First synthetic yeast chromosome built .


An international team of scientists has synthesised the first working chromosome in yeast, the latest step in the quest to make the world’s first synthetic yeast genome.

The research, reported today the journal Science, could lead to the development of new strains of the organism to help produce industrial chemicals, medicines and biofuels.

An international team of scientists has synthesised the first working chromosome in yeast, the latest step in the quest to make the world’s first synthetic yeast genome.

The research, reported today the journal Science, could lead to the development of new strains of the organism to help produce industrial chemicals, medicines and biofuels.

Instead of just copying nature, the team extensively modified their chromosome, deleting unwanted genes here and there.

It then successfully incorporated the designer chromosome into living yeast cells, endowing them with new capabilities not found in naturally occurring yeast.

“It is the most extensively altered chromosome ever built,” says study leader Jef Boeke of New York University’s Langone Medical Center.

While other teams have synthesised bacterium and viral DNA, Boeke’s project is the first report of a synthetic chromosome in a eukaryote, an organism whose cells contain a nucleus, like human cells.

The achievement, which took seven years, involved the use of computer-aided design to construct one of 16 chromosomes in brewer’s yeast, known scientifically as Saccharomyces cerevisiae.

The synthetic version, which the scientists call synIII, is a slimmed-down version of the yeast’s naturally occurring chromosome III, which has 316,667 base pairs. The team picked this chromosome because it is the smallest and controls how yeast cells mate and undergo genetic change.

“We have shown that yeast cells carrying this synthetic chromosome are remarkably normal. They behave almost identically to wild yeast cells, only they now possess new capabilities and can do things that wild yeast cannot,” says Boeke.

Such methods could be used to improve yeast’s ability to thrive in harsh environments, such as very high concentrations of alcohol.

Tour-de-force in synthetic biology
Jim Collins of Boston University and a pioneer in the field called Boeke’s work a “tour-de-force in synthetic biology,” an emerging field of science which applies the principles of engineering to living systems.

“This development enables new experiments on genome evolution and highlights our ever-expanding ability to modify and engineer DNA,” says Collins, whose lab is engineering a probiotic yogurt bacterium to neutralise cholera infections.

Synthetic biology is best known for work done by genome scientist and entrepreneur Craig Venter, who in 2010 reported he had built the first synthetic genome of a bacterium out of chemicals.

That work generated a lot of hype and considerable worry that scientists were tinkering with nature.

Boeke says the work in his lab and many others is much less like “playing God” and more akin to genetic engineering, but on a broader scale.

Chromosome scrambling
For their designer yeast chromosome, Boeke and his team made more than 500 changes, removing repeating sections of nearly 50,000 base pairs of DNA they deemed unnecessary to chromosome reproduction and growth.

They also removed what has been called “junk DNA” – parts of the genetic code that do not make proteins – and segments known as “jumping genes,” stretches of DNA that randomly hop around the genome and can cause mutations.

Despite all of those changes, Boeke says, “we still have a chromosome that works.”

He is most excited about the ability to selectively delete or rearrange the letters of the chromosome, a process he calls chromosome scrambling. To make this happen, the scientists added in stretches of DNA known as loxP, a gene sequence that works as a genetic switch that can be activated by a protein.

“What’s really exciting is in addition to yeast being healthy and happy, we’ve also endowed this chromosome with this almost magical property of being able to rearrange its structure when we wave our magic wand and generate millions of variant chromosomes,” says Boeke.

Having the ability to produce new synthetic strains of yeast could result in some very useful types of yeast that could be used to make rare medicines, such as artemisinin for malaria, or certain vaccines, including for hepatitis B, which is derived from yeast, says Boeke.

Synthetic yeast could also be used to make more efficient biofuels, such as alcohol, butanol, and biodiesel.

Lei Wang, assistant professor in the Chemical Biology and Proteomics Laboratory at the Salk Institute for Biological Studies in La Jolla, California, says the work “will enable us to artificially speed up the evolution process in the lab.”

Wang, who was not involved in the research, says he is impressed to see the yeast behaving normally after so many changes, which suggests “you can do very bold things to the organism.”

Labs in United States, Britain, China and India are working toward making synthetic versions of all of the organism’s 16 chromosomes by 2017, and Boeke thinks there could be at least one or two more yeast chromosomes published this year.

Tags: biotechnology, research, genetics

Instead of just copying nature, the team extensively modified their chromosome, deleting unwanted genes here and there.

It then successfully incorporated the designer chromosome into living yeast cells, endowing them with new capabilities not found in naturally occurring yeast.

“It is the most extensively altered chromosome ever built,” says study leader Jef Boeke of New York University’s Langone Medical Center.

While other teams have synthesised bacterium and viral DNA, Boeke’s project is the first report of a synthetic chromosome in a eukaryote, an organism whose cells contain a nucleus, like human cells.

