Posts tagged genetics
Articles and news from the latest research reports.
Mice have system to handle smell of fear
July 23, 2012
Mice appear to have a specialized system for detecting and at least initially processing instinctually important smells such as those that denote predators. The finding raises a question about whether their response to those smells is hardwired.
A separate subsystem for the smell of fear. Experiments in mice suggest neurons that detect odors associated with an instinctive response — like fleeing when an approaching predator is detected — are configured differently than other olfactory neurons. Further research could determine whether this system automatically triggers flight or other primal behaviors.Credit: Mike Cohea/Brown University
PROVIDENCE, R.I. [Brown University] — A new study finds that mice have a distinct neural subsystem that links the nose to the brain and is associated with instinctually important smells such as those emitted by predators. That insight, published online this week in Proceedings of the National Academy of Sciences, prompts the question whether mice and other mammals have specially hardwired neural circuitry to trigger instinctive behavior in response to certain smells.
In the series of experiments and observations described in the paper, the authors found that nerve cells in the nose that express members of the gene family of trace amine-associated receptors (TAAR) have several key biological differences from the much more common and diverse neurons that express members of the olfactory receptor gene family. Those other nerve cells detect a much broader range of smells, said corresponding author Gilad Barnea, the Robert and Nancy Carney Assistant Professor of Neuroscience at Brown University.
The differences between TAAR neurons and olfactory receptor neurons led Barnea and his co-authors to conclude that they form an independent subsystem for certain smells.
“Our observations suggest that the TAAR-expressing sensory neurons constitute a distinct olfactory subsystem that extracts specific environmental cues that then elicit innate responses,” Barnea said.
A protein essential for metabolism and recently associated with neurodegenerative diseases also occurs in several brain-specific forms. This discovery emerged in the course of a research project funded by the Austrian Science Fund FWF, the findings of which have now been published in the journal Human Molecular Genetics. The scientists working on the project discovered a large new region in the genetic code of the protein PGC-1alpha. Previously unknown variations of the protein, which can be found specifically in the brain, are produced from this region. This discovery may provide tissue-specific starting points for the development of new treatments for neurodegenerative diseases like Huntington’s, Parkinson’s and Alzheimer’s.
PGC-1alpha is a real jack-of-all-trades. As a central regulator of metabolic genes that coordinate energy metabolism, the protein, which functions as a “transcriptional coactivator”, influences major body functions. The extent to which the protein also influences medical conditions like obesity, diabetes and metabolic syndrome is unclear, and was under further investigation as part of a research project funded by the Austrian Science Fund FWF. In the course of their research, however, the scientists stumbled on unexpected findings with a particular relevance for neurodegenerative diseases.
Major Difference
A research team headed by Prof. Wolfgang Patsch from the Departments of Pharmacology and Toxicology, and Laboratory Medicine at the Paracelsus Medical University established that the gene which codes for PGC-1alpha (PPARGC1A) is six times larger than hitherto assumed. A new promoter was actually found at some distance (ca. 580 kb) from the previously known gene. A promoter is a DNA segment usually occurring upstream from a gene that can ultimately control how that gene is expressed as a protein. The transmission of genetic information from DNA to RNA molecules, i.e. transcription, is an important intermediate step in this process.
Transcripts, which are produced from the newly discovered promoter, were now examined in detail as part of the research project. “These transcripts differ in important regions from those encoded by the previously characterized - reference - PPARGC1A locus. Based on these differences, we were able to show that these previously unknown transcripts are produced specifically in human brain cells and are at least as common there as the reference transcripts,” explains Dr. Selma M. Soyal, first author of the article currently published in Human Molecular Genetics. Further analyzes showed that the differences in the transcripts lead to the formation of proteins which differ from the protein that acts as a reference, in particular at the N-terminus. Other differences were found within the PGC-1alpha amino acid chain.
When the different PGC-1alpha proteins were localized in human cells (SH-SY5Y), another surprise awaited the scientists: whereas the reference protein was located mainly in the cell nucleus, one of the newly discovered variants was mainly found in the surrounding cytoplasm; another was found both in the nucleus and in the cytoplasm. According to Prof. Patsch: “It is likely that the differences we found in the transcripts influence mechanisms in the finished proteins which control their localization in the cell.”
