proteins. About 98.5 percent involve the things that make us human. If those things are all RNA, then that’s the future. It has to be important for health and disease. That’s how I wound up in the field. Why did you come to UNC? I think UNC is a unique place when it comes to RNA, biophysics, and biochemistry. Our department is very collaborative, people are very collegial, and students are very active and enthusiastic. We all understand each other. Leaders in the department, [the UNC Lineberger Comprehensive] Cancer Center, and the School of Medicine are all very supportive. We have a fantastic atmosphere here. We also have state-of-the-art techniques and facilities that are essential for developing my technologies. Our NMR people have done so much work to make this place a very exciting place to work. And then there’s the RNA work; I think UNC is one of the top universities in this field. Also, there’s the environment of the neighboring universities plus NIEHS [the National Institute for Environmental Health Sciences]. I would say, for me, UNC is the perfect spot for technology development and for the kind of research I want to do with that technology. What is x-ray crystallography and nuclear magnetic resonance spectroscopy, and how do you use these techniques, as well as computational and biochemical approaches, in your research? The critical aspect of my work involves building new techniques to study miRNA instead of relying on existing techniques. When I was in graduate school, we developed new techniques that allowed us to make a video to see how RNA moves. As a postdoc I built more techniques. And now here at UNC, I’m still developing new techniques based in NMR spectroscopy that allow us to show RNA movement at a slower time scale. This cannot be done by any other techniques. NMR is like MRI (magnetic resonance imaging). The difference is that MRI shows images of the body. NMR images atoms. It’s at a much higher resolution. NMR allows us to look at every single atom so we can determine the structure of a molecule that can control gene expression. We can create images in three dimensions on a nanometer scale. We can show its very interesting shape. X-Ray crystallography involves the same principle. Instead of creating x-rays of bones, we x-ray atoms to look at molecules at the atomic level Our techniques allow us to look at atoms at a specific time and to “watch” how the atoms move. We can generate a video. That’s what we want – not only what a molecule looks like but how it acts while it performs a function. This is important because everything in biology is moving. Molecules have to communicate with each other. They need to change shape depending on whether there’s an intruder or not, or during cancer. So, NMR is a powerful tool. Think of it like this: if we really want to understand how a story is developing, it’s ok to see a couple photos, but it’s better to watch a movie to see how it starts, how it ends, and what happens in between. So, for us – as researchers – motion pictures are better when studying human biology and how disease occurs. We can take high-resolution motion pictures so we can know how molecules respond to different environments and how they work. And when something goes wrong, we can see it and search for a way to repair it. This is why computer programs are crucial. Once we generate motion pictures, we have to be able stitch them together so we can see how molecules work on the atomic level and find a way to repair them. If molecules are dysfunctional, they cause disease. This is why basic science is so important. It describes the fundamentals of all biological processes, and when something goes wrong you end up in a kind of disease state. That’s what we’re interested in. What has your research revealed thus far, and why is this kind of work important for improving health and treating diseases? We want to use research techniques we’ve developed to solve biological puzzles. We’re trying to study how “misregulation” of genes contributes to major diseases, such as heart disease and cancer. One thing we study is that if you get rid of a particular microRNA, a tumor disappears. That means it’s an oncogene. This little bit of RNA – 22 nucleotides – once thought of as genetic junk or noise turns out to be very important. We’re trying to understand how this tiny piece of RNA wound up here and to be so important for human health. How are miRNAs made? A lot of people study what miRNA strands do and how they affect other biology. We’re interested in that, too, but we’re more interested in how the miRNA winds up in the role of regulation. We’re interested in the upstream situation of a disease state – can we prevent that miRNA from being the cause of a problem? To us, that’s a more important, and a more fundamental scientific question. What we’ve found, when studying miRNA from its origin, is that these strands are very dynamic. They move around. A lot of miRNAs as regulatory genes are very dynamic. Now we want to watch how they move and identify different proteins that can use this moving target as a regulator for a downstream effect to cause disease. It is no doubt very complex. The human condition is astonishing to think about. The better we get at figuring out what’s going on inside a healthy person, the more we reveal how much we don’t really know. I think the more we know about biology the more it seems almost like magic. I have two boys, and it’s almost magic to see that they were born healthy. An incredible number of things could go wrong, but they usually don’t, even though the human body is an intense synergistic system. All the parts of the body talk to each other to make sure every part of our body works. It’s really amazing. The more I do science the more I find that every single living species is just amazing. That motivates me even more to do science, to understand what’s going on, and to find a way to restore that synergy for people who have a disease.
