Saturday, May 30, 2009
Genetic survey finds healthy human skin is crawling with bacteria
Think a good antibacterial hand soap is keeping your skin relatively microbe and bacteria free? You might want to think again. Scientists and germophobes alike have long known that human skin—from head to toe—is literally crawling with bacteria and microbes. And a new study, published today in Science shows that skin is host to many, many more of the tiny organisms than previously thought. Researchers at the National Institutes of Health's (NIH) new Human Microbiome Project sequenced genes from skin samples from volunteers and found bacteria that hailed from 19 different phyla, 205 genera and possessed more than 112,000 individual gene sequences. (Previous studies of skin cultures supposed that just one type of bacteria, Staphylococcus—a virulent strain of which is responsible for staph infections—was the main resident of human skin.) But no need to overdo it on the antibacterials; most of the tiny organisms aren't doing any harm. All of these samples were collected from 20 different disease-prone spots on the bodies of 10 healthy volunteers—from forehead to heel, with stops such as the buttock and inner elbow along the way.After completing this initial survey, researchers aim to establish a bacterial baseline so as to better treat skin diseases, such as acne or eczema, where bacterial populations might be out of whack. "The skin is…an ecosystem, harboring microbial communities that live in a range of physiologically and topographically distinct niches," the study authors write. "For example, hairy, moist underarms lie a short distance from smooth, dry forearms, but these two niches are as ecologically dissimilar as rainforests are to deserts." Can you guess the location with the most types of bacteria? No, it's not the "rainforest" or below the belt. Try the forearm, which boasts an average of 44 different species.
Largest Ever Autism Study Identifies Two Genetic Culprits
The largest genome scan ever conducted to get to the bottom of autism has pinpointed two locations in the human genetic makeup that may trigger the mysterious mental condition. The Autism Genome Project, a collaboration of 120 scientists representing 19 countries and 50 institutions, compared the genomes of 1,168 families that each had at least two autism sufferers in them to try to track down the regions. The consortium reports its findings in this week's issue of Nature Genetics.
Autism is a mental disorder characterized by behavioral problems that may include a lack of social and communications skills, such as failure to respond to one's own name, intense tantrums and general detachment. In the last decade the diagnosis of autism has increased 10-fold. It is now believed to affect one in 166 children born in the U.S. and four boys for every girl.
"Although we know autism is highly inheritable, complex gene interactions and submicroscopic anomalies create a din of statistical noise that drowns out detection of signals from linked sites in the genome," says study co-author Bernie Devlin, a human geneticist at the University of Pittsburgh. "To amplify these signals, we brought to bear gene chip technology with a huge sample, and also screened for these fine-level anomalies, factoring them into the analysis."
Using a DNA microarray, or gene chip, the team was able to scan large stretches of sequence for tiny deletions common within the study families. They also sought out copy number variations and large-scale insertions or deletions of genetic material. In the two-fold analysis, the researchers implicated the gene neurexin 1, located on chromosome 2, as well as a swath of sequence on chromosome 11.
Neurexin 1 is part of a three-member family of genes coding for proteins involved in communication between neurons. It is associated with glutamate, the neurotransmitter known to elevate neuronal activity and play a role in wiring the brain during early development. Glutamate functioning has been implicated in other syndromes involving mental retardation of which autism is often a symptom, such as fragile X syndrome and tuberous sclerosis. Neurexin 1 is specifically believed to be involved in building glutamate synapses, the links through which glutamate neurons send and receive electrical signals.
"Often you don't have any idea of what a gene does, but in this case we know neurexin 1 is involved at sites where the neurotransmitter glutamate is released," says study coauthor Gerard Schellenberg, a medical researcher at the University of Washington. "As for the chromosome 11 location, we think there is another susceptibility gene there and we are actively pursuing it. We are in the neighborhood and have a plan to find it. The section of chromosome 11 identified in the study has been linked to proteins that ferry glutamate across synapses.
Genetic anomalies, from tiny deletions or substitutions of single bases to large stretches of missing code or even multiple copies of the same code, often crop up in the human genome and, occasionally, can create a disposition to a particular type of disorder. Among the variations found in the Autism Genome Project subjects was the deletion of the neurexin 1 gene. Much of the autism research community believes there may be roughly six major genes involved in autism, and maybe 30 others that may confer some risk. A combination of mutations in any of these genes could contribute to the likelihood of being born with autism. Because a number of different genetic factors may contribute to this disease, identifying these markers is made very difficult and large sample sizes are needed to get significant results.
"These findings are a piece of the puzzle," says Geraldine Dawson, director of the University of Washington's Autism Center. "As we identify these genes we will be able to screen young children for autism at an early age and begin interventions earlier, which can have a dramatic effect for some children."
These results are the culmination of phase 1 of the Autism Genome Project, which began in 2002 with the sharing of samples and data from labs around the world. Phase 2 will follow up on the leads discovered in the first phase. The $14.5 million project will receive funding from various institutions such as the National Institutes of Health and Autism Speaks, an organization dedicated to increasing the awareness of and finding a cure for autism spectrum disorders.
"Autism is a very difficult condition for families—communication is taken for granted by parents of healthy children but is so greatly missed by those with autistic children," says study co-author, Jonathan Green, a child psychiatrist at the University of Manchester in England. "We hope that these exciting results may represent a step on the way to further new treatments in the future."
Autism is a mental disorder characterized by behavioral problems that may include a lack of social and communications skills, such as failure to respond to one's own name, intense tantrums and general detachment. In the last decade the diagnosis of autism has increased 10-fold. It is now believed to affect one in 166 children born in the U.S. and four boys for every girl.
"Although we know autism is highly inheritable, complex gene interactions and submicroscopic anomalies create a din of statistical noise that drowns out detection of signals from linked sites in the genome," says study co-author Bernie Devlin, a human geneticist at the University of Pittsburgh. "To amplify these signals, we brought to bear gene chip technology with a huge sample, and also screened for these fine-level anomalies, factoring them into the analysis."
Using a DNA microarray, or gene chip, the team was able to scan large stretches of sequence for tiny deletions common within the study families. They also sought out copy number variations and large-scale insertions or deletions of genetic material. In the two-fold analysis, the researchers implicated the gene neurexin 1, located on chromosome 2, as well as a swath of sequence on chromosome 11.
Neurexin 1 is part of a three-member family of genes coding for proteins involved in communication between neurons. It is associated with glutamate, the neurotransmitter known to elevate neuronal activity and play a role in wiring the brain during early development. Glutamate functioning has been implicated in other syndromes involving mental retardation of which autism is often a symptom, such as fragile X syndrome and tuberous sclerosis. Neurexin 1 is specifically believed to be involved in building glutamate synapses, the links through which glutamate neurons send and receive electrical signals.
"Often you don't have any idea of what a gene does, but in this case we know neurexin 1 is involved at sites where the neurotransmitter glutamate is released," says study coauthor Gerard Schellenberg, a medical researcher at the University of Washington. "As for the chromosome 11 location, we think there is another susceptibility gene there and we are actively pursuing it. We are in the neighborhood and have a plan to find it. The section of chromosome 11 identified in the study has been linked to proteins that ferry glutamate across synapses.
Genetic anomalies, from tiny deletions or substitutions of single bases to large stretches of missing code or even multiple copies of the same code, often crop up in the human genome and, occasionally, can create a disposition to a particular type of disorder. Among the variations found in the Autism Genome Project subjects was the deletion of the neurexin 1 gene. Much of the autism research community believes there may be roughly six major genes involved in autism, and maybe 30 others that may confer some risk. A combination of mutations in any of these genes could contribute to the likelihood of being born with autism. Because a number of different genetic factors may contribute to this disease, identifying these markers is made very difficult and large sample sizes are needed to get significant results.
"These findings are a piece of the puzzle," says Geraldine Dawson, director of the University of Washington's Autism Center. "As we identify these genes we will be able to screen young children for autism at an early age and begin interventions earlier, which can have a dramatic effect for some children."
These results are the culmination of phase 1 of the Autism Genome Project, which began in 2002 with the sharing of samples and data from labs around the world. Phase 2 will follow up on the leads discovered in the first phase. The $14.5 million project will receive funding from various institutions such as the National Institutes of Health and Autism Speaks, an organization dedicated to increasing the awareness of and finding a cure for autism spectrum disorders.
"Autism is a very difficult condition for families—communication is taken for granted by parents of healthy children but is so greatly missed by those with autistic children," says study co-author, Jonathan Green, a child psychiatrist at the University of Manchester in England. "We hope that these exciting results may represent a step on the way to further new treatments in the future."
A study on a large scale identify the genes implicated in mental retardation
X-linked mental retardation (XLMR) is a common cause of moderate to severe intellectual disability in males. XLMR is very heterogeneous, and about two-thirds of patients have clinically indistinguishable non-syndromic (NS-XLMR) forms, which has greatly hampered their molecular elucidation. A few years ago, international consortia overcame this impasse by collecting DNA and cell lines from large cohorts of XLMR families, thereby paving the way for the systematic study of the molecular causes of XLMR. Mutations in known genes might already account for 50% of the families with NS-XLMR, and various genes have been pinpointed that seem to be of particular diagnostic importance. Eventually, even therapy of XLMR might become possible, as suggested by the unexpected plasticity of the neuronal wiring in the brain, and the recent successful drug treatment of a fly model for fragile X syndrome.
Wednesday, May 27, 2009
NEW 'OME' IN TOWN
We're living in an "omic" world. Some of these "omes," such as the genome and the proteome, are familiar; others, less so. Now the metabonome, one of the newest omes in name if not in reality, has joined the pantheon of global biological measurements.
METHOD OF CHOICE NMR is the most popular method for metabonomics experiments. The NMR facility at Imperial College is shown here.COURTESY OF JEREMY NICHOLSON The "omics" suffix has come to signify the measurement of the entire complement of a given level of biological molecules and information. Therefore, genomics measures the entire genetic makeup of an organism, while proteomics measures all the proteins expressed under given conditions. Metabonomics is no different. As the name might imply, metabonomics is defined as measurement of the complete metabolic response of an organism to an environmental stimulus or genetic modification. Some people use the term metabolomics to refer to metabonomics at the level of a single cell type, rather than a larger system.
The omics can provide information for basic biological research and for pharmaceutical and clinical applications. One of the challenges is integrating the information from the various omics, something that really is only beginning. The goal of a meeting held last month in San Francisco by the California Separation Science Society was just such an integration. In the process, the organizers coined yet another word--systeomics--which was defined as the integration of genomics, proteomics, and metabonomics.
Despite the goal of integration, scientists appear to be sticking with their favorite ome. Most speakers concentrated on one of the areas without addressing how to fit the three together.
Metabonomics may be the most recently named of the omics, but it's one of the oldest. In fact, metabonomics harkens back to old-fashioned biochemistry, with its emphasis on metabolism, the sum of the processes to acquire and use energy in an organism, to biosynthesize cellular components, and to catabolize wastes.
"We've been doing toxicological and disease diagnostics based on metabolic profiling for more than 20 years. That's before genomics or proteomics raised their ugly heads," Jeremy Nicholson, professor of biological chemistry at Imperial College of Science, Technology & Medicine in London, told C&EN.
Nicholson believes that metabonomics is "more closely related to things in the clinical world" than either genomics or proteomics, owing to the fact that metabonomic signatures reflect both genetic information and environmental influences.