A Protein With Impact
The detailed functional characterization of the brain-specific proteins could prove significant, as PGC-1alpha is associated with various neurodegenerative diseases such as Huntington’s disease, Parkinson’s and Alzheimer’s - a link that was also confirmed by the project. Using complex statistical analyses, sequence differences in the new promoter were examined in 1.706 Huntington patients as part of a collaboration with the European Huntington’s Disease Network. A clear correlation emerged here between different sequence patterns and the age of onset of the disease in the patients. In addition, the scientists were also able to show that the newly discovered promoter is active in nerve tissue. This indicates that it may actually play an important role in the only partly known links between PGC-1alpha and the neurodegenerative diseases in question.
Overall, the findings of this project, which is funded by the Austrian Science Fund FWF, indicate complex functions of PGC-1alpha in humans. If the scientists succeed in reaching a better understanding of this complexity, PGC-1alpha could provide new possibilities for future therapeutic intervention in key neurodegenerative diseases.
Discovery May Lead to New Treatment for ALS
ScienceDaily (July 18, 2012) — Researchers at Oregon Health & Science University School of Dentistry have discovered that TDP-43, a protein strongly linked to ALS (amyotrophic lateral sclerosis) and other neurodegenerative diseases, appears to activate a variety of different molecular pathways when genetically manipulated. The findings have implications for understanding and possibly treating ALS and neurodegenerative diseases such as Alzheimer’s and Parkinson’s.
ALS affects two in 100,000 adults in the United States annually and the prognosis for patients is grim.The new discovery is published online in G3: Genes, Genomes, Genetics (and the July 2012 print issue of G3).
Using a fruit fly model, the OHSU team genetically increased or eliminated TDP-43 to study its effect on the central nervous system. By using massively parallel sequencing methods to profile the expression of genes in the central nervous system, the team found that the loss of TDP-43 results in widespread gene activation and altered splicing, much of which is reversed by rescue of TDP-43 expression. Although previous studies have implicated both absence and over expression of TDP-43 in ALS, the OHSU study showed little overlap in the gene expression between these two manipulations, suggesting that the bulk of the genes affected are different.
"Our data suggest that TDP-43 plays a role in synaptic transmission, synaptic release and endocytosis," said Dennis Hazelett, Ph.D., lead author of the study. "We also uncovered a potential novel regulation of several pathways, many targets of which appear to be conserved."
Source: Science Daily
Researchers identify mechanisms that allow embryonic stem cells to become any cell in the human body
July 18, 2012
(Phys.org) — New research at the Hebrew University of Jerusalem sheds light on pluripotency—the ability of embryonic stem cells to renew themselves indefinitely and to differentiate into all types of mature cells. Solving this problem, which is a major challenge in modern biology, could expedite the use of embryonic stem cells in cell therapy and regenerative medicine. If scientists can replicate the mechanisms that make pluripotency possible, they could create cells in the laboratory which could be implanted in humans to cure diseases characterized by cell death, such as Alzheimer’s, Parkinson’s, diabetes and other degenerative diseases.
To shed light on these processes, researchers in the lab of Dr. Eran Meshorer, in the Department of Genetics at the Hebrew University’s Alexander Silberman Institute of Life Sciences, are combining molecular, microscopic and genomic approaches. Meshorer’s team is focusing on epigenetic pathways—which cause biological changes without a corresponding change in the DNA sequence—that are specific to embryonic stem cells.
The molecular basis for epigenetic mechanisms is chromatin, which is comprised of a cell’s DNA and structural and regulatory proteins. In groundbreaking research performed by Shai Melcer, a PhD student in the Meshorer lab, the mechanisms which support an “open” chromatin conformation in embryonic stem cells were examined. The researchers found that chromatin is less condensed in embryonic stem cells, allowing them the flexibility or “functional plasticity” to turn into any kind of cell.
A distinct pattern of chemical modifications of chromatin structural proteins (referred to as the acetylation and methylation of histones) enables a looser chromatin configuration in embryonic stem cells. During the early stages of differentiation, this pattern changes to facilitate chromatin compaction.