The achievement, which took seven years, involved the use of computer-aided design to construct one of 16 chromosomes in brewer’s yeast, known scientifically as Saccharomyces cerevisiae.

The synthetic version, which the scientists call synIII, is a slimmed-down version of the yeast’s naturally occurring chromosome III, which has 316,667 base pairs. The team picked this chromosome because it is the smallest and controls how yeast cells mate and undergo genetic change.

“We have shown that yeast cells carrying this synthetic chromosome are remarkably normal. They behave almost identically to wild yeast cells, only they now possess new capabilities and can do things that wild yeast cannot,” says Boeke.

Such methods could be used to improve yeast’s ability to thrive in harsh environments, such as very high concentrations of alcohol.

Tour-de-force in synthetic biology
Jim Collins of Boston University and a pioneer in the field called Boeke’s work a “tour-de-force in synthetic biology,” an emerging field of science which applies the principles of engineering to living systems.

“This development enables new experiments on genome evolution and highlights our ever-expanding ability to modify and engineer DNA,” says Collins, whose lab is engineering a probiotic yogurt bacterium to neutralise cholera infections.

Synthetic biology is best known for work done by genome scientist and entrepreneur Craig Venter, who in 2010 reported he had built the first synthetic genome of a bacterium out of chemicals.

That work generated a lot of hype and considerable worry that scientists were tinkering with nature.

Boeke says the work in his lab and many others is much less like “playing God” and more akin to genetic engineering, but on a broader scale.

Chromosome scrambling
For their designer yeast chromosome, Boeke and his team made more than 500 changes, removing repeating sections of nearly 50,000 base pairs of DNA they deemed unnecessary to chromosome reproduction and growth.

They also removed what has been called “junk DNA” – parts of the genetic code that do not make proteins – and segments known as “jumping genes,” stretches of DNA that randomly hop around the genome and can cause mutations.

Despite all of those changes, Boeke says, “we still have a chromosome that works.”

He is most excited about the ability to selectively delete or rearrange the letters of the chromosome, a process he calls chromosome scrambling. To make this happen, the scientists added in stretches of DNA known as loxP, a gene sequence that works as a genetic switch that can be activated by a protein.

“What’s really exciting is in addition to yeast being healthy and happy, we’ve also endowed this chromosome with this almost magical property of being able to rearrange its structure when we wave our magic wand and generate millions of variant chromosomes,” says Boeke.

Bakers yeast

Having the ability to produce new synthetic strains of yeast could result in some very useful types of yeast that could be used to make rare medicines, such as artemisinin for malaria, or certain vaccines, including for hepatitis B, which is derived from yeast, says Boeke.

Synthetic yeast could also be used to make more efficient biofuels, such as alcohol, butanol, and biodiesel.

Lei Wang, assistant professor in the Chemical Biology and Proteomics Laboratory at the Salk Institute for Biological Studies in La Jolla, California, says the work “will enable us to artificially speed up the evolution process in the lab.”

Wang, who was not involved in the research, says he is impressed to see the yeast behaving normally after so many changes, which suggests “you can do very bold things to the organism.”

Labs in United States, Britain, China and India are working toward making synthetic versions of all of the organism’s 16 chromosomes by 2017, and Boeke thinks there could be at least one or two more yeast chromosomes published this year.

 

Is the STEM skills shortage overblown or even non-existent?


With the rising emphasis on tech across the business landscape, STEM (science, technology, engineering and mathematics) skills appear to be in high demand. Yet, one analysis finds the alleged shortfall of these skills isn’t all it appears to be.

Robert Charette, writing in IEEE Spectrum,  says that despite the handwringing, “there are more STEM workers than suitable jobs.” He points to a study by the Economic Policy Institute that found that wages for U.S. IT and mathematics-related professionals have not grown appreciably over the past decade, and that they, too, have had difficulty finding jobs in the past five years. He lists a number of studies that refute the presence of a global STEM skills shortage. The U.S. Bureau of Labor Statistics, for one, estimates that there was a net loss of  370 000 science and engineering jobs in the U.S. in 2011.

There isn’t even agreement on what STEM jobs are, Charette points out. Even agencies of the U.S. government don’t agree. The U.S. Department of Commerce puts the number of STEM jobs at7.6 million, which “includes professional and technical support occupations in the fields of computer science and mathematics, engineering, and life and physical sciences as well as management,” he relates. The National Science Foundation, on the other hand, estimates there are 12.4 million STEM jobs, taking in health-care workers,  psychologists and social scientists. Other data from Georgetown University finds that a majority of STEM graduates actually leave the STEM field altogether after ten years.

Perhaps what is needed is more polymath skills — blending STEM with other disciplines such as business, law, or even the arts — to drive innovation and entrepreneurship. Building a software company takes more than programming abilities — it takes business savvy and vision.