John Lindon, another professor of biological chemistry at Imperial College, agrees. "Genomics and proteomics are in 'omics world.' They're not in the real world," Lindon said. "What you're trying to do is relate changes in gene expression or changes in protein level with some real-world endpoints that relate to a disease or toxic episode."
Adelbert Roscher, professor of biochemical genetics on the medical faculty at the University of Munich, said that metabolite profiling "measures the real outcome of potential changes suggested by genomics and proteomics."
Image is available in( Adobe PDF format only)
BIG PICTURE Metabonomics offers the opportunity to find patterns and changes in the entire metabolism, represented here by the metabolic pathways chart designed by Donald E. Nicholson, retired from the University of Leeds.©INTERNATIONAL UNION OF BIOCHEMISTRY & MOLECULAR BIOLOGYTHE VALUE OF genomic and proteomic measurements, Nicholson believes, is "considerably more limited than most people think." For example, changes in gene and protein expression needn't result in an "endpoint change." That is, the change in one gene or protein could be compensated elsewhere, resulting in no net change. "That's always the big problem with genes and proteins," Nicholson said. "Their up or down regulation can be part of the overall homeostatic or corrective process of the cell, not necessarily part of the pathology."
Nicholson suspects that most diseases have a metabolic signature at some level. The challenge is finding that signature. Finding the right matrix is important, whether it be urine, blood, cerebrospinal fluid, or solid tissue.
"Urine carries information on almost everything, because [the kidney is] your ultimate excretory organ, where homeostasis is maintained," Nicholson said. "There's a tremendous amount of information that can be obtained from urine, if you can analyze all the thousands of metabolites that are in there."
Metabonomics experiments are carried out by analyzing biological fluids or tissue extracts with techniques--such as nuclear magnetic resonance spectroscopy, mass spectrometry, or infrared spectroscopy--that provide many data points simultaneously. Even intact tissue samples taken during biopsies can be analyzed, using the NMR technique known as magic angle spinning.
The metabonomic profile is dominated by molecules smaller than 1,000 daltons. That molecular weight range "incorporates pretty much all energy pathways, all catabolic pathways, and many biosynthetic pathways," Nicholson told C&EN.
Nicholson and his colleagues focus on NMR measurements. The subtle differences in NMR spectra are practically impossible to identify just by visual inspection. Data mining and statistical techniques must be used to pull out what Nicholson calls "latent diagnostic information."
METHOD OF CHOICE NMR is the most popular method for metabonomics experiments. The NMR facility at Imperial College is shown here.COURTESY OF JEREMY NICHOLSON The "omics" suffix has come to signify the measurement of the entire complement of a given level of biological molecules and information. Therefore, genomics measures the entire genetic makeup of an organism, while proteomics measures all the proteins expressed under given conditions. Metabonomics is no different. As the name might imply, metabonomics is defined as measurement of the complete metabolic response of an organism to an environmental stimulus or genetic modification. Some people use the term metabolomics to refer to metabonomics at the level of a single cell type, rather than a larger system.
The omics can provide information for basic biological research and for pharmaceutical and clinical applications. One of the challenges is integrating the information from the various omics, something that really is only beginning. The goal of a meeting held last month in San Francisco by the California Separation Science Society was just such an integration. In the process, the organizers coined yet another word--systeomics--which was defined as the integration of genomics, proteomics, and metabonomics.
Despite the goal of integration, scientists appear to be sticking with their favorite ome. Most speakers concentrated on one of the areas without addressing how to fit the three together.
Metabonomics may be the most recently named of the omics, but it's one of the oldest. In fact, metabonomics harkens back to old-fashioned biochemistry, with its emphasis on metabolism, the sum of the processes to acquire and use energy in an organism, to biosynthesize cellular components, and to catabolize wastes.
"We've been doing toxicological and disease diagnostics based on metabolic profiling for more than 20 years. That's before genomics or proteomics raised their ugly heads," Jeremy Nicholson, professor of biological chemistry at Imperial College of Science, Technology & Medicine in London, told C&EN.
Nicholson believes that metabonomics is "more closely related to things in the clinical world" than either genomics or proteomics, owing to the fact that metabonomic signatures reflect both genetic information and environmental influences.
John Lindon, another professor of biological chemistry at Imperial College, agrees. "Genomics and proteomics are in 'omics world.' They're not in the real world," Lindon said. "What you're trying to do is relate changes in gene expression or changes in protein level with some real-world endpoints that relate to a disease or toxic episode."
Adelbert Roscher, professor of biochemical genetics on the medical faculty at the University of Munich, said that metabolite profiling "measures the real outcome of potential changes suggested by genomics and proteomics."
Image is available in( Adobe PDF format only)
BIG PICTURE Metabonomics offers the opportunity to find patterns and changes in the entire metabolism, represented here by the metabolic pathways chart designed by Donald E. Nicholson, retired from the University of Leeds.©INTERNATIONAL UNION OF BIOCHEMISTRY & MOLECULAR BIOLOGYTHE VALUE OF genomic and proteomic measurements, Nicholson believes, is "considerably more limited than most people think." For example, changes in gene and protein expression needn't result in an "endpoint change." That is, the change in one gene or protein could be compensated elsewhere, resulting in no net change. "That's always the big problem with genes and proteins," Nicholson said. "Their up or down regulation can be part of the overall homeostatic or corrective process of the cell, not necessarily part of the pathology."
Nicholson suspects that most diseases have a metabolic signature at some level. The challenge is finding that signature. Finding the right matrix is important, whether it be urine, blood, cerebrospinal fluid, or solid tissue.
"Urine carries information on almost everything, because [the kidney is] your ultimate excretory organ, where homeostasis is maintained," Nicholson said. "There's a tremendous amount of information that can be obtained from urine, if you can analyze all the thousands of metabolites that are in there."
Metabonomics experiments are carried out by analyzing biological fluids or tissue extracts with techniques--such as nuclear magnetic resonance spectroscopy, mass spectrometry, or infrared spectroscopy--that provide many data points simultaneously. Even intact tissue samples taken during biopsies can be analyzed, using the NMR technique known as magic angle spinning.
The metabonomic profile is dominated by molecules smaller than 1,000 daltons. That molecular weight range "incorporates pretty much all energy pathways, all catabolic pathways, and many biosynthetic pathways," Nicholson told C&EN.
Nicholson and his colleagues focus on NMR measurements. The subtle differences in NMR spectra are practically impossible to identify just by visual inspection. Data mining and statistical techniques must be used to pull out what Nicholson calls "latent diagnostic information."
Metabolomics: Is it just another Omics?
The omics
One would not be mistaken for thinking that a new omics word enters our scientific vocabulary every week, from behaviouromics and cytomics to transgenomics and vaccinomics [ref www.genomicglossaries.com/content/omes.asp]. By far the most important and widely established omics terms include genomics - the high throughput analyses of multiple genes including gene sequencing and function; transcriptomics – the study of mRNAs transcribed from a cell’s genome; and proteomics – the determination of the structures and functions of all proteins in a cell or organism. The complete characterisation of cellular processes, whether associated with normal homoeostasis or as a result of disease, toxic insult or genetic manipulation, also requires information on the metabolic status of the cell or organism. Indeed it can be argued that the cellular metabolic status is the most functional measure of the cell’s phenotype (Figure 1). The twenty first century has witnessed the rapid explosion of a new omics science associated with the measurement of metabolites.
What’s in a name?
So what name do we give to the high throughput and comprehensive analysis of metabolites within a cell or organism under a defined physiological state? Metabolomics has emerged as the obvious terminology, although many other variants exist such as metabolic profiling, metabolic fingerprinting and metabonomics. The latter originated from Professor Jeremy Nicholson’s laboratory at Imperial College London, a pioneer of the field, who defines metabonomics as ‘the quantitative measurement of the dynamic multiparametric metabolic response of living systems to pathophysiological stimuli or genetic modification’ (Nicholson, et al. 1999 #3). As with any new research field the definitions continue to evolve, and a formal nomenclature will soon be decided by the new Metabolomics Society.
Applications in the biological and clinical sciences
To date, relatively few metabolomics studies have been published that provide significant new insight into biological processes. Noteworthy papers include the application of metabolomics to the study of drug toxicity (Nicholson, et al. 2002 #2), identification of the phenotype of silent gene mutations (Raamsdonk, et al. 2001 #4), and clinical applications such as the diagnosis of coronary heart disease (Brindle, et al. 2002 #1). Metabolomics has simply had insufficient time to prove itself compared with the more mature omics approaches of genomics and transcriptomics. Indeed, considerable work still remains in developing the bioanalytical and bioinformatic technologies that underpin this science, without which its full potential will never be realised. One of the two primary goals of my research group is exactly that, to develop and optimise metabolomics methodologies at Birmingham, which can then be applied to a range of applications (Figure 2) (Viant, 2003 #5). My group’s other focus is to apply these methods to study the effects of environmental stressors on fish and aquatic invertebrates. To that end I was fortunate to be awarded an NERC Advanced Fellowship, which started in November 2003.
Metabolomics technologies
Birmingham attracted me for several reasons, not least because of it’s new £7.7m nuclear magnetic resonance (NMR) facility named the Henry Wellcome Building for Biomolecular NMR Spectroscopy (HWB•NMR), under the Executive Directorship of Professor Michael Overduin in the School of Medicine. This national facility, which opened officially in November 2004, houses state-of-the-art NMR equipment including the world’s most powerful 900 MHz spectrometer. NMR spectroscopy is currently the most widely used bioanalytical technique for metabolomics, and following recent NERC and BBSRC awards the HWB•NMR is now purchasing additional equipment dedicated to Birmingham’s emerging metabolomics program (Figure 3). Mass spectrometry is an equally important toolset for metabolomics and also proteomics, and the School of Biosciences is currently purchasing an ultra-high mass precision FT ICR mass spectrometer for ‘omics’ research, under the direction of Professor John Heath, Head of School, and Dr Helen Cooper, a newly appointed Wellcome Trust University Technology Fellow. Collectively these instruments and associated expertise have the potential to position Birmingham as an international centre of excellence for metabolomics. In addition, we are well placed to develop the necessary spectral processing tools and bioinformatics for metabolomics studies that are needed to extract the metabolic information from the NMR and mass spectra. This draws upon extensive expertise from across campus and includes Drs. Ulrich Günther and Christian Ludwig (HWB•NMR), Drs. Francesco Falciani and Dov Stekel (School of Biosciences) and Dr. Theo Arvanitis (School of Engineering).
Environmental metabolomics
Metabolomics is ideal for studying the impact of stressors such as pollution and climate change on environmental species, not least because no species-specific DNA sequence information is required. Lactate is lactate whether you are studying a fish, earthworm or human! Current environmental projects at Birmingham, funded by the NERC, include developing a predictive biomarker model for the marine and estuarine environments, based upon metabolomic and bioinformatic methods that use the European flounder and common mussel as sentinel species (Figure 4). This project complements research by Professor Kevin Chipman’s group who are using transcriptomics to characterise the responses of flounder to several classes of toxicants. Recently we have secured a £1.6m NERC Consortium grant, coordinated by Birmingham and in collaboration with a number of UK universities, to identify and define the bases of individual and population susceptibility and adaptation to environmental pollutants in fish using an integrated ‘omic’ approach. Disease processes are also amenable to study. On-going projects include an investigation of withering syndrome in the red abalone, a marine shellfish, in collaboration with the University of California, Davis (Figure 5) (Viant, et al. 2003), and a collaboration with the Centre for Environment, Fisheries and Aquaculture Science at Weymouth in which we are characterising the metabolic consequences of tumour formation in the liver of dab, a marine flatfish.