But even more interestingly, the authors found that a nuclear lamina protein, lamin A, is also a part of the secret. In all differentiated cell types, lamin A binds compacted domains of chromatin and anchors them to the cell’s nuclear envelope. Lamin A is absent from embryonic stem cells and this may enable the freer, more dynamic chromatin state in the cell nucleus. The authors believe that chromatin plasticity is tantamount to functional plasticity since chromatin is made up of DNA that includes all genes and codes for all proteins in any living cell. Understanding the mechanisms that regulate chromatin function will enable intelligent manipulations of embryonic stem cells in the future.
"If we can apply this new understanding about the mechanisms that give embryonic stem cells their plasticity, then we can increase or decrease the dynamics of the proteins that bind DNA and thereby increase or decrease the cells’ differentiation potential," concludes Dr. Meshorer. “This could expedite the use of embryonic stem cells in cell therapy and regenerative medicine, by enabling the creation of cells in the laboratory which could be implanted in humans to cure diseases characterized by cell death, such as Alzheimer’s, Parkinson’s, diabetes and other degenerative diseases.”
Source: PHYS.ORG
Scientists have developed a statistical method using evolutionary information to significantly enhance the likelihood of identifying disease-associated alleles in the genome that show better consistency across populations.
The group’s research appeared in the advanced online issue of the journal Molecular Biology and Evolution. The new method is now available to use via the web, so that researchers worldwide can apply it as an aid to discovering disease-associated mutations that are more consistently reproducible and therefore useable as diagnostic markers. Kumar refers to this new approach, combining standard comparative genomic studies with phylogenetic data as phylomedicine, a rapidly developing field that promises to streamline genomic information and improve its diagnostic power.
Read more: Evolutionary information improves discovery of mutations associated with diseases
Genetic Link to Rapid Weight Gain from Antipsychotics Discovered
ScienceDaily (July 17, 2012) — Scientists have discovered two genetic variants associated with the substantial, rapid weight gain occurring in nearly half the patients treated with antipsychotic medications, according to two studies involving the Centre for Addiction and Mental Health (CAMH).
These results could eventually be used to identify which patients have the variations, enabling clinicians to choose strategies to prevent this serious side-effect and offer more personalized treatment.
"Weight gain occurs in up to 40 per cent of patients taking medications called second-generation or atypical antipsychotics, which are used because they’re effective in controlling the major symptoms of schizophrenia," says CAMH Scientist Dr. James Kennedy, senior author on the most recent study published online in the Archives of General Psychiatry.
This weight gain can lead to obesity, type 2 diabetes, heart problems and a shortened life span. “Identifying genetic risks leading to these side-effects will help us prescribe more effectively,” says Dr. Kennedy, head of the new Tanenbaum Centre for Pharmacogenetics, which is part of CAMH’s Campbell Family Mental Health Research Institute. Currently, CAMH screens for two other genetic variations that affect patients’ responses to psychiatric medications.
Each study identified a different variation near the melanocortin-4 receptor (MC4R) gene, which is known to be linked to obesity.
In the Archives of General Psychiatry study, people carrying two copies of a variant gained about three times as much weight as those with one or no copies, after six to 12 weeks of treatment with atypical antipsychotics. (The difference was approximately 6 kg versus 2 kg.) The study had four patient groups: two from the U.S., one in Germany and one from a larger European study.
"The weight gain was associated with this genetic variation in all these groups, which included pediatric patients with severe behaviour or mood problems, and patients with schizophrenia experiencing a first episode or who did not respond to other antipsychotic treatments," says CAMH Scientist Dr. Daniel Müller. "The results from our genetic analysis combined with this diverse set of patients provide compelling evidence for the role of this MC4R variant. Our research group has discovered other gene variants associated with antipsychotic-induced weight gain in the past, but this one appears to be the most compelling finding thus far."
Three of the four groups had never previously taken atypical antipsychotics. Different groups were treated with drugs such as olanzapine, risperidone, aripiprazole or quetiapine, and compliance was monitored to ensure the treatment regime was followed. Weight and other metabolic-related measures were taken at the start and during treatment.