STEM skills do have an important role in economic growth, Charette opines. “There is indeed a shortage — a STEM knowledge shortage.” While a STEM-based university degree isn’t necessary, “improving everyone’s STEM skills would clearly be good for the workforce and for people’s employment prospects, for public policy debates, and for everyday tasks like balancing checkbooks and calculating risks.”

Ironically, while many non-STEM jobs require some level of STEM skills, many STEM jobs themselves are being displaced. Many of the skills needed in today’s marketplace — from auto repair to graphic arts to accounting — call for computer proficiency, as they now entail work built on software. At the same time, many functions that may have required engineers and mathematicians are being automated — algorithms have replaced many high-level mental tasks and processes. Even computer programmers and operators are finding their jobs are being automated. Perhaps non-STEM professionals need more STEM, but STEM professionals need more liberal arts.

Turning human stem cells into brain cells sheds light on neural development.


Medical researchers have manipulated human stem cells into producing types of brain cells known to play important roles in neurodevelopmental disorders such as epilepsy, schizophrenia and autism. The new model cell system allows neuroscientists to investigate normal brain development, as well as to identify specific disruptions in biological signals that may contribute to neuropsychiatric diseases.

brainsondema

Scientists from The Children’s Hospital of Philadelphia and the Sloan-Kettering Institute for Cancer Research led a study team that described their research in the journal Cell Stem Cell, published online today.

The research harnesses human embryonic stem cells (hESCs), which differentiate into a broad range of different cell types. In the current study, the scientists directed the stem cells into becoming cortical interneurons—a class of brain cells that, by releasing theneurotransmitter GABA, controls electrical firing in brain circuits.

“Interneurons act like an orchestra conductor, directing other excitatory brain cells to fire in synchrony,” said study co-leader Stewart A. Anderson, M.D., a research psychiatrist at The Children’s Hospital of Philadelphia. “However, when interneurons malfunction, the synchrony is disrupted, and seizures or mental disorders can result.”

Anderson and study co-leader Lorenz Studer, M.D., of the Center for Stem Cell Biologyat Sloan-Kettering, derived interneurons in a laboratory model that simulates how neurons normally develop in the human forebrain.

“Unlike, say, liver diseases, in which researchers can biopsy a section of a patient’s liver, neuroscientists cannot biopsy a living patient’s brain tissue,” said Anderson. Hence it is important to produce a cell culture model of brain tissue for studying neurological diseases. Significantly, the human-derived cells in the current study also “wire up” in circuits with other types of brain cells taken from mice, when cultured together. Those interactions, Anderson added, allowed the study team to observe cell-to-cell signaling that occurs during forebrain development.

In ongoing studies, Anderson explained, he and colleagues are using their cell model to better define molecular events that occur during brain development. By selectively manipulating genes in the interneurons, the researchers seek to better understand how gene abnormalities may disrupt brain circuitry and give rise to particular diseases. Ultimately, those studies could help inform drug development by identifying molecules that could offer therapeutic targets for more effective treatments of neuropsychiatric diseases.

In addition, Anderson’s laboratory is studying interneurons derived from stem cells made from skin samples of patients with chromosome 22q.11.2 deletion syndrome, a genetic disease which has long been studied at The Children’s Hospital of Philadelphia. In this multisystem disorder, about one third of patients have autistic spectrum disorders, and a partially overlapping third of patients develop schizophrenia. Investigating the roles of genes and signaling pathways in their model cells may reveal specific genes that are crucial in those patients with this syndrome who have neurodevelopmental problems.

 

Source:Nature

 

 

 

Mesenchymal stem cells.


Mesenchymal stem cells (MSCs) are multipotent adult stem cells that have regenerative capability and exert paracrine actions on damaged tissues. Since peritoneal fibrosis is a serious complication of peritoneal dialysis, we tested whether MSCs suppress this using a chlorhexidine gluconate model in rats. Although MSCs isolated from green fluorescent protein–positive rats were detected for only 3 days following their injection, immunohistochemical staining showed that MSCs suppressed the expression of mesenchymal cells, their effects on the deposition of extracellular matrix proteins, and the infiltration of macrophages for 14 days. Moreover, MSCs reduced the functional impairment of the peritoneal membrane. Cocultures of MSCs and human peritoneal mesothelial cells using a Transwell system indicated that the beneficial effects of MSCs on the glucose-induced upregulation of transforming growth factor-β1(TGF-β1) and fibronectin mRNA expression in the human cells were likely due to paracrine actions. Preincubation in MSC-conditioned medium suppressed TGF-β1-induced epithelial-to-mesenchymal transition, α-smooth muscle actin, and the decrease in zonula occludens-1 in cultured human peritoneal mesothelial cells. Although bone morphogenic protein 7 was not detected, MSCs secreted hepatocyte growth factor and a neutralizing antibody to this inhibited TGF-β1 signaling. Thus, our findings imply that MSCs ameliorate experimental peritoneal fibrosis by suppressing inflammation and TGF-β1 signaling in a paracrine manner.