Birmingham’s Metabolomics Initiative
The application of metabolomics to cancer extends far beyond environmental studies, and not surprisingly this involves the Institute for Cancer Studies in the School of Medicine at Birmingham. In particular, a newly-funded EU project with Dr. Ulrich Günther, Dr. Chris Bunce (School of Biosciences) and me, aims to develop advanced NMR technologies for metabolomics and to use these to investigate the role of specific enzymes in cancer. Other projects include Dr Andrew Peet’s metabolomics studies in paediatric neuro-oncology at the Birmingham Children’s Hospital. Aside from medical studies, metabolomics projects are now starting in several Schools across the campus, including an investigation of acid stress in E. coli by Dr. Pete Lund in Biosciences, and projects by Professor Anton Wagenmakers in Sport and Exercise Sciences and Professor Mohamed Al-Rubeai in Chemical Engineering. In summary, Birmingham is now entering an extremely exciting and productive period of metabolomics research that includes three important components – state of the art equipment and infrastructure, experts in bioanalytical and bioinformatic method development, and world class biological and clinical scientists – and crucial to our success is the highly collaborative environment on which The University of Birmingham thrives.
One would not be mistaken for thinking that a new omics word enters our scientific vocabulary every week, from behaviouromics and cytomics to transgenomics and vaccinomics [ref www.genomicglossaries.com/content/omes.asp]. By far the most important and widely established omics terms include genomics - the high throughput analyses of multiple genes including gene sequencing and function; transcriptomics – the study of mRNAs transcribed from a cell’s genome; and proteomics – the determination of the structures and functions of all proteins in a cell or organism. The complete characterisation of cellular processes, whether associated with normal homoeostasis or as a result of disease, toxic insult or genetic manipulation, also requires information on the metabolic status of the cell or organism. Indeed it can be argued that the cellular metabolic status is the most functional measure of the cell’s phenotype (Figure 1). The twenty first century has witnessed the rapid explosion of a new omics science associated with the measurement of metabolites.
What’s in a name?
So what name do we give to the high throughput and comprehensive analysis of metabolites within a cell or organism under a defined physiological state? Metabolomics has emerged as the obvious terminology, although many other variants exist such as metabolic profiling, metabolic fingerprinting and metabonomics. The latter originated from Professor Jeremy Nicholson’s laboratory at Imperial College London, a pioneer of the field, who defines metabonomics as ‘the quantitative measurement of the dynamic multiparametric metabolic response of living systems to pathophysiological stimuli or genetic modification’ (Nicholson, et al. 1999 #3). As with any new research field the definitions continue to evolve, and a formal nomenclature will soon be decided by the new Metabolomics Society.
Applications in the biological and clinical sciences
To date, relatively few metabolomics studies have been published that provide significant new insight into biological processes. Noteworthy papers include the application of metabolomics to the study of drug toxicity (Nicholson, et al. 2002 #2), identification of the phenotype of silent gene mutations (Raamsdonk, et al. 2001 #4), and clinical applications such as the diagnosis of coronary heart disease (Brindle, et al. 2002 #1). Metabolomics has simply had insufficient time to prove itself compared with the more mature omics approaches of genomics and transcriptomics. Indeed, considerable work still remains in developing the bioanalytical and bioinformatic technologies that underpin this science, without which its full potential will never be realised. One of the two primary goals of my research group is exactly that, to develop and optimise metabolomics methodologies at Birmingham, which can then be applied to a range of applications (Figure 2) (Viant, 2003 #5). My group’s other focus is to apply these methods to study the effects of environmental stressors on fish and aquatic invertebrates. To that end I was fortunate to be awarded an NERC Advanced Fellowship, which started in November 2003.
Metabolomics technologies
Birmingham attracted me for several reasons, not least because of it’s new £7.7m nuclear magnetic resonance (NMR) facility named the Henry Wellcome Building for Biomolecular NMR Spectroscopy (HWB•NMR), under the Executive Directorship of Professor Michael Overduin in the School of Medicine. This national facility, which opened officially in November 2004, houses state-of-the-art NMR equipment including the world’s most powerful 900 MHz spectrometer. NMR spectroscopy is currently the most widely used bioanalytical technique for metabolomics, and following recent NERC and BBSRC awards the HWB•NMR is now purchasing additional equipment dedicated to Birmingham’s emerging metabolomics program (Figure 3). Mass spectrometry is an equally important toolset for metabolomics and also proteomics, and the School of Biosciences is currently purchasing an ultra-high mass precision FT ICR mass spectrometer for ‘omics’ research, under the direction of Professor John Heath, Head of School, and Dr Helen Cooper, a newly appointed Wellcome Trust University Technology Fellow. Collectively these instruments and associated expertise have the potential to position Birmingham as an international centre of excellence for metabolomics. In addition, we are well placed to develop the necessary spectral processing tools and bioinformatics for metabolomics studies that are needed to extract the metabolic information from the NMR and mass spectra. This draws upon extensive expertise from across campus and includes Drs. Ulrich Günther and Christian Ludwig (HWB•NMR), Drs. Francesco Falciani and Dov Stekel (School of Biosciences) and Dr. Theo Arvanitis (School of Engineering).
Environmental metabolomics
Metabolomics is ideal for studying the impact of stressors such as pollution and climate change on environmental species, not least because no species-specific DNA sequence information is required. Lactate is lactate whether you are studying a fish, earthworm or human! Current environmental projects at Birmingham, funded by the NERC, include developing a predictive biomarker model for the marine and estuarine environments, based upon metabolomic and bioinformatic methods that use the European flounder and common mussel as sentinel species (Figure 4). This project complements research by Professor Kevin Chipman’s group who are using transcriptomics to characterise the responses of flounder to several classes of toxicants. Recently we have secured a £1.6m NERC Consortium grant, coordinated by Birmingham and in collaboration with a number of UK universities, to identify and define the bases of individual and population susceptibility and adaptation to environmental pollutants in fish using an integrated ‘omic’ approach. Disease processes are also amenable to study. On-going projects include an investigation of withering syndrome in the red abalone, a marine shellfish, in collaboration with the University of California, Davis (Figure 5) (Viant, et al. 2003), and a collaboration with the Centre for Environment, Fisheries and Aquaculture Science at Weymouth in which we are characterising the metabolic consequences of tumour formation in the liver of dab, a marine flatfish.
Birmingham’s Metabolomics Initiative
The application of metabolomics to cancer extends far beyond environmental studies, and not surprisingly this involves the Institute for Cancer Studies in the School of Medicine at Birmingham. In particular, a newly-funded EU project with Dr. Ulrich Günther, Dr. Chris Bunce (School of Biosciences) and me, aims to develop advanced NMR technologies for metabolomics and to use these to investigate the role of specific enzymes in cancer. Other projects include Dr Andrew Peet’s metabolomics studies in paediatric neuro-oncology at the Birmingham Children’s Hospital. Aside from medical studies, metabolomics projects are now starting in several Schools across the campus, including an investigation of acid stress in E. coli by Dr. Pete Lund in Biosciences, and projects by Professor Anton Wagenmakers in Sport and Exercise Sciences and Professor Mohamed Al-Rubeai in Chemical Engineering. In summary, Birmingham is now entering an extremely exciting and productive period of metabolomics research that includes three important components – state of the art equipment and infrastructure, experts in bioanalytical and bioinformatic method development, and world class biological and clinical scientists – and crucial to our success is the highly collaborative environment on which The University of Birmingham thrives.
Environmental Metabolomics: The Study of Disease and Toxicity in Wildlife
With the completion of the Human Genome Project, we have now truly entered the exciting era of post-genomics biology. Several new scientific disciplines have emerged of which metabolomics holds significant promise for the understanding and diagnosis of diseases both in humans and wildlife. This introduction to the new field of metabolomics will describe several applications of this approach for monitoring the health of organisms in the environment.
The inside of a Californian red abalone shell, Haliotis rufescens (compare size to the coin in photo). The shellfish is susceptible to a disease called withering syndrome. Source: Wikimedia Commons.
Introduction to metabolomics
It’s the study of small naturally occurring molecules.
Metabolomics is the study of all the naturally occurring small molecules, called metabolites, in biological samples such as cells, biofluids, or tissues. These small molecules are the products of metabolism and include, for example, sugars (or carbohydrates), fats (or lipids), and amino acids. The collection of all the metabolites within a cell is called the metabolome. Scientists have started to characterize the metabolome in a quest to better understand and diagnose disease.
It requires input from various disciplines, such as chemistry.
Metabolomics incorporates the use of bioinformatics, the application of computer and statistical techniques to the understanding and management of biological information, to search for unique patterns of metabolites that are indicative of a particular disease.
Metabolomics is a multidisciplinary approach involving biologists, computer scientists, and analytical chemists. The tools used to measure the metabolites are more commonly associated with chemistry laboratories and include nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry.
It measures the interactions of genes with the environment.
The advantage of metabolomics for disease diagnosis, whether in humans or wildlife, stems from the fact that this approach measures the phenotype of an organism, the biological characteristics of an organism that result from the interaction of its genetic make-up with the environment. When an organism becomes diseased or stressed, thus triggering specific molecular changes, the phenotype becomes altered. This change can then, in principle, be measured using metabolomics.
Current applications in human disease diagnosis
A person’s health can be assessed quickly and comprehensively.
For many years doctors have been measuring specific metabolites in a patient’s blood or urine to diagnose particular diseases. Perhaps the most familiar is the measurement of glucose to diagnose diabetes. Metabolomics is opening up new horizons as hundreds of metabolites can be measured rapidly and simultaneously, providing a much more comprehensive assessment of a patient’s health status. Recently, notable applications of metabolomics in the study of human diseases have begun to emerge:
It helps diagnose heart disease and some neurological conditions.
Detection of the presence and severity of coronary heart disease using NMR-based metabolomics.1 This noninvasive approach identified the disease from human serum samples and in the future could reduce the use of angiography, which is highly invasive.
Prediction of the clinical outcome of a sudden hemorrhage of a blood vessel over the surface of the brain (termed subarachnoid hemorrhage), by means of metabolomics analysis of cerebral spinal fluid.2
Classification of patients with progressive neurological diseases (e.g., amyotrophic lateral sclerosis, in which loss of nerve cells produces muscle paralysis) into clinically relevant groups on the basis of metabolite profiles in serum samples.3
Metabolomics in the environmental sciences
Researchers have been developing and applying these methods to study the effects of both diseases and chemicals on wildlife species, or “environmental organisms.” This is a particularly important area of science for several reasons, ranging from concern over the health of the environment to maximizing profits for the aquaculture industry. Environmental metabolomics may prove of major benefit in a variety of ways:
Certain species are used to monitor environmental health.
Environmental monitoring using so-called “sentinel species” of vertebrate and invertebrate animals. Many organizations, typically government related, monitor the prevalence of diseases in certain species of wildlife as indicators of the health of the environment. For example, within the United Kingdom the National Marine Monitoring Program collects several fish species to assess the effects of disease, pollutants, and other stressors such as climate change on fish stocks and biodiversity in the aquatic environment.