A genome-wide association study was conducted on pediatric patients by the study’s lead researcher, Dr. Anil Malhotra, at the Zucker Hillside Hospital in Glen Oaks, NY. In this type of study, variations are sought across a person’s entire set of genes to identify those associated with a particular trait. The result pointed to the MC4R gene.
This gene’s role in antipsychotic-induced weight gain had been identified in a CAMH study published earlier this year in The Pharmacogenomics Journal, involving Drs. Müller and Kennedy, and conducted by PhD student Nabilah Chowdhury. They found a different variation on MC4R that was linked to the side-effect.
For both studies, CAMH researchers did genotyping experiments to identify the single changes to the sequence of the MC4R gene — known as single nucleotide polymorphisms (SNPs) — related to the drug-induced weight gain side-effect.
The MC4R gene encodes a receptor involved in the brain pathways regulating weight, appetite and satiety. “We don’t know exactly how the atypical antipsychotics disrupt this pathway, or how this variation affects the receptor,” says Dr. Müller. “We need further studies to validate this result and eventually turn this into a clinical application.”
Source: Science Daily
Gene Therapy Treatment Extends Lives of Mice with Fatal Disease, Spinal Muscular Atrophy
July 16th, 2012
Spinal Muscular Atrophy affects one in 6,000 children and has no known cure.
A team of University of Missouri researchers has found that introducing a missing gene into the central nervous system could help extend the lives of patients with Spinal Muscular Atrophy (SMA) – the leading genetic cause of infantile death in the world.
SMA is a rare genetic disease that is inherited by one in 6,000 children who often die young because there is no cure. Children who inherit SMA are missing a gene that produces a protein which directs nerves in the spine to give commands to muscles.
The MU team, led by Christian Lorson, professor in the Department of Veterinary Pathobiology and the Department of Molecular Microbiology and Immunology, introduced the missing gene into mice born with SMA through two different methods: intravenously and directly into the mice’s central nervous systems. While both methods were effective in extending the lives of the mice, Lorson found that introducing the missing gene directly into the central nervous system extended the lives of the mice longer.
Mice born with spinal muscular atrophy typically only live five or six days. Researchers introduced the SMN gene into the mice’s central nervous systems and were able to extend their lives 10-25 days longer. The mice in the picture have spinal muscular atrophy.
“Typically, mice born with SMA only live five or six days, but by introducing the missing SMN gene into the mice’s central nervous systems, we were able to extend their lives 10-25 days longer than SMA mice who go untreated,” said Lorson, who works in the MU Bond Life Sciences Center and the College of Veterinary Medicine. “While this system is still not perfect, what our study did show is that the direct administration of the missing gene into the central nervous system provides some degree of rescue and a profound extension of survival.”
There are several different types of SMA that appear in humans, depending on the age that symptoms begin to appear. Lorson believes that introducing the missing gene through the central nervous system is a way to potentially treat humans regardless of what SMA type they have.
“This is a treatment method that is very close to being a reality for human patients,” Lorson said. “Clinical trials of SMA treatment using gene therapy are likely to begin in next 12-18 months, barring any unforeseen problems.”
Source: Neuroscience News
![Research teams from The University of Texas Health Science Center at Houston (UTHealth) and Paris, France have discovered a gene defect linked to a cluster of systemic complications, including life-threatening thoracic aortic disease and intracranial aneurysms. The new syndrome is similar, but distinct from known syndromes such as Marfan and Loeys-Dietz syndrome.
Read more: Researchers Discover Gene Defect for New Syndrome
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Research teams from The University of Texas Health Science Center at Houston (UTHealth) and Paris, France have discovered a gene defect linked to a cluster of systemic complications, including life-threatening thoracic aortic disease and intracranial aneurysms. The new syndrome is similar, but distinct from known syndromes such as Marfan and Loeys-Dietz syndrome.
Read more: Researchers Discover Gene Defect for New Syndrome
Activity of Rare Genetic Variant in Glioma Validated
ScienceDaily (July 2, 2012) — Researchers at Moffitt Cancer Center working with colleagues at three other institutions have validated a link between a rare genetic variant and the risk of glioma, the most common and lethal type of brain tumor. The validation study also uncovered an association between the same rare genetic variant and improved rates of survival for patients with glioma.