Source: Nature.

Hans-Peter Kiem genetically manipulates stem cells to treat HIV, genetic diseases and cancers.


Fred Hutch oncologist, stem cell and gene therapy researcher

Imagine if we could treat deadly diseases by generating healthier versions of the very building blocks of our bodies—blood stem cells. That’s the vision of Dr. Hans-Peter Kiem, whose Hutchinson Center laboratory is working to make such therapies a reality.

“Not long ago, this was science fiction,” he said.

Kiem’s cutting edge research reflects his longstanding interest in blood stem cell transplantation, now one of the standard treatments for many blood cancers, in which the patient receives an infusion of blood stem cells, either from a donor or from the patient’s own multiplied cells. The idea is that the new stem cells will grow into disease-free blood cells—a concept that Kiem’s research takes a step further.

“Stem cells can do everything,” said Kiem, who first came to the Hutchinson Center as a fellow in 1992 and joined the faculty five years later. “If we can correct defective stem cells, we can cure diseases.”

Kiem and his colleagues investigate how stem cells can be extracted from sick patients, manipulated at a genetic level and then delivered back to them to treat a range of diseases, from infections like HIV to genetic diseases to aggressive cancers.

One ongoing research effort confronts a major challenge in cancer treatment: Patients can receive only so much chemotherapy at a time, or else their blood cell counts may drop to a level that invites infections, anemia, excessive bleeding and other serious health complications. In such a scenario, the patient must stop receiving chemotherapy until the cell counts recover to healthy levels—but meanwhile, the cancer can worsen.

Kiem’s lab has developed a way to extract a patient’s blood stem cells and insert a special “resistance” gene that is designed to protect the cells from damage by common chemotherapy drugs such as temozolomide and BCNU. An infusion of these enhanced cells could give new hope to patients with the most aggressive form of brain cancer—glioblastoma—which is very difficult to treat. A small study for glioblastoma patients that Kiem started in fall 2009 is showing promising initial results and continuing to expand.

Kiem is also planning a study of patients with AIDS and lymphoma, who would receive blood stem cells with two inserted genes: one that counteracts the HIV infection and one that protects the patient from chemotherapy’s effects.

More recently Kiem has extended his work to derive blood stem cells from a new class of stem cells called induced pluripotent stem cells. What makes pluripotent stem cells promising for new treatments is that they can be derived from readily accessible adult tissues, such as skin cells, and can mature into many other types of tissues and cells, including blood stem cells. These blood stem cells could in turn be expanded and used for blood stem cell transplantations, offering a new treatment option for patients with defective marrow or immune function.

Kiem’s groundbreaking work led to his selection in 2009 as the recipient of the first José Carreras/E. Donnall Thomas Endowed Chair for Cancer Research. The award is named for internationally known tenor and leukemia survivor Carreras and Thomas, who developed bone marrow transplantation.

Don Thomas was pursuing something that was at that time viewed as very difficult,” Kiem said. “It’s a bit of the same thing right now for gene therapy in stem cells. I hope that in 10 or 20 years it will be like what Don has achieved.”

Source: Fred Hutchinson Cancer Research Center

 

 

 

Highly potent human haemopoietic stem cells first emerge in the intraembryonic aorta-gonad-mesonephros region.


Abstract

Background

Haemopoietic stem cells (HSCs) are used in the clinic to treat various haematological disorders. These cells emerge during early embryogenesis and maintain haemopoiesis in the adult organism. In the vertebrate embryo, HSCs develop in multiple locations. Little is known about the embryonic development of human HSCs.

Methods

Human embryonic and fetal tissues were obtained after elective termination of pregnancy. Preconditioned immunodeficient mice were used as recipients for human HSCs. Transplanted mice were bled every 1—2 months to assess human HSC contribution.

Findings

We have found that human HSCs emerge first in the aorta-gonad-mesonephros (AGM) region and only later appear in the yolk sac, liver, and placenta. Transplantation of human AGM region cells into immunodeficient mice provides long-term high-level multilineage haemopoietic repopulation. We have shown that, despite the low number of HSCs in the human AGM region, their self-renewal potential is enormous. A single HSC derived from the AGM region generates around 600 daughter HSCs in primary recipients, which disseminate throughout the entire recipient bone marrow and are retransplantable.

Interpretation

We provide a systematic spatiotemporal analysis of HSC emergence in the early human embryo and identify the AGM region as the primary source of powerful HSCs with enormous self-renewal capacity. This high potency of the first HSCs sets a new standard for in-vitro generation of HSCs from pluripotent stem cells for the purpose of regenerative medicine.

Source: Lancet