Chemical risk assessment of pharmaceuticals, pesticides, and other household and industrial chemicals. Prior to the use of any new chemicals in society, the company that has developed and manufactured the chemical must assess the risk posed to wildlife and the environment. Only if a new chemical poses minimal harm can it be licensed and sold.
Metabolomics can ensure healthy animal stocks.
Maintenance of healthy stocks of animals in the aquaculture industry, including fish and invertebrates. As with any type of intensive farming, rearing large numbers of animals in close proximity can drastically increase the occurrence and spread of diseases. Maintaining healthy animals is important for both animal welfare and productivity.
Identification of cancer in marine flatfish
Studies identified liver cancer in fish.
Metabolomics and proteomics, the study of thousands of proteins simultaneously, have been used to study liver cancer in a marine flatfish species called dab (Limanda limanda).4 Scientists had noted high levels of tumours in up to 14 percent of the fish collected from the open sea and estuaries around the United Kingdom. It was hypothesised that metabolomics and proteomics could identify differences between healthy and diseased dab livers, and that these differences, or biomarkers, could be used to rapidly diagnose liver cancer in the future.
Initial studies using mass spectrometry did indeed find molecular differences between healthy and diseased livers, although the exact metabolites remain unidentified. The goal of the investigation is to identify the specific causes within the environment that may be responsible for the disease. Potential causes include chemical pollutants that are ingested by the bottom-feeding dab or biological factors such as bacteria or viruses.
Chemical risk assessment in fish, mammals, and earthworms
Many chemicals in the environment can be monitored simultaneously.
A number of research groups have been developing and using metabolomics to study the effects of chemicals on organisms in the environment. In addition to the work on aquatic organisms, several studies on terrestrial invertebrates have been conducted, and a limited number of studies on terrestrial mammals have been reported. The advantage of metabolomics over traditional approaches for assessing the effects of chemical toxicity is that earlier methods tend to measure only a small number of responses. With metabolomics, hundreds of metabolites can be monitored simultaneously, providing a much more comprehensive snapshot of the effects that a particular chemical has on a living organism.
It gives a snapshot of what a particular chemical does to an organism.
Studies were conducted using Japanese medaka (Oryzias latipes), a species that is widely used in toxicity testing, to investigate the effects of trichloroethylene, an environmental pollutant, and the pesticide dinoseb on the development of fish embryos.5,6
Other metabolomics studies have identified biomarker patterns in earthworms (Eisenia veneta) following exposure to pollutants such as a nitrophenol7 and fluorinated anilines.8
The effects of arsenic, a common environmental contaminant, on kidney metabolism in the bank vole (Clethrionomys glareolus) have also been investigated using NMR-based metabolomics.9
A bacterial infection has been decimating abalone populations.
Monitoring withering syndrome in California red abalone
Red abalone (Haliotis rufescens), an important shellfish species that lives along the Pacific Coast of the United States, is susceptible to a disease called withering syndrome. This fatal disease is caused by a bacterial infection and is known to have decimated more than 90 percent of the related black abalone (Haliotis cracherodii) population in southern California.
Abalone aquaculture is economically important in the US.
The potential impact of withering disease on the aquaculture industry prompted the use of metabolomics to identify and measure multiple biomarkers associated with the disease. Using NMR-based metabolomics, characteristic fingerprints of metabolites were detected in the foot muscle, digestive gland, and hemolymph (blood) in diseased abalone that were different from those in healthy animals.10
Metabolomics provides a biomarker indicating the health of abalone.
Building upon this research, scientists have since investigated the influence of food availability, temperature, and bacterial infection on the health status of the red abalone.11 They have shown that withering syndrome depends on bacterial infection, and that metabolomics correlate well with the more painstaking inspection of the tissue under a microscope.
Furthermore, scientists confirmed that a particular ratio of two metabolites, glucose and homarine, in foot muscle serves as a biomarker for distinguishing diseased animals from both healthy and starved abalone.
Metabolomics have also been used to determine whether treatment with an antibiotic, oxytetracycline, can reverse the effects of withering syndrome. The results from this study are still pending (for further information, check the websites listed at the end of this article).
Future developments in environmental metabolomics
The goal is to diagnose health and identify factors that cause disease.
Although much progress has been made in environmental metabolomics in the past few years, researchers have only scratched the surface in terms of potential applications. This is partly because this approach is still technically complicated, limiting its widespread introduction into environmental laboratories. Indeed, considerable work still remains in developing the chemical and computational technologies that underpin this science. As the technology advances, we will better realize and exploit the advantages of metabolomics for studying disease and toxicity in wildlife. The point is to be able to diagnose the health of organisms using metabolomics analyses of minute blood samples, and then to relate these measurements on individuals to the overall health of the environment, particularly the impacts of pollution, climate change, and other manmade stressors.
The inside of a Californian red abalone shell, Haliotis rufescens (compare size to the coin in photo). The shellfish is susceptible to a disease called withering syndrome. Source: Wikimedia Commons.
Introduction to metabolomics
It’s the study of small naturally occurring molecules.
Metabolomics is the study of all the naturally occurring small molecules, called metabolites, in biological samples such as cells, biofluids, or tissues. These small molecules are the products of metabolism and include, for example, sugars (or carbohydrates), fats (or lipids), and amino acids. The collection of all the metabolites within a cell is called the metabolome. Scientists have started to characterize the metabolome in a quest to better understand and diagnose disease.
It requires input from various disciplines, such as chemistry.
Metabolomics incorporates the use of bioinformatics, the application of computer and statistical techniques to the understanding and management of biological information, to search for unique patterns of metabolites that are indicative of a particular disease.
Metabolomics is a multidisciplinary approach involving biologists, computer scientists, and analytical chemists. The tools used to measure the metabolites are more commonly associated with chemistry laboratories and include nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry.
It measures the interactions of genes with the environment.
The advantage of metabolomics for disease diagnosis, whether in humans or wildlife, stems from the fact that this approach measures the phenotype of an organism, the biological characteristics of an organism that result from the interaction of its genetic make-up with the environment. When an organism becomes diseased or stressed, thus triggering specific molecular changes, the phenotype becomes altered. This change can then, in principle, be measured using metabolomics.
Current applications in human disease diagnosis
A person’s health can be assessed quickly and comprehensively.
For many years doctors have been measuring specific metabolites in a patient’s blood or urine to diagnose particular diseases. Perhaps the most familiar is the measurement of glucose to diagnose diabetes. Metabolomics is opening up new horizons as hundreds of metabolites can be measured rapidly and simultaneously, providing a much more comprehensive assessment of a patient’s health status. Recently, notable applications of metabolomics in the study of human diseases have begun to emerge:
It helps diagnose heart disease and some neurological conditions.
Detection of the presence and severity of coronary heart disease using NMR-based metabolomics.1 This noninvasive approach identified the disease from human serum samples and in the future could reduce the use of angiography, which is highly invasive.
Prediction of the clinical outcome of a sudden hemorrhage of a blood vessel over the surface of the brain (termed subarachnoid hemorrhage), by means of metabolomics analysis of cerebral spinal fluid.2
Classification of patients with progressive neurological diseases (e.g., amyotrophic lateral sclerosis, in which loss of nerve cells produces muscle paralysis) into clinically relevant groups on the basis of metabolite profiles in serum samples.3
Metabolomics in the environmental sciences
Researchers have been developing and applying these methods to study the effects of both diseases and chemicals on wildlife species, or “environmental organisms.” This is a particularly important area of science for several reasons, ranging from concern over the health of the environment to maximizing profits for the aquaculture industry. Environmental metabolomics may prove of major benefit in a variety of ways:
Certain species are used to monitor environmental health.
Environmental monitoring using so-called “sentinel species” of vertebrate and invertebrate animals. Many organizations, typically government related, monitor the prevalence of diseases in certain species of wildlife as indicators of the health of the environment. For example, within the United Kingdom the National Marine Monitoring Program collects several fish species to assess the effects of disease, pollutants, and other stressors such as climate change on fish stocks and biodiversity in the aquatic environment.
Chemical risk assessment of pharmaceuticals, pesticides, and other household and industrial chemicals. Prior to the use of any new chemicals in society, the company that has developed and manufactured the chemical must assess the risk posed to wildlife and the environment. Only if a new chemical poses minimal harm can it be licensed and sold.
Metabolomics can ensure healthy animal stocks.
Maintenance of healthy stocks of animals in the aquaculture industry, including fish and invertebrates. As with any type of intensive farming, rearing large numbers of animals in close proximity can drastically increase the occurrence and spread of diseases. Maintaining healthy animals is important for both animal welfare and productivity.
Identification of cancer in marine flatfish
Studies identified liver cancer in fish.
Metabolomics and proteomics, the study of thousands of proteins simultaneously, have been used to study liver cancer in a marine flatfish species called dab (Limanda limanda).4 Scientists had noted high levels of tumours in up to 14 percent of the fish collected from the open sea and estuaries around the United Kingdom. It was hypothesised that metabolomics and proteomics could identify differences between healthy and diseased dab livers, and that these differences, or biomarkers, could be used to rapidly diagnose liver cancer in the future.
Initial studies using mass spectrometry did indeed find molecular differences between healthy and diseased livers, although the exact metabolites remain unidentified. The goal of the investigation is to identify the specific causes within the environment that may be responsible for the disease. Potential causes include chemical pollutants that are ingested by the bottom-feeding dab or biological factors such as bacteria or viruses.
Chemical risk assessment in fish, mammals, and earthworms
Many chemicals in the environment can be monitored simultaneously.
A number of research groups have been developing and using metabolomics to study the effects of chemicals on organisms in the environment. In addition to the work on aquatic organisms, several studies on terrestrial invertebrates have been conducted, and a limited number of studies on terrestrial mammals have been reported. The advantage of metabolomics over traditional approaches for assessing the effects of chemical toxicity is that earlier methods tend to measure only a small number of responses. With metabolomics, hundreds of metabolites can be monitored simultaneously, providing a much more comprehensive snapshot of the effects that a particular chemical has on a living organism.
It gives a snapshot of what a particular chemical does to an organism.
Studies were conducted using Japanese medaka (Oryzias latipes), a species that is widely used in toxicity testing, to investigate the effects of trichloroethylene, an environmental pollutant, and the pesticide dinoseb on the development of fish embryos.5,6
Other metabolomics studies have identified biomarker patterns in earthworms (Eisenia veneta) following exposure to pollutants such as a nitrophenol7 and fluorinated anilines.8
The effects of arsenic, a common environmental contaminant, on kidney metabolism in the bank vole (Clethrionomys glareolus) have also been investigated using NMR-based metabolomics.9
A bacterial infection has been decimating abalone populations.
Monitoring withering syndrome in California red abalone
Red abalone (Haliotis rufescens), an important shellfish species that lives along the Pacific Coast of the United States, is susceptible to a disease called withering syndrome. This fatal disease is caused by a bacterial infection and is known to have decimated more than 90 percent of the related black abalone (Haliotis cracherodii) population in southern California.
Abalone aquaculture is economically important in the US.
The potential impact of withering disease on the aquaculture industry prompted the use of metabolomics to identify and measure multiple biomarkers associated with the disease. Using NMR-based metabolomics, characteristic fingerprints of metabolites were detected in the foot muscle, digestive gland, and hemolymph (blood) in diseased abalone that were different from those in healthy animals.10
Metabolomics provides a biomarker indicating the health of abalone.