The study, the first to confirm a rare susceptibility variant in glioma, appeared in a recent issue of the Journal of Medical Genetics, a journal published by the British Medical Association.
"Glioma is a poorly understood cancer with high morbidity and devastating outcomes," said study lead author Kathleen M. Egan, Sc.D., interim program leader of Cancer Epidemiology and vice chair of the Department of Cancer Epidemiology. "However, the discovery of the association of the TP53 genetic variant rs78378222 with glioma provides new insights into these tumors and offers better prospects for identifying people at risk."
According to the authors, their study “genotyped’ the single nucleotide polymorphism (SNP, or “snip”) rs78378222 in TP53, an important tumor suppressor gene. The researchers said the SNP disrupts the TP53 signal and, because of its activity, has been linked to a variety of cancers. This study linked the presence of the rare form of rs78378222 to deadly glioma.
The researchers conducted a large, clinic-based, case-control study of individuals age 18 and older with a recent glioma diagnosis. A total of 566 glioma cases and 603 controls were genotyped for the rs78378222 variant.
Study results reveal that the odds of developing glioma were increased 3.5 times among the rare variant allele carriers. However, when researchers examined the impact of rs78378222 on survival, they found an approximately 50 percent reduction in death rates for those who were variant allele carriers.
"That the variant increased survival chances was an unexpected finding," Egan said. "It is tempting to speculate that the presence of the risk allele could direct tumor development into a less aggressive path."
The researchers concluded that their study results “may shed light on the etiology and progression of these tumors.”
Source: Science Daily
Genes May Play Role in Educational Achievement
ScienceDaily (July 2, 2012) — Researchers have identified genetic markers that may influence whether a person finishes high school and goes on to college, according to a national longitudinal study of thousands of young Americans.
The study is in the July issue of Developmental Psychology, a publication of the American Psychological Association.
"Being able to show that specific genes are related in any way to academic achievement is a big step forward in understanding the developmental pathways among young people," said the study’s lead author, Kevin Beaver, PhD, a professor at the College of Criminology and Criminal Justice at Florida State University.
The three genes identified in the study — DAT1, DRD2 and DRD4 — have been linked to behaviors such as attention regulation, motivation, violence, cognitive skills and intelligence, according to the study. Previous research has explored the genetic underpinnings of intelligence but virtually none has examined genes that potentially contribute to educational attainment in community samples, said Beaver.
He and his colleagues analyzed data from the National Longitudinal Study of Adolescent Health, also known as Add Health. Add Health is a four-wave study of a nationally representative sample of American youths who were enrolled in middle or high school in 1994 and 1995. The study continued until 2008, when most of the respondents were between the ages of 24 and 32. The participants completed surveys, provided DNA samples and were interviewed, along with their parents. The sample used for this analysis consisted of 1,674 respondents.
The genes identified in this research are known as dopamine transporter and receptor genes. Every person has the genes DAT1, DRD2 and DRD4, but what is of interest are molecular differences within the genes, known as alleles, according to Beaver. Subjects who possessed certain alleles within these genes achieved the highest levels of education, according to the findings.
Dopamine transporter genes assist in the production of proteins that regulate levels of the neurotransmitter dopamine in the brain, while dopamine receptor genes are involved in neurotransmission. Previous research has shown that dopamine levels play a role in regulating impulsive behavior, attention and intelligence.
The presence of the alleles alone did not guarantee higher levels of education, the study found. Having a lower IQ was more strongly associated with lower levels of education. Also, living in poverty and essentially “running with a bad crowd” resulted in lower levels of education despite the genetic effects.
Even though the genetic variants were found to be associated with educational levels, having a specific allele does not determine whether someone will graduate from high school or earn a college degree, according to Beaver. Rather, these genes work in a probabilistic way, with the presence of certain alleles simply increasing or decreasing the likelihood of educational outcomes, he said. “No one gene is going to say, ‘Sally will graduate from high school’ or ‘Johnny will earn a college degree,’” he said. “These genetic effects operate indirectly, through memory, violent tendencies and impulsivity, which are all known predictors of how well a kid will succeed in school. If we can keep moving forward and identify more genetic markers for educational achievement, we can begin to truly understand how genetics play a role in how we live and succeed in life.”
Source: Science Daily