Genetic Sensor Boosts Biofuel Production

Designer microbes regulate their pathways to optimise fuel production, boosting yields threefold.

• BY SUSAN YOUNG

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Give bacteria a bit of self-awareness and they can be smarter about producing biofuel.  

That's the conclusion from researchers at the University of California, Berkeley, who report a genetic sensor that enables bacteria to adjust their gene expression in response to varying levels of key intermediates for making biodiesel. As a result, the microbes produced three times as much fuel. Such a sensor-regulator system could eventually make advanced biofuels cheaper and bring them closer to being an economically viable replacement to petroleum-based products.

One issue that has limited the amount of biofuels a microbe makes is an imbalance of the different biological ingredients, or precursors, used to make the final fuel product. In a study published this week in Nature Biotechnology, Jay Keasling, professor of chemical engineering and bioengineering at UC Berkeley, and colleagues describe a biological sensor system that lets bacteria regulate genes in its biofuel-production pathways according to the amount of specific precursors in the cell.

The researchers augmented a previously reported strain of engineered E. coli that creates biodiesel from two biological building blocks—fatty acids and ethanol. Over the life cycle of that strain, one precursor can be produced at a higher level than another, an inefficient and sometimes harmful situation.

"The pathways weren't in balance," says Keasling. "The cells were wasting resources producing one precursor at a higher level than another." He says biofuel production would sometimes consume too many fatty acids, which the bacteria need at certain stages of their life cycle, making the strain unstable.

Keasling and coworkers designed a microbe using a naturally occurring sensor that responds to the amounts of internal fatty acids and related molecules and tunes the activity of its pathways accordingly. When limited amounts of fatty acid are in the cell, the sensor-regulator molecules put the brakes on both the ethanol-producing and fatty acid-converting pathways. Conversely, when the bacteria contain higher levels of fatty acids, the brakes on these pathways are released.

The sensor-regulator system improves the engineered bacteria in two ways, says Keasling: the metabolic pathways are better balanced so that one precursor isn't overproduced relative to the other, and the modified bacteria are more stable because the biofuel production isn't robbing the cell of the ability to grow. This "self-awareness" increased the amount of biodiesel made by the bacteria to 28 per cent of the theoretical maximum, a threefold increase over the previously reported strain.  

Although the improvement is significant, biodiesel production still needs to be expanded to bring the fuel into the mainstream. "There are many issues, including metabolic imbalances, that need to be solved to make biofuels a reality," said Keasling in an e-mail. For instance, expanding these largely experimental cultures to a commercial scale—on the order of a million litres—will be a challenge.

While the genetic regulator will not be the only key to opening up the nascent biofuels field, it is an elegant strategy for improving yields, says James Liao, a biomolecular engineer at the University of California, Los Angeles. "The sensor-regulator system will be a handy tool in our current toolbox."