Vieira C.B.,Instituto Oswaldo Cruz IOC |
de Abreu Correa A.,Instituto Oswaldo Cruz IOC |
de Jesus M.S.,Instituto Leonidas e Maria Deane ILMD |
Luz S.L.B.,Instituto Leonidas e Maria Deane ILMD |
And 4 more authors.
Food and Environmental Virology | Year: 2016
The Negro River is located in the Amazon basin, the largest hydrological catchment in the world. Its water is used for drinking, domestic activities, recreation and transportation and water quality is significantly affected by anthropogenic impacts. The goals of this study were to determine the presence and concentrations of the main viral etiological agents of acute gastroenteritis, such as group A rotavirus (RVA) and genogroup II norovirus (NoV GII), and to assess the use of human adenovirus (HAdV) and JC polyomavirus (JCPyV) as viral indicators of human faecal contamination in the aquatic environment of Manaus under different hydrological scenarios. Water samples were collected along Negro River and in small streams known as igarapés. Viruses were concentrated by an organic flocculation method and detected by quantitative PCR. From 272 samples analysed, HAdV was detected in 91.9 %, followed by JCPyV (69.5 %), RVA (23.9 %) and NoV GII (7.4 %). Viral concentrations ranged from 102 to 106 GC L−1 and viruses were more likely to be detected during the flood season, with the exception of NoV GII, which was detected only during the dry season. Statistically significant differences on virus concentrations between dry and flood seasons were observed only for RVA. The HAdV data provides a useful complement to faecal indicator bacteria in the monitoring of aquatic environments. Overall results demonstrated that the hydrological cycle of the Negro River in the Amazon Basin affects the dynamics of viruses in aquatic environments and, consequently, the exposure of citizens to these waterborne pathogens. © 2016, Springer Science+Business Media New York.
PubMed | Aberystwyth University, National Institute for Environmental Health, Instituto Oswaldo Cruz IOC and Instituto Leonidas e Maria Deane ILMD
Type: Comparative Study | Journal: Food and environmental virology | Year: 2016
The Negro River is located in the Amazon basin, the largest hydrological catchment in the world. Its water is used for drinking, domestic activities, recreation and transportation and water quality is significantly affected by anthropogenic impacts. The goals of this study were to determine the presence and concentrations of the main viral etiological agents of acute gastroenteritis, such as group A rotavirus (RVA) and genogroup II norovirus (NoV GII), and to assess the use of human adenovirus (HAdV) and JC polyomavirus (JCPyV) as viral indicators of human faecal contamination in the aquatic environment of Manaus under different hydrological scenarios. Water samples were collected along Negro River and in small streams known as igaraps. Viruses were concentrated by an organic flocculation method and detected by quantitative PCR. From 272 samples analysed, HAdV was detected in 91.9%, followed by JCPyV (69.5%), RVA (23.9%) and NoV GII (7.4%). Viral concentrations ranged from 10(2) to 10(6) GC L(-1) and viruses were more likely to be detected during the flood season, with the exception of NoV GII, which was detected only during the dry season. Statistically significant differences on virus concentrations between dry and flood seasons were observed only for RVA. The HAdV data provides a useful complement to faecal indicator bacteria in the monitoring of aquatic environments. Overall results demonstrated that the hydrological cycle of the Negro River in the Amazon Basin affects the dynamics of viruses in aquatic environments and, consequently, the exposure of citizens to these waterborne pathogens.
Barna Z.,National Institute for Environmental Health |
Antmann K.,Semmelweiss University |
Paszti J.,National Center for Epidemiology |
Banfi R.,National Institute for Environmental Health |
And 5 more authors.