Building upon this research, scientists have since investigated the influence of food availability, temperature, and bacterial infection on the health status of the red abalone.11 They have shown that withering syndrome depends on bacterial infection, and that metabolomics correlate well with the more painstaking inspection of the tissue under a microscope.
Furthermore, scientists confirmed that a particular ratio of two metabolites, glucose and homarine, in foot muscle serves as a biomarker for distinguishing diseased animals from both healthy and starved abalone.
Metabolomics have also been used to determine whether treatment with an antibiotic, oxytetracycline, can reverse the effects of withering syndrome. The results from this study are still pending (for further information, check the websites listed at the end of this article).
Future developments in environmental metabolomics
The goal is to diagnose health and identify factors that cause disease.
Although much progress has been made in environmental metabolomics in the past few years, researchers have only scratched the surface in terms of potential applications. This is partly because this approach is still technically complicated, limiting its widespread introduction into environmental laboratories. Indeed, considerable work still remains in developing the chemical and computational technologies that underpin this science. As the technology advances, we will better realize and exploit the advantages of metabolomics for studying disease and toxicity in wildlife. The point is to be able to diagnose the health of organisms using metabolomics analyses of minute blood samples, and then to relate these measurements on individuals to the overall health of the environment, particularly the impacts of pollution, climate change, and other manmade stressors.
Transgenic Animals: Their Benefits To Human Welfare
Nowadays, breakthroughs in molecular biology are happening at an unprecedented rate. One of them is the ability to engineer transgenic animals, i.e., animals that carry genes from other species. The technology has already produced transgenic animals such as mice, rats, rabbits, pigs, sheep, and cows. Although there are many ethical issues surrounding transgenesis, this article focuses on the basics of the technology and its applications in agriculture, medicine, and industry.
What is a transgenic animal?
There are various definitions for the term transgenic animal. The Federation of European Laboratory Animal Associations defines the term as an animal in which there has been a deliberate modification of its genome, the genetic makeup of an organism responsible for inherited characteristics.5
A transgenic animal is one whose genome has been changed to carry genes from other species.
The nucleus of all cells in every living organism contains genes made up of DNA. These genes store information that regulates how our bodies form and function. Genes can be altered artificially, so that some characteristics of an animal are changed. For example, an embryo can have an extra, functioning gene from another source artificially introduced into it, or a gene introduced which can knock out the functioning of another particular gene in the embryo. Animals that have their DNA manipulated in this way are knows as transgenic animals.20
The majority of transgenic animals produced so far are mice, the animal that pioneered the technology. The first successful transgenic animal was a mouse.6 A few years later, it was followed by rabbits, pigs, sheep, and cattle.8,14,15,16
Why are these animals being produced? The two most common reasons are:
Transgenic animals are useful as disease models and producers of substances for human welfare.
Some transgenic animals are produced for specific economic traits. For example, transgenic cattle were created to produce milk containing particular human proteins, which may help in the treatment of human emphysema.
Other transgenic animals are produced as disease models (animals genetically manipulated to exhibit disease symptoms so that effective treatment can be studied). For example, Harvard scientists made a major scientific breakthrough when they received a U.S. patent (the company DuPont holds exclusive rights to its use) for a genetically engineered mouse, called OncoMouse® or the Harvard mouse, carrying a gene that promotes the development of various human cancers.22
How are transgenic animals produced?
Since the discovery of the molecular structure of DNA by Watson and Crick in 1953, molecular biology research has gained momentum. Molecular biology technology combines techniques and expertise from biochemistry, genetics, cell biology, developmental biology, and microbiology.2
Scientists can now produce transgenic animals because, since Watson and Crick’s discovery, there have been breakthroughs in:
The insertion of a foreign gene (transgene) into an animal is successful only if the gene is inherited by offspring.
The success rate for transgenesis is very low and successful transgenic animals need to be cloned or mated.
recombinant DNA (artificially-produced DNA)
genetic cloning
analysis of gene expression (the process by which a gene gives rise to a protein)
genomic mapping
The underlying principle in the production of transgenic animals is the introduction of a foreign gene or genes into an animal (the inserted genes are called transgenes). The foreign genes “must be transmitted through the germ line, so that every cell, including germ cells, of the animal contain the same modified genetic material.”26 (Germ cells are cells whose function is to transmit genes to an organism’s offspring.)
To date, there are three basic methods of producing transgenic animals:
DNA microinjection
Retrovirus-mediated gene transfer
Embryonic stem cell-mediated gene transfer
Gene transfer by microinjection is the predominant method used to produce transgenic farm animals. Since the insertion of DNA results in a random process, transgenic animals are mated to ensure that their offspring acquire the desired transgene. However, the success rate of producing transgenic animals individually by these methods is very low and it may be more efficient to use cloning techniques to increase their numbers. For example, gene transfer studies revealed that only 0.6% of transgenic pigs were born with a desired gene after 7,000 eggs were injected with a specific transgene.27
DNA microinjection is the predominant transgenesis method.
1. DNA Microinjection
The mouse was the first animal to undergo successful gene transfer using DNA microinjection.6 This method involves:
transfer of a desired gene construct (of a single gene or a combination of genes that are recombined and then cloned) from another member of the same species or from a different species into the pronucleus of a reproductive cell19
the manipulated cell, which first must be cultured in vitro (in a lab, not in a live animal) to develop to a specific embryonic phase, is then transferred to the recipient female
2. Retrovirus-Mediated Gene Transfer
The second method produces chimeras, altered animals with mixed DNA.
A retrovirus is a virus that carries its genetic material in the form of RNA rather than DNA. This method involves:26
retroviruses used as vectors to transfer genetic material into the host cell, resulting in a chimera, an organism consisting of tissues or parts of diverse genetic constitution
chimeras are inbred for as many as 20 generations until homozygous (carrying the desired transgene in every cell) transgenic offspring are born
The method was successfully used in 1974 when a simian virus was inserted into mice embryos, resulting in mice carrying this DNA.10
3. Embryonic Stem Cell-Mediated Gene Transfer
The presence of transgenes can be tested at the embryonic state in this third method.
This method involves:7,19,26
isolation of totipotent stem cells (stem cells that can develop into any type of specialized cell) from embryos
the desired gene is inserted into these cells
cells containing the desired DNA are incorporated into the host’s embryo, resulting in a chimeric animal
Unlike the other two methods, which require live transgenic offspring to test for the presence of the desired transgene, this method allows testing for transgenes at the cell stage.
How do transgenic animals contribute to human welfare?
The benefits of these animals to human welfare can be grouped into areas:
Agriculture
Medicine
Industry
The examples below are not intended to be complete but only to provide a sampling of the benefits.
1. Agricultural Applications
Transgenesis will allow larger herds with specific traits.
a) breeding Farmers have always used selective breeding to produce animals that exhibit desired traits (e.g., increased milk production, high growth rate).11,15,17 Traditional breeding is a time-consuming, difficult task. When technology using molecular biology was developed, it became possible to develop traits in animals in a shorter time and with more precision. In addition, it offers the farmer an easy way to increase yields.
Scientists can improve the size of livestock genetically.
b) quality Transgenic cows exist that produce more milk or milk with less lactose or cholesterol12, pigs and cattle that have more meat on them8,17, and sheep that grow more wool18. In the past, farmers used growth hormones to spur the development of animals but this technique was problematic, especially since residue of the hormones remained in the animal product.
Disease-resistant livestock is not a reality just yet.
c) disease resistance Scientists are attempting to produce disease-resistant animals, such as influenza-resistant pigs, but a very limited number of genes are currently known to be responsible for resistance to diseases in farm animals.19
2. Medical Applications
Transplant organs may soon come from transgenic animals.
a) xenotransplantation Patients die every year for lack of a replacement heart, liver, or kidney. For example, about 5,000 organs are needed each year in the United Kingdom alone.25 Transgenic pigs may provide the transplant organs needed to alleviate the shortfall.9 Currently, xenotransplantation is hampered by a pig protein that can cause donor rejection but research is underway to remove the pig protein and replace it with a human protein.25
Milk-producing transgenic animals are especially useful for medicines.
b) nutritional supplements and pharmaceuticals Products such as insulin, growth hormone, and blood anti-clotting factors may soon be or have already been obtained from the milk of transgenic cows, sheep, or goats.3,12,23 Research is also underway to manufacture milk through transgenesis for treatment of debilitating diseases such as phenylketonuria (PKU), hereditary emphysema, and cystic fibrosis.3,13,23,25
In 1997, the first transgenic cow, Rosie, produced human protein-enriched milk at 2.4 grams per litre. This transgenic milk is a more nutritionally balanced product than natural bovine milk and could be given to babies or the elderly with special nutritional or digestive needs.4,21,23 Rosie’s milk contains the human gene alpha-lactalbumin.
A transgenic cow exists that produces a substance to help human red cells grow.
c) human gene therapy Human gene therapy involves adding a normal copy of a gene (transgene) to the genome of a person carrying defective copies of the gene. The potential for treatments for the 5,000 named genetic diseases is huge and transgenic animals could play a role. For example, the A. I. Virtanen Institute in Finland produced a calf with a gene that makes the substance that promotes the growth of red cells in humans.24
Uses in industry include material fabrication and safety tests of chemicals.
3. Industrial Applications
In 2001, two scientists at Nexia Biotechnologies in Canada spliced spider genes into the cells of lactating goats. The goats began to manufacture silk along with their milk and secrete tiny silk strands from their body by the bucketful. By extracting polymer strands from the milk and weaving them into thread, the scientists can create a light, tough, flexible material that could be used in such applications as military uniforms, medical microsutures, and tennis racket strings.1
Toxicity-sensitive transgenic animals have been produced for chemical safety testing. Microorganisms have been engineered to produce a wide variety of proteins, which in turn can produce enzymes that can speed up industrial chemical reactions.20
What are the ethical concerns surrounding transgenesis?
This article focuses on the benefits of the technology; however, thoughtful ethical decision-making cannot be ignored by the biotechnology industry, scientists, policy-makers, and the public. These ethical issues, better served in their own article, include questions such as:
Ethical concerns must be addressed as the technology grows, including the issue of lab animal welfare.
Should there be universal protocols for transgenesis?
Should such protocols demand that only the most promising research be permitted?
Is human welfare the only consideration? What about the welfare of other life forms?
Should scientists focus on in vitro (cultured in a lab) transgenic methods rather than, or before, using live animals to alleviate animal suffering?
Will transgenic animals radically change the direction of evolution, which may result in drastic consequences for nature and humans alike?
Should patents be allowed on transgenic animals, which may hamper the free exchange of scientific research?
Conclusion: Transgenic technology holds great potential in agriculture, medicine, and industry.
Conclusion
Interestingly, the creation of transgenic animals has resulted in a shift in the use of laboratory animals — from the use of higher-order species such as dogs to lower-order species such as mice — and has decreased the number of animals used in such experimentation,26 especially in the development of disease models. This is certainly a good turn of events since transgenic technology holds great potential in many fields, including agriculture, medicine, and industry.
Acknowledgements: The updated information in this article is based on the author’s graduate student paper written for the course, Introduction to Science Philosophy (PPS 702), in 2001. The author is deeply grateful to professors Rudy C. Tarumingkeng, Ph.D. and Zahrial Coto, Ph.D. for their help.