A Miserable Existence

“Those miscreants who are grossly foolish, lowest among mankind, whose knowledge is stolen by illusion, and who partake of the atheistic nature of demons, do not surrender unto Me.” (Lord Krishna, Bhagavad-gita, 7.15) The decision to follow the righteous path in life is made so much easier by the visible behavior of those who follow any other path. As if they were trying to steer us in the right direction on purpose, their actions and demeanor prove that, at the very least, the path recommended by the saintly class of men fulfills a higher immediate destiny, with a calm disposition and a love for humanity engulfing the previously bitter and competitive living entity. From the noticeable dichotomy the sober thinking individual can take a further interest in the enlightened path and make steady progress in that most important endeavor. The importance of the association of saints cannot be overemphasized. The famous Vaishnava poet Goswami Tulsidas prays in his Vinai Patrika to always have the association of the saintly class in whatever birth follows. According to Vedic information, depending on the type of consciousness one has at the time of death, their residence in the next life can be pretty much anywhere. Have a mind concentrated on money, you’ll take birth in circumstances where you can compete with your fellow man to deliver a good or service to the public for the intended result of a profit. While at the moment of quitting the body if you are focused on meeting the base demands of the senses, you’ll be granted birth in an animal species in the subsequent existence, wherein you’ll get to cater to the desires for eating, sleeping, defending and mating without impediment. The saintly class can rescue any person, from any walk of life. Tulsidas points to the examples of Prahlada Maharaja, Valmiki, Jatayu, and a few others to remind the sincere listener of the power of good association. The saintly class has outward features which are definable. A person who doesn’t even know that someone is following the righteous path as a way of life can at least notice that a saint has a unique demeanor. They are kind, sweet, compassionate, instructive and knowledgeable. The most noticeable feature is their equal disposition towards all creatures. “The humble sage, by virtue of true knowledge, sees with equal vision a learned and gentle brahmana, a cow, an elephant, a dog and a dog-eater [outcaste] .”  (Lord Krishna, Bhagavad-gita, 5.18) Why would this feature stand out? How many people do you know that treat a stranger just as well as they treat a friend? How many people view the cat, the dog, the elephant, the learned sage and the dog-eater as being equal on a spiritual level? The visible variety in outward forms makes acquiring the equal vision of a saint very difficult. For starters, why would we treat something as wild as a tiger the same as a human baby? They have very different inclinations. A tiger will jump at the chance to kill you, while the infant human is the essence of innocence. The saint isn’t a sentimentalist who irrationally follows gentleness under all circumstances. Rather, real kindness is defined by showing compassion upon creatures and knowing what will benefit them in the future. The tiger does not have the ability to accept sober instruction on the meaning of life. Though the tiger is a spirit soul at the core, because of the features it assumed at the time of birth, its potential for knowledge gathering is limited. The human being, on the other hand, can mature to the point that it can take instruction from others and be benefitted from those kind words of advice. The saint proves to be beneficial in all circumstances. They may not always preach openly with their words, but they configure their actions to meet the situation at hand, finding a way to help others with their association. With Prahlada, the association of Narada while within the womb helped him to be devoted to God right from the time of birth. Valmiki was a highway robber who stole for a living, but through the association of Narada he was transformed into a staunch devotee whose heart was so pure that he could author the wonderful Ramayana, a poem which chronicles the life and pastimes of Lord Rama. Birth after birth, the association of the saints is so valuable that it is equivalent to having God’s direct company. In one sense the saints are no different than God, for they chant His names all the time, “Hare Krishna Hare Krishna, Krishna Krishna, Hare Hare, Hare Rama Hare Rama, Rama Rama, Hare Hare”. They have the Lord on the mind all the time, so naturally that consciousness will influence their behavior. People who have the association of such a spiritually enriched person can only find benefits. The saints also know the true meaning of advaita. The Sanskrit term means “non-dual”, so one who understands it knows that God pervades all of space. We say that God is not personally present in a particular area because of our limitations. The sun sets at night, but it does not disappear. The position of the earth has changed, and because our sense perceptions are limited, we are no longer able to see the sun. This lasts for only a brief period, until the next morning. “O son of Kunti [Arjuna], I am the taste of water, the light of the sun and the moon, the syllable om in the Vedic mantras; I am the sound in ether and ability in man.”  (Lord Krishna, Bg. 7.8) With the Supreme Lord, His influence is felt in the nature at large. He is the taste of water, the sound in ether, and the original fragrance of the earth. The results of the actions of the individual are delivered by God in His unmanifest form, which pervades the space as Brahman and also lives locally within the heart of every creature as the Supersoul. The saints understand this presence, so at every second they are seeing the divine. More than just trying to get a glimpse of Him for a moment and then proclaiming life to be a success, the saints take the sight of God as fuel for their actions. They notice His presence everywhere and then use that vision to make every place a playing field for devotional activities; this is the true meaning to advaita. But how do we know that the saints are correct? What if they just have good qualities but are actually following a bogus system of spirituality? Thankfully for us, the people who don’t follow the purported righteous path are full of bad qualities. Thieves, liars and cheats may outwardly claim to be religious, but based on their behavior we know that they have no understanding of advaita. Even if they should openly profess to follow spirituality, donning the garb of a saint, based on their miserable disposition, their utter hatred for humanity, and the lack of any positive influence they have on others, we know that their knowledge of the highest matters of spiritual life is lacking. If you were to make an honest comparison between the saint and the atheist, you’d see that the saint is calm and peaceful, while the atheist is always in angst. They are never happy about their condition, even if they should have millions of dollars in the bank. They come up with their own philosophies for what the meaning of life should be. Perhaps they want to give money to the poor or open hospitals; thus essentially admitting that only some people are worthy of help. The fact that money doesn’t bring happiness to the rich person is overlooked, for the belief is that if the well-off aren’t doing so well mentally, it’s their fault. “They probably deserve it for having exploited others, preventing them from acquiring wealth.” The concept of hating your country or community can only come through ignorance of the all-pervasiveness of spirit. Spirit is also glorious in its attributes. The Supreme Spirit is full of bliss, eternality and knowledge, and those features are inherited by His innumerable sparks that roam this and many other lands. If you hate your country, you’re essentially saying that you dislike your neighbors. The person who lives next to you is part of your country. The people you run into in the supermarket and restaurants are your community. If you have blanket hatred for them you are not very intelligent, for you know nothing about them. “They believe that to gratify the senses unto the end of life is the prime necessity of human civilization. Thus there is no end to their anxiety. Being bound by hundreds and thousands of desires, by lust and anger, they secure money by illegal means for sense gratification.”  (Lord Krishna, Bg. 16.11-12) The atheist doctrine is to gratify the senses as much as possible before death comes, for the afterlife is considered just a mythical concept concocted by spiritualists who couldn’t deal with death. But the flaw with this logic is that the life of hedonism proves to be miserable. If more drinking and gambling were the answer to life’s problems, the entire world today would be filled with happy people. The society at large would embody good qualities, the fraternal spirit. We see that just the opposite is true, as with each foray into sense gratification, the senses become conditioned to temporary happiness. So the next time it will take more sense gratification to reach satiation. Then there is the competition factor. Others are also struggling to find that happiness, so you better get “yours” before someone else takes it from you. Contrast this with the life of the saint. He lives peacefully, with very little, and stays in a neutral position mentally. He has high regard for every single creature. He doesn’t only pity the destitute human being for their materially impoverished condition. Rather, every living entity has the potential to acquire the divine qualities, to know and learn about God and use that knowledge to better their condition. Just looking at the two results, we see that the saints are superior. If we’re comparing the outcomes as a type of experiment, there is no question that the test case of atheism brings inferior results. Who would want to be miserable all day? Who would want to increase their hatred of humanity as they matured through life? Who would want to grow old and be stuck with boring activities that don’t take you any place meaningful? The saint grants the benediction of God’s association through a variety of mediums. The holy name is the entry point and also the solid foundation for the spiritually enlivened soul. That name is the true wealth of the saints, who hold on to it for dear life. The example of the atheist and the dichotomy they create helps to clear up the right choice in life. The greatest skeptic of religion still is interested in meeting a beneficial end, a future condition that is positive. By taking the association of the saints and learning from their behavior, the immediate aftermath is a kinder, gentler and wiser person. The reward of God’s permanent association in the afterlife is the mature fruit that results from steady practice in bhakti-yoga, which only brings increased happiness with each passing day. In Closing: To have an existence should be pleasurable, But without acknowledging God life miserable. Atheist divine consciousness they live without, Days then filled with misery, worry and doubt. Saints, on the other hand, always at peace, With equal vision, duality and anger cease. Make an experiment, do a visible test, Results will tell you which method is best. With their behavior saints show what is right, Bhakti under guidance to reach bliss’s height.