Journal of Water and Health | Year: 2014
Hospital tap water is a potential source of pathogenic bacteria associated with nosocomial infections. Infection control should include preventive measures to reduce the risk of waterborne infection. The efficiency of point-of-use water filters in infection control was assessed in the intensive care unit of a Hungarian hospital with long history of nosocomial Pseudomonas aeruginosa cases. All taps in the unit were fitted with disposable point-of-use filters. The incidence of nosocomial P. aeruginosa infections decreased from 2.71 to 0 cases/100 patient days when the filters were in place. Legionnaires' disease was not observed either during or outside the study period. Before the application of the filters, both P. aeruginosa and Legionella sp. were shown to colonize five of the seven taps. Filtration eliminated both bacteria completely, though secondary contamination was observed. Total genome restriction profiling of environmental and clinical P. aeruginosa isolates have shown the ubiquitous presence of a single genotype. The same genotype was detected in five of the seven previous nosocomial cases, which supports the assumption of water-derived infection. The results demonstrate that point-of-use filters are effective and cost-efficient measures in reducing health-care associated infections. © IWA Publishing 2014.
Rusinol M.,University of Barcelona |
Fernandez-Cassi X.,University of Barcelona |
Hundesa A.,University of Barcelona |
Vieira C.,Oswaldo Cruz Institute |
And 11 more authors.
Water Research | Year: 2014
Integrated river basin management planning to mitigate the impacts of economic, demographic and climate change is an important issue for the future protection of water resources. Identifying sources of microbial contamination via the emerging science of Microbial Source Tracking (MST) plays a key role in risk assessment and the design of remediation strategies. Following an 18-month surveillance program within the EU-FP7-funded VIROCLIME project, specific MST tools were used to assess human markers such as adenoviruses (HAdV) and JC polyomaviruses (JCPyV) and porcine and bovine markers such as porcine adenoviruses (PAdV) and bovine polyomaviruses (BPyV) via quantification with real-time PCR to analyze surface water collected from five sites within different climatic zones: the Negro River (Brazil), Glafkos River (Greece), Tisza River (Hungary), Llobregat River (Spain) and Umeälven River (Sweden). The utility of the viral MST tools and the prevalence and abundance of specific human and animal viruses in the five river catchments and adjacent seawater, which is impacted by riverine contributions from the upstream catchments, were examined. In areas where no sanitation systems have been implemented, sewage can directly enter surface waters, and river water exhibited high viral loads; HAdV and JCPyV could be detected at mean concentrations of 105 and 104 Genome Copies/Liter (GC/L), respectively. In general, river water samples upstream of urban discharges presented lower human viral loads than downstream sampling sites, and those differences appeared to increase with urban populations but decrease in response to high river flow, as the elevated river water volume dilutes microbial loads. During dry seasons, river water flow decreases dramatically, and secondary effluents can represent the bulk of the riverine discharge. We also observed that ice cover that formed over the river during the winter in the studied areas in North Europe could preserve viral stability due to the low temperatures and/or the lack of solar inactivation. Porcine and bovine markers were detected where intensive livestock and agricultural activities were present; mean concentration values of 103GC/L indicated that farms were sometimes unexpected and important sources of fecal contamination in water. During spring and summer, when livestock is outdoors and river flows are low, animal pollution increases due to diffuse contamination and direct voiding of feces onto the catchment surface. The field studies described here demonstrate the dynamics of fecal contamination in all catchments studied, and the data obtained is currently being used to develop dissemination models of fecal contamination in water with respect to future climate change scenarios. The results concerning human and animal targets presented in this study demonstrate the specificity and applicability of the viral quantitative parameters developed to widely divergent geographical areas and their high interest as new indicators of human and animal fecal contamination in water and as MST tools. © 2014 Elsevier Ltd.