What is a transgenic animal?
There are various definitions for the term transgenic animal. The Federation of European Laboratory Animal Associations defines the term as an animal in which there has been a deliberate modification of its genome, the genetic makeup of an organism responsible for inherited characteristics.5
A transgenic animal is one whose genome has been changed to carry genes from other species.
The nucleus of all cells in every living organism contains genes made up of DNA. These genes store information that regulates how our bodies form and function. Genes can be altered artificially, so that some characteristics of an animal are changed. For example, an embryo can have an extra, functioning gene from another source artificially introduced into it, or a gene introduced which can knock out the functioning of another particular gene in the embryo. Animals that have their DNA manipulated in this way are knows as transgenic animals.20
The majority of transgenic animals produced so far are mice, the animal that pioneered the technology. The first successful transgenic animal was a mouse.6 A few years later, it was followed by rabbits, pigs, sheep, and cattle.8,14,15,16
Why are these animals being produced? The two most common reasons are:
Transgenic animals are useful as disease models and producers of substances for human welfare.
Some transgenic animals are produced for specific economic traits. For example, transgenic cattle were created to produce milk containing particular human proteins, which may help in the treatment of human emphysema.
Other transgenic animals are produced as disease models (animals genetically manipulated to exhibit disease symptoms so that effective treatment can be studied). For example, Harvard scientists made a major scientific breakthrough when they received a U.S. patent (the company DuPont holds exclusive rights to its use) for a genetically engineered mouse, called OncoMouse® or the Harvard mouse, carrying a gene that promotes the development of various human cancers.22
How are transgenic animals produced?
Since the discovery of the molecular structure of DNA by Watson and Crick in 1953, molecular biology research has gained momentum. Molecular biology technology combines techniques and expertise from biochemistry, genetics, cell biology, developmental biology, and microbiology.2
Scientists can now produce transgenic animals because, since Watson and Crick’s discovery, there have been breakthroughs in:
The insertion of a foreign gene (transgene) into an animal is successful only if the gene is inherited by offspring.
The success rate for transgenesis is very low and successful transgenic animals need to be cloned or mated.
recombinant DNA (artificially-produced DNA)
genetic cloning
analysis of gene expression (the process by which a gene gives rise to a protein)
genomic mapping
The underlying principle in the production of transgenic animals is the introduction of a foreign gene or genes into an animal (the inserted genes are called transgenes). The foreign genes “must be transmitted through the germ line, so that every cell, including germ cells, of the animal contain the same modified genetic material.”26 (Germ cells are cells whose function is to transmit genes to an organism’s offspring.)
To date, there are three basic methods of producing transgenic animals:
DNA microinjection
Retrovirus-mediated gene transfer
Embryonic stem cell-mediated gene transfer
Gene transfer by microinjection is the predominant method used to produce transgenic farm animals. Since the insertion of DNA results in a random process, transgenic animals are mated to ensure that their offspring acquire the desired transgene. However, the success rate of producing transgenic animals individually by these methods is very low and it may be more efficient to use cloning techniques to increase their numbers. For example, gene transfer studies revealed that only 0.6% of transgenic pigs were born with a desired gene after 7,000 eggs were injected with a specific transgene.27
DNA microinjection is the predominant transgenesis method.
1. DNA Microinjection
The mouse was the first animal to undergo successful gene transfer using DNA microinjection.6 This method involves:
transfer of a desired gene construct (of a single gene or a combination of genes that are recombined and then cloned) from another member of the same species or from a different species into the pronucleus of a reproductive cell19
the manipulated cell, which first must be cultured in vitro (in a lab, not in a live animal) to develop to a specific embryonic phase, is then transferred to the recipient female
2. Retrovirus-Mediated Gene Transfer
The second method produces chimeras, altered animals with mixed DNA.
A retrovirus is a virus that carries its genetic material in the form of RNA rather than DNA. This method involves:26
retroviruses used as vectors to transfer genetic material into the host cell, resulting in a chimera, an organism consisting of tissues or parts of diverse genetic constitution
chimeras are inbred for as many as 20 generations until homozygous (carrying the desired transgene in every cell) transgenic offspring are born
The method was successfully used in 1974 when a simian virus was inserted into mice embryos, resulting in mice carrying this DNA.10
3. Embryonic Stem Cell-Mediated Gene Transfer
The presence of transgenes can be tested at the embryonic state in this third method.
This method involves:7,19,26
isolation of totipotent stem cells (stem cells that can develop into any type of specialized cell) from embryos
the desired gene is inserted into these cells
cells containing the desired DNA are incorporated into the host’s embryo, resulting in a chimeric animal
Unlike the other two methods, which require live transgenic offspring to test for the presence of the desired transgene, this method allows testing for transgenes at the cell stage.
How do transgenic animals contribute to human welfare?
The benefits of these animals to human welfare can be grouped into areas:
Agriculture
Medicine
Industry
The examples below are not intended to be complete but only to provide a sampling of the benefits.
1. Agricultural Applications
Transgenesis will allow larger herds with specific traits.
a) breeding Farmers have always used selective breeding to produce animals that exhibit desired traits (e.g., increased milk production, high growth rate).11,15,17 Traditional breeding is a time-consuming, difficult task. When technology using molecular biology was developed, it became possible to develop traits in animals in a shorter time and with more precision. In addition, it offers the farmer an easy way to increase yields.
Scientists can improve the size of livestock genetically.
b) quality Transgenic cows exist that produce more milk or milk with less lactose or cholesterol12, pigs and cattle that have more meat on them8,17, and sheep that grow more wool18. In the past, farmers used growth hormones to spur the development of animals but this technique was problematic, especially since residue of the hormones remained in the animal product.
Disease-resistant livestock is not a reality just yet.
c) disease resistance Scientists are attempting to produce disease-resistant animals, such as influenza-resistant pigs, but a very limited number of genes are currently known to be responsible for resistance to diseases in farm animals.19
2. Medical Applications
Transplant organs may soon come from transgenic animals.
a) xenotransplantation Patients die every year for lack of a replacement heart, liver, or kidney. For example, about 5,000 organs are needed each year in the United Kingdom alone.25 Transgenic pigs may provide the transplant organs needed to alleviate the shortfall.9 Currently, xenotransplantation is hampered by a pig protein that can cause donor rejection but research is underway to remove the pig protein and replace it with a human protein.25
Milk-producing transgenic animals are especially useful for medicines.
b) nutritional supplements and pharmaceuticals Products such as insulin, growth hormone, and blood anti-clotting factors may soon be or have already been obtained from the milk of transgenic cows, sheep, or goats.3,12,23 Research is also underway to manufacture milk through transgenesis for treatment of debilitating diseases such as phenylketonuria (PKU), hereditary emphysema, and cystic fibrosis.3,13,23,25
In 1997, the first transgenic cow, Rosie, produced human protein-enriched milk at 2.4 grams per litre. This transgenic milk is a more nutritionally balanced product than natural bovine milk and could be given to babies or the elderly with special nutritional or digestive needs.4,21,23 Rosie’s milk contains the human gene alpha-lactalbumin.
A transgenic cow exists that produces a substance to help human red cells grow.
c) human gene therapy Human gene therapy involves adding a normal copy of a gene (transgene) to the genome of a person carrying defective copies of the gene. The potential for treatments for the 5,000 named genetic diseases is huge and transgenic animals could play a role. For example, the A. I. Virtanen Institute in Finland produced a calf with a gene that makes the substance that promotes the growth of red cells in humans.24
Uses in industry include material fabrication and safety tests of chemicals.
3. Industrial Applications
In 2001, two scientists at Nexia Biotechnologies in Canada spliced spider genes into the cells of lactating goats. The goats began to manufacture silk along with their milk and secrete tiny silk strands from their body by the bucketful. By extracting polymer strands from the milk and weaving them into thread, the scientists can create a light, tough, flexible material that could be used in such applications as military uniforms, medical microsutures, and tennis racket strings.1
Toxicity-sensitive transgenic animals have been produced for chemical safety testing. Microorganisms have been engineered to produce a wide variety of proteins, which in turn can produce enzymes that can speed up industrial chemical reactions.20
What are the ethical concerns surrounding transgenesis?
This article focuses on the benefits of the technology; however, thoughtful ethical decision-making cannot be ignored by the biotechnology industry, scientists, policy-makers, and the public. These ethical issues, better served in their own article, include questions such as:
Ethical concerns must be addressed as the technology grows, including the issue of lab animal welfare.
Should there be universal protocols for transgenesis?
Should such protocols demand that only the most promising research be permitted?
Is human welfare the only consideration? What about the welfare of other life forms?
Should scientists focus on in vitro (cultured in a lab) transgenic methods rather than, or before, using live animals to alleviate animal suffering?
Will transgenic animals radically change the direction of evolution, which may result in drastic consequences for nature and humans alike?
Should patents be allowed on transgenic animals, which may hamper the free exchange of scientific research?
Conclusion: Transgenic technology holds great potential in agriculture, medicine, and industry.
Conclusion
Interestingly, the creation of transgenic animals has resulted in a shift in the use of laboratory animals — from the use of higher-order species such as dogs to lower-order species such as mice — and has decreased the number of animals used in such experimentation,26 especially in the development of disease models. This is certainly a good turn of events since transgenic technology holds great potential in many fields, including agriculture, medicine, and industry.
Acknowledgements: The updated information in this article is based on the author’s graduate student paper written for the course, Introduction to Science Philosophy (PPS 702), in 2001. The author is deeply grateful to professors Rudy C. Tarumingkeng, Ph.D. and Zahrial Coto, Ph.D. for their help.
Primer on Ethics and Crossing Species Boundaries
Ancient Greek mythology is replete with references to part-human animals. There is the monstrous half-human, half-bull Minotaur; the Gorgon sisters (one of whom is Medusa) with hair of writhing snakes; the Sirens who are sweet singing sea nymphs each with the head of a woman and the body of a bird; and, not to be forgotten, there is the infamous Sphinx with the head and breasts of a woman, the body of a lion, and the wings of a bird. Part-human creatures are also a staple of modern science fiction, as in H. G. Wells’ The Island of Dr Moreau,1 where animals are vivisected into part-human creatures, or George Langelaan’s The Fly, in which a scientist emerges from his disintegrator-reintegrator machine with the head and arms of a fly.2
But part-human animals are not only science fiction—they are also science fact. While not as monstrous as the creatures of lore, part-human laboratory animals raise some important ethical and societal issues.
What does it mean to cross species boundaries?
First, from a biological perspective, it is surprisingly difficult to answer the question What does it mean to cross species boundaries? This is true not only because of the number of species concepts (according to some, as many as 22),3 but also because species boundaries are not fixed.
How do we define a species?
Is the boundary between species real or artificial?
Species concepts: One classic definition of species is the biological species concept. This definition emphasizes the importance of reproductive isolation or lack of genetic exchange that separates species.4 By this account, crossing species boundaries would involve the transfer of genetic materials between populations of organisms that do not interbreed. In cases where such interbreeding can be achieved artificially, as in the laboratory, the raison d’etre of the biological species concept is undermined. Other accounts of species may be brought to bear in place of the biological species concept, but the consensus among biologists is that no single species concept will be sufficient for all situations.
Species boundaries: One of the consequences of our evolutionary past is that genes, gene regulatory networks, epigenetic developmental processes, and features of the biophysical environment are widely shared by different kinds of creatures. The idea of fixed or rigid breaks between species plays no role whatsoever in contemporary biology. Indeed, the fluidity of species boundaries has been revealed through the techniques of comparative genomics, warning against the interpretation of species as unique types.
Crossing the boundary implies combining genetic or cellular material from two organisms.
Given the difficulty in defining species once and for all, and also the flexibility of species boundaries,5 what does it mean to cross species boundaries?
When we refer to species and the crossing of species boundaries,5 we do so based on the following simple idea: Every individual human contains a human genome. In all likelihood, this genome will not be representative of other human genomes and will contain a lot of DNA that is contained in many other kinds of organisms, thanks to our evolution from a common ancestor. The same will be true with nonhuman organisms, such as a rose or a rat or a Rhesus macaque. As such, when we refer to crossing species boundaries, we refer to the combination of genetic or cellular material from two organisms that would generally be understood, in lay terms, as belonging to different species: a human as understood by most lay people, a Rhesus macaque as understood by most lay people, and so on.6
Parents of hybrids are different species.
Genetically modified food is a transgenic product.
Chimeras have cells from two genetically distinct organisms.
Hybrids, transgenics, and chimeras
A geep: a sheep-goat chimera produced by combining the embryos of a goat and a sheep. Not to be confused with a sheep-goat hybrid, which can result when a goat mates with a sheep. Photo: Dr. Gary B. Anderson of Univ. of California, Davis.
There are many types of interspecies organisms including hybrids, transgenics, and chimeras, each of which is created through different sorts of processes. Hybrids are created through breeding. Transgenics are produced through genetic manipulation and modification. Chimeras are the result of cell or tissue transplants.
Hybrids are created by breeding across species. Hybrids are generally the result of combining an egg from one species with sperm from another to form a single embryo. Hybrids contain recombined genetic material throughout their genome and throughout all the tissues in their body.
Transgenics are the result of gene transfer. Typically, transgenics contain transferred or manipulated genes in addition to the host nuclear and mitochondrial DNA. One exception may be a transgenic embryo comprised of the entire complement of nuclear DNA from one organism fused with an enucleated egg cell from another.
Chimeras comprise a mixture of cells from two or more genetically distinct organisms of the same or different species. They are mosaics at the cellular level; individual cells are derived from either the host or the donor but not both.7
Note that chimeras and transgenics need not cross species boundaries, whereas hybrids are always interspecific.
Multiple applications
Crossing species boundaries happens all the time in nature and in agricultural settings, and it has a long history in developmental biology and immunology laboratories. Consider just a few examples:
Nature and breeding programs cross boundaries.
lateral gene transfer between bacteria, whereby genetic material is transmitted horizontally from one organism to another8
the crossing of strains of wheat; the insertion of genes from a plant (or an animal) into a plant to improve crop yield and robustness9
the mating of a horse with a donkey to create a mule; the fusion of sheep and goat cells to create a “geep”10
the transplantation of cells and tissues from one species of frog to another, and of neural tissue from quails to chickens, to study the complex processes of development11-13
Gene transfer from animals to humans and vice versa is common.
Crossing species boundaries between human and nonhuman animals is also commonplace:
Animal tissues, cells, and their derivatives are often transferred to humans, whether by using insulin produced from pig or cow pancreases, injecting flu vaccines cultured in fertilized chicken eggs, or transplanting heart valves from pigs into humans.
Human genes and cells are often transferred to animal hosts to create humanized animal models (such as OncoMouse, which develops human cancers14), to grow humanized tissues that can be transplanted back into humans (such as sheep with human livers15), or to test the developmental potential of transplants.16
Stem cell research
Stem cell research and cloning ignited debate.
In the first few years of human stem cell research, most of the ethics discussions centered on the use of human embryos as sources of stem cells. Research to derive human embryonic stem (hES) cells involves removing cells from the inner cell mass of a human blastocyst, which destroys the developing embryo. While this debate continued, further debate on the ethics of cloning to produce children, and cloning for biomedical research, emerged. This debate arose in response to claims about the anticipated benefit of future stem cell therapies using cells from cloned embryos, which would allow patients to receive transplants of cells containing their own DNA.17
The debate has encompassed part-human animals.
While these issues remain ethically contentious, a new debate has recently emerged concerning the ethics of crossing species boundaries to make part-human chimeras. Stem cell scientists and others insist that this cross-species work is important to basic science and a necessary step on the path to regenerative medicine. They maintain that it would be unethical to involve humans in stem cell transplantation research without first having studied the safety and efficacy of the human cells in nonhuman animals.
Ethical controversy
Issues of health and safety, especially given the possibility of zoonosis, or the transfer of a disease from nonhuman animals to humans, have long been front and center in the ethics debate about cross-species work.18 In the last decade or so, with the increase in science options for the crossing of species boundaries, other ethical issues have come to the fore.
Attempts to patent a humanzee failed but caused a stir.
In 1997, Stuart Newman, a developmental biologist sponsored by biotechnology activist Jeremy Rifkin, sought to preclude the creation of a humanzee—a part-human, part-chimpanzee chimera. Together, Newman and Rifkin tried to patent the relevant technology so that they would be able to restrict its use and to promote a vigorous social dialogue about the desirability of such part-human beings.19 They were unsuccessful in obtaining the patent, leaving open the possibility that humanzees may soon walk among us, with or without patent protection. Examples of recent research involving the transplantation of cells and tissues into prenatal nonhuman animals (embryos and fetuses), the transplantation of cells and tissues into nonhuman animal brains, and the transplantation of cells and tissues into the brains of nonhuman primates, serve to make this point:
Part-human animals already exist.
Scientists want to test human cells in other primates.
Scientists at Harvard University have published their research involving the transfer of human neural stem cells into the developing fetal brain of bonnet monkeys.20
Scientists in Israel have reported that human embryonic stem cells transplanted into chick embryos differentiated into neurons.21
Scientists in Nevada have reported on inserting human neural stem cells into fetal sheep to assess their developmental potential.22
Scientists in California have reported on the development of functional neurons in mouse brains, where the neurons were derived from human embryonic stem cells.23
While this research is ongoing, a debate has erupted about the ethics of creating part-human beings in response to proposals from some stem cell scientists to use nonhuman primates as an assay system for testing the developmental potential of human stem cells. The fact that biologists are especially interested in transplanting human neural stem cells into the brains of nonhuman primates24 intensifies the controversy about humanzee-like chimeras.
The ethics of creating part-human beings
Is it natural and moral to develop part-human animals?
The ethical debate has been multivocal, with moral considerations raised from many perspectives, both religious and secular. The central moral concerns with creating part-human beings include worries about the following:
the unnaturalness and intuitive repugnance of certain kinds of creatures, such as part-human combinations25
the threat of intensified moral confusion regarding the creation of novel part-human beings who violate the pragmatically clear moral demarcation line between species upon which current institutions, structures, and social practices are based5
the potential for transferring moral status to nonhuman animals by conferring on them characteristically human cognitive capacities, which may or may not threaten human dignity24,26
the possibility that enhanced animals would deserve to be treated as if they were human subjects but would continue being treated as if they were unenhanced nonhuman animals27
the moral status of nonhuman animals, especially primates, as experimental animals28
Some see the medical benefits of the research.
Others see it as a way to improve humans.
Scientists and others who advocate cross-species work argue that the part-human animals will be useful as disease models, assay systems, or organ sources.16,29 They dismiss the worries about repugnance, deny the potential for moral confusion, and endeavor to sidestep concerns about moral status and potential threats to human dignity. They also rely heavily on current norms for research involving humans to legitimate preclinical cross-species research in nonhuman animals.
Additionally, advocates of transhumanism, the movement to enhance humans using biotechnology, argue that the creation of hybrids, transgenics, and chimeras may be useful in the quest to radically alter humans.30 They see an opportunity to improve upon human nature and to enhance cognitive and physical performance—an idea that is itself morally controversial.31
More debate is needed about the value and ethics of such research.
Toward a constructive public debate
Unfortunately, much of the public debate on the ethics of crossing species boundaries is characterized by sensationalism and political posturing. While some commentators have attempted to explore the moral dimensions of interspecies research in careful and respectful terms, many of the media reports have exaggerated the conflict, providing more heat than light. Even so, attempts at public education and public engagement have tended to reveal the persistence of the moral controversy. This suggests the need for scientists, ethicists, and others to take seriously the ethical concerns that have been raised. The voluntary guidelines for human embryonic stem cell research recently published by the National Academy of Sciences arguably are an attempt to do just this.32 As we have argued elsewhere, however, considerably more debate and discussion is needed about the fundamental underlying values.33,34
But part-human animals are not only science fiction—they are also science fact. While not as monstrous as the creatures of lore, part-human laboratory animals raise some important ethical and societal issues.
What does it mean to cross species boundaries?
First, from a biological perspective, it is surprisingly difficult to answer the question What does it mean to cross species boundaries? This is true not only because of the number of species concepts (according to some, as many as 22),3 but also because species boundaries are not fixed.
How do we define a species?
Is the boundary between species real or artificial?
Species concepts: One classic definition of species is the biological species concept. This definition emphasizes the importance of reproductive isolation or lack of genetic exchange that separates species.4 By this account, crossing species boundaries would involve the transfer of genetic materials between populations of organisms that do not interbreed. In cases where such interbreeding can be achieved artificially, as in the laboratory, the raison d’etre of the biological species concept is undermined. Other accounts of species may be brought to bear in place of the biological species concept, but the consensus among biologists is that no single species concept will be sufficient for all situations.
Species boundaries: One of the consequences of our evolutionary past is that genes, gene regulatory networks, epigenetic developmental processes, and features of the biophysical environment are widely shared by different kinds of creatures. The idea of fixed or rigid breaks between species plays no role whatsoever in contemporary biology. Indeed, the fluidity of species boundaries has been revealed through the techniques of comparative genomics, warning against the interpretation of species as unique types.
Crossing the boundary implies combining genetic or cellular material from two organisms.
Given the difficulty in defining species once and for all, and also the flexibility of species boundaries,5 what does it mean to cross species boundaries?
When we refer to species and the crossing of species boundaries,5 we do so based on the following simple idea: Every individual human contains a human genome. In all likelihood, this genome will not be representative of other human genomes and will contain a lot of DNA that is contained in many other kinds of organisms, thanks to our evolution from a common ancestor. The same will be true with nonhuman organisms, such as a rose or a rat or a Rhesus macaque. As such, when we refer to crossing species boundaries, we refer to the combination of genetic or cellular material from two organisms that would generally be understood, in lay terms, as belonging to different species: a human as understood by most lay people, a Rhesus macaque as understood by most lay people, and so on.6
Parents of hybrids are different species.
Genetically modified food is a transgenic product.
Chimeras have cells from two genetically distinct organisms.
Hybrids, transgenics, and chimeras
A geep: a sheep-goat chimera produced by combining the embryos of a goat and a sheep. Not to be confused with a sheep-goat hybrid, which can result when a goat mates with a sheep. Photo: Dr. Gary B. Anderson of Univ. of California, Davis.
There are many types of interspecies organisms including hybrids, transgenics, and chimeras, each of which is created through different sorts of processes. Hybrids are created through breeding. Transgenics are produced through genetic manipulation and modification. Chimeras are the result of cell or tissue transplants.