Torokne A.,National Institute for Environmental Health |
Toro K.,National Institute for Environmental Health
Environmental Toxicology | Year: 2010
The aim of this study is to compare the responses of two different ecotoxicological methods for the determination of the toxic hazard of river or creek sediments in Hungary. Since water quality is intrinsically linked to sediment quality, the ecotoxicological control of sediments is also very important in the water quality policy. The 2000/60 EC Water Framework Directive aims at achieving a good qualitative and quantitative status of all water bodies by 2015. Fifteen sediments and four sludges were collected at different sites in Hungary, which are contaminated by industrial sewage. The first assay is the acute toxicity test with the crustacean Daphnia magna Straus (OECD 202) using larvae less than 1 day old, and an exposure time of 2 days. The second assay is the Ostracodtoxkit F with freshly hatched larvae of the crustacean Heterocypris incongruens and an exposure time of 6 days. The Ostracodtoxkit F test is a "direct sediment contact" bioassay, in which the test organisms are in continuous contact with the sediments. The Daphnia tests were applied on water extracts of the sediment without any contact of the test organisms with the contaminated sediment. The same 1:4 water/sediment ratio has been applied to both tests. The results showed higher toxic effects of the sediments to H. incongruens than to D. magna confirming the need to complement "water only" tests with "solid phase" assays for a meaningful evaluation of the toxic hazard of aquatic environments. The sensitivity of H. incongruens is similar to that of the other test species which are currently used for solid-phase assays. The growth inhibition of H. incongruens is a very sensitive endpoint for sediment toxicity testing. The sediment toxicity tested by ostracods showed strong correlation with concentration of total chromium, lead, and cadmium together. © 2010 Wiley Periodicals, Inc.
Felfoldi T.,Eötvös Loránd University |
Heeger Z.,Eötvös Loránd University |
Vargha M.,National Institute for Environmental Health |
Marialigeti K.,Eötvös Loránd University
Clinical Microbiology and Infection | Year: 2010
The drinking water distribution system of a hospital was investigated using standard cultivation techniques, taxon-specific PCRs targeting pathogenic bacteria, denaturing gradient gel electrophoresis, cloning and sequencing. The results obtained verify the higher sensitivity of PCR compared to cultivation for detecting Legionella and Pseudomonas aeruginosa. Moreover, several other opportunistic pathogenic bacteria, such as Escherichia albertii, Acinetobacter lwoffi and Corynebacterium tuberculostrearicum, were detected, emphasizing that drinking water systems, especially those with stagnant water sections, could be the source of nosocomial infections. © 2009 The Authors. Journal Compilation © 2009 European Society of Clinical Microbiology and Infectious Diseases.
Kern A.,National Institute for Environmental Health |
Kadar M.,National Institute for Environmental Health |
Szomor K.,National Diagnostics |
Berencsi G.,National Diagnostics |
And 2 more authors.
Journal of Water and Health | Year: 2013
Waterborne viruses infect the human population through the consumption of contaminated drinking water and by direct contact with polluted surface water during recreational activity. Although water related viral outbreaks are a major public health concern, virus detection is not a part of the water quality monitoring scheme, mainly due to the absence of routine analysis methods. In the present study, we implemented various approaches for water concentration and virus detection, and tested on Hungarian surface water samples. Eighty samples were collected from 16 sites in Hungary. Samples were concentrated by glass wool and membrane filtration. Human adenoviruses were detected by conventional and quantitative real-time polymerase chain reaction (PCR) methods in 56% (45/80) of the samples; viral titers ranged from 8.60 × 101 to 3.91 × 104 genome copies per liter. Noroviruses and enteroviruses were detected in 30% (24/80) and 13% (10/80) of samples, respectively, by reverse transcription-PCR assays. Results indicate a high prevalence of viral human pathogens in surface waters, suggesting the necessity of a detailed survey focusing on the quality of natural bathing waters and drinking water sources. © IWA Publishing 2013.
PubMed | National Diagnostics, Stanford University and National Institute for Environmental Health
Type: Journal Article | Journal: Journal of water and health | Year: 2013
Waterborne viruses infect the human population through the consumption of contaminated drinking water and by direct contact with polluted surface water during recreational activity. Although water related viral outbreaks are a major public health concern, virus detection is not a part of the water quality monitoring scheme, mainly due to the absence of routine analysis methods. In the present study, we implemented various approaches for water concentration and virus detection, and tested on Hungarian surface water samples. Eighty samples were collected from 16 sites in Hungary. Samples were concentrated by glass wool and membrane filtration. Human adenoviruses were detected by conventional and quantitative real-time polymerase chain reaction (PCR) methods in 56% (45/80) of the samples; viral titers ranged from 8.60 10(1) to 3.91 10(4) genome copies per liter. Noroviruses and enteroviruses were detected in 30% (24/80) and 13% (10/80) of samples, respectively, by reverse transcription-PCR assays. Results indicate a high prevalence of viral human pathogens in surface waters, suggesting the necessity of a detailed survey focusing on the quality of natural bathing waters and drinking water sources.