Hybrids are created by breeding across species. Hybrids are generally the result of combining an egg from one species with sperm from another to form a single embryo. Hybrids contain recombined genetic material throughout their genome and throughout all the tissues in their body.
Transgenics are the result of gene transfer. Typically, transgenics contain transferred or manipulated genes in addition to the host nuclear and mitochondrial DNA. One exception may be a transgenic embryo comprised of the entire complement of nuclear DNA from one organism fused with an enucleated egg cell from another.
Chimeras comprise a mixture of cells from two or more genetically distinct organisms of the same or different species. They are mosaics at the cellular level; individual cells are derived from either the host or the donor but not both.7
Note that chimeras and transgenics need not cross species boundaries, whereas hybrids are always interspecific.
Multiple applications
Crossing species boundaries happens all the time in nature and in agricultural settings, and it has a long history in developmental biology and immunology laboratories. Consider just a few examples:
Nature and breeding programs cross boundaries.
lateral gene transfer between bacteria, whereby genetic material is transmitted horizontally from one organism to another8
the crossing of strains of wheat; the insertion of genes from a plant (or an animal) into a plant to improve crop yield and robustness9
the mating of a horse with a donkey to create a mule; the fusion of sheep and goat cells to create a “geep”10
the transplantation of cells and tissues from one species of frog to another, and of neural tissue from quails to chickens, to study the complex processes of development11-13
Gene transfer from animals to humans and vice versa is common.
Crossing species boundaries between human and nonhuman animals is also commonplace:
Animal tissues, cells, and their derivatives are often transferred to humans, whether by using insulin produced from pig or cow pancreases, injecting flu vaccines cultured in fertilized chicken eggs, or transplanting heart valves from pigs into humans.
Human genes and cells are often transferred to animal hosts to create humanized animal models (such as OncoMouse, which develops human cancers14), to grow humanized tissues that can be transplanted back into humans (such as sheep with human livers15), or to test the developmental potential of transplants.16
Stem cell research
Stem cell research and cloning ignited debate.
In the first few years of human stem cell research, most of the ethics discussions centered on the use of human embryos as sources of stem cells. Research to derive human embryonic stem (hES) cells involves removing cells from the inner cell mass of a human blastocyst, which destroys the developing embryo. While this debate continued, further debate on the ethics of cloning to produce children, and cloning for biomedical research, emerged. This debate arose in response to claims about the anticipated benefit of future stem cell therapies using cells from cloned embryos, which would allow patients to receive transplants of cells containing their own DNA.17
The debate has encompassed part-human animals.
While these issues remain ethically contentious, a new debate has recently emerged concerning the ethics of crossing species boundaries to make part-human chimeras. Stem cell scientists and others insist that this cross-species work is important to basic science and a necessary step on the path to regenerative medicine. They maintain that it would be unethical to involve humans in stem cell transplantation research without first having studied the safety and efficacy of the human cells in nonhuman animals.
Ethical controversy
Issues of health and safety, especially given the possibility of zoonosis, or the transfer of a disease from nonhuman animals to humans, have long been front and center in the ethics debate about cross-species work.18 In the last decade or so, with the increase in science options for the crossing of species boundaries, other ethical issues have come to the fore.
Attempts to patent a humanzee failed but caused a stir.
In 1997, Stuart Newman, a developmental biologist sponsored by biotechnology activist Jeremy Rifkin, sought to preclude the creation of a humanzee—a part-human, part-chimpanzee chimera. Together, Newman and Rifkin tried to patent the relevant technology so that they would be able to restrict its use and to promote a vigorous social dialogue about the desirability of such part-human beings.19 They were unsuccessful in obtaining the patent, leaving open the possibility that humanzees may soon walk among us, with or without patent protection. Examples of recent research involving the transplantation of cells and tissues into prenatal nonhuman animals (embryos and fetuses), the transplantation of cells and tissues into nonhuman animal brains, and the transplantation of cells and tissues into the brains of nonhuman primates, serve to make this point:
Part-human animals already exist.
Scientists want to test human cells in other primates.
Scientists at Harvard University have published their research involving the transfer of human neural stem cells into the developing fetal brain of bonnet monkeys.20
Scientists in Israel have reported that human embryonic stem cells transplanted into chick embryos differentiated into neurons.21
Scientists in Nevada have reported on inserting human neural stem cells into fetal sheep to assess their developmental potential.22
Scientists in California have reported on the development of functional neurons in mouse brains, where the neurons were derived from human embryonic stem cells.23
While this research is ongoing, a debate has erupted about the ethics of creating part-human beings in response to proposals from some stem cell scientists to use nonhuman primates as an assay system for testing the developmental potential of human stem cells. The fact that biologists are especially interested in transplanting human neural stem cells into the brains of nonhuman primates24 intensifies the controversy about humanzee-like chimeras.
The ethics of creating part-human beings
Is it natural and moral to develop part-human animals?
The ethical debate has been multivocal, with moral considerations raised from many perspectives, both religious and secular. The central moral concerns with creating part-human beings include worries about the following:
the unnaturalness and intuitive repugnance of certain kinds of creatures, such as part-human combinations25
the threat of intensified moral confusion regarding the creation of novel part-human beings who violate the pragmatically clear moral demarcation line between species upon which current institutions, structures, and social practices are based5
the potential for transferring moral status to nonhuman animals by conferring on them characteristically human cognitive capacities, which may or may not threaten human dignity24,26
the possibility that enhanced animals would deserve to be treated as if they were human subjects but would continue being treated as if they were unenhanced nonhuman animals27
the moral status of nonhuman animals, especially primates, as experimental animals28
Some see the medical benefits of the research.
Others see it as a way to improve humans.
Scientists and others who advocate cross-species work argue that the part-human animals will be useful as disease models, assay systems, or organ sources.16,29 They dismiss the worries about repugnance, deny the potential for moral confusion, and endeavor to sidestep concerns about moral status and potential threats to human dignity. They also rely heavily on current norms for research involving humans to legitimate preclinical cross-species research in nonhuman animals.
Additionally, advocates of transhumanism, the movement to enhance humans using biotechnology, argue that the creation of hybrids, transgenics, and chimeras may be useful in the quest to radically alter humans.30 They see an opportunity to improve upon human nature and to enhance cognitive and physical performance—an idea that is itself morally controversial.31
More debate is needed about the value and ethics of such research.
Toward a constructive public debate
Unfortunately, much of the public debate on the ethics of crossing species boundaries is characterized by sensationalism and political posturing. While some commentators have attempted to explore the moral dimensions of interspecies research in careful and respectful terms, many of the media reports have exaggerated the conflict, providing more heat than light. Even so, attempts at public education and public engagement have tended to reveal the persistence of the moral controversy. This suggests the need for scientists, ethicists, and others to take seriously the ethical concerns that have been raised. The voluntary guidelines for human embryonic stem cell research recently published by the National Academy of Sciences arguably are an attempt to do just this.32 As we have argued elsewhere, however, considerably more debate and discussion is needed about the fundamental underlying values.33,34
DEAFNESS GENE
MicroRNA mir-96 mutation leads to loss of hearing if it is present in a single copy and deafness if it is present in two copies.
The results of a search conducted under the projects "Sirocco" and "Eurohear" which was funded by the European Union was posted in nature genetics journal.The association between a new type of gene and progressive loss of hearing is concerned in this discovery.The mir-96 gene is a small piece of RNA that affect the process of generation of other molecules in sensory hair cells of the inner ear .
The results came from the collaboration of two research groups, one Spanish and one English.
Karen Steel who was one of the coordinators of the team of British Sanger Institute, said "We were able to demonstrate relatively quickly if the mice that were carriers of one copy of the variant of this gene suffer from progressive loss of hearing, and if they were carrying both genes, they were suffering from severe hearing loss. The main principal questions to be answered concerning the possibility to determine which variant was involved and how influences on hearing ".
Chromosome 7 which was identified recently is the possible location of the gene altered the two groups of researchers have sequenced the gene in each "homologous genomic regions in man and mouse that are associated with hearing loss" and it has showed the presence of a mutation in the gene mir - 96.
Miguel Angel Moreno-Pelayois is the author of the study and researcher at the Hospital Ramon y Cajal in Spain.He said "We know a number of genes associated with deafness in humans and mice, but we discovered with surprise that this belongs to a new class of MicroRNA genes defined. No one had observed a mutation that can cause disease in a couple of MicroRNA sequence. This is the first MicroRNA gene associated with hearing loss and e 'is significant that the first to be associated with a hereditary condition. "
Experts recognized that the MicroRNA may bind to the active messengers in the generation of cell protein, effectively stopping the process and now have discovered that it is possible to analyze the role of mutation in mice. It also seems that the sensory hair cells in the mutant mice are affected by mir-96 gene, while mice carrying two copies of the gene mutant hair cells are deformed from birth and cells subjected to a degeneration in the early stages of life.
Morag Lewis of the Sanger Institute who discovered the mutation had commented that "The mutation, or variation of a single letter of genetic code from A to T in this tiny extension, is sufficient to cause a serious loss in mice".
This mechanism may also occur in human beings.But, according to analysis of the two families used as a sample, the mutation does not happen ever in the same regions where the mouse, although affect neighboring regions, and always very important for the proper functioning of mir-96 .
The results of a search conducted under the projects "Sirocco" and "Eurohear" which was funded by the European Union was posted in nature genetics journal.The association between a new type of gene and progressive loss of hearing is concerned in this discovery.The mir-96 gene is a small piece of RNA that affect the process of generation of other molecules in sensory hair cells of the inner ear .
The results came from the collaboration of two research groups, one Spanish and one English.
Karen Steel who was one of the coordinators of the team of British Sanger Institute, said "We were able to demonstrate relatively quickly if the mice that were carriers of one copy of the variant of this gene suffer from progressive loss of hearing, and if they were carrying both genes, they were suffering from severe hearing loss. The main principal questions to be answered concerning the possibility to determine which variant was involved and how influences on hearing ".
Chromosome 7 which was identified recently is the possible location of the gene altered the two groups of researchers have sequenced the gene in each "homologous genomic regions in man and mouse that are associated with hearing loss" and it has showed the presence of a mutation in the gene mir - 96.
Miguel Angel Moreno-Pelayois is the author of the study and researcher at the Hospital Ramon y Cajal in Spain.He said "We know a number of genes associated with deafness in humans and mice, but we discovered with surprise that this belongs to a new class of MicroRNA genes defined. No one had observed a mutation that can cause disease in a couple of MicroRNA sequence. This is the first MicroRNA gene associated with hearing loss and e 'is significant that the first to be associated with a hereditary condition. "
Experts recognized that the MicroRNA may bind to the active messengers in the generation of cell protein, effectively stopping the process and now have discovered that it is possible to analyze the role of mutation in mice. It also seems that the sensory hair cells in the mutant mice are affected by mir-96 gene, while mice carrying two copies of the gene mutant hair cells are deformed from birth and cells subjected to a degeneration in the early stages of life.
Morag Lewis of the Sanger Institute who discovered the mutation had commented that "The mutation, or variation of a single letter of genetic code from A to T in this tiny extension, is sufficient to cause a serious loss in mice".
This mechanism may also occur in human beings.But, according to analysis of the two families used as a sample, the mutation does not happen ever in the same regions where the mouse, although affect neighboring regions, and always very important for the proper functioning of mir-96 .
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