OM SAI RAM........

__._,_.___

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Awesome Computer Mouse!

Rare cells key to immune system

[White blood cells in the blood stream. The recently characterised immune cell may help the immune system to 'remember' an attacker. Image: Henrik5000/iStockphoto The characterisation of a rare immune cell’s involvement in antibody production and ability to ‘remember’ infectious agents could help to improve vaccination and lead to new treatments for immune disorders, say researchers from the Walter and Eliza Hall Institute. The cells, called T follicular helper cells, represent less than half of one per cent of all immune cells, but play a critical role in antibody production and developing long-lasting immunity. However, the cells are also dramatically increased in chronic inflammatory disease, suggesting that they could be a therapeutic target for treating these diseases. The research team, led by Dr Katja Lüthje and Associate Professor David Tarlinton, from the institute’s Immunology division, and Dr Stephen Nutt from the institute’s Molecular Immunology division, discovered a means of identifying the rare T follicular helper cells while they are actually involved in instructing the immune response, revealing for the first time the possible fates of these cells. The research was published today in the journal Nature Immunology. Dr Lüthje said the research team discovered T follicular helper cells were essential for developing strong and specific antibody responses to infectious agents. “Antibodies are fundamental to the body’s defence against infection,” Dr Lüthje said. “Antibody production critically relies on the interaction of two cell types: B cells that produce antibody, and helper T cells that recruit and ‘teach’ the B cells how to respond to infectious agents. In this study, we used a special fluorescent protein to help identify exactly which cells were involved in the process, and discovered that, amongst the rare T follicular helper cells, only a subset were actively involved in instructing B cells in antibody production.” Dr Nutt said that one of the key findings made by the research team was that T follicular helper cells can remember being exposed to infectious agents, allowing them to rapidly react to subsequent attacks. “The success of vaccines relies on antibody production and long-term immune ‘memory’; without these, most routinely-used vaccines, including measles, mumps and tetanus, do not work,” Dr Nutt said. “It is well established that antibody-producing B cells can remember a particular infectious agent and rapidly respond if and when they come across it again. Our study shows, for the first time, that T follicular helper cells also develop memory to rapidly respond to infection.” “This finding is incredibly important for the development of vaccines, which relies on immune memory to prevent subsequent infections,” Dr Nutt said. “Some vaccines, such as polio are very effective at establishing long-term immunity, while others, such as the cholera vaccine are not particularly effective and need ongoing boosters. It may be that the vaccines are not establishing good T follicular helper cell memory, and this could be something to look at for developing new vaccines for diseases that currently do not have good preventive treatments.” Associate Professor Tarlinton said another key finding was that T follicular helper cells show a remarkable flexibility in their role in immunity. “We found that T follicular helper cells are pretty flexible, adapting to carry out several different functions depending on where they are needed,” he said. He said the research team also discovered that T follicular helper cell numbers are tightly controlled by the immune system, which might explain why increases in their numbers are associated with chronic inflammatory diseases, which include rheumatoid arthritis, type 1 diabetes, lupus and multiple sclerosis. “In some models, a large increase in the numbers of T follicular helper cells is associated with the development of chronic inflammatory, or what we call autoimmune, diseases in which the immune system attacks its own tissues,” Associate Professor Tarlinton said. “In fact, it has been found that T follicular helper cells, in mouse models, were actually the cause of an autoimmune disease very much like lupus in humans. This suggests that modulating these cells could be a potential treatment for autoimmune conditions.” The research was supported by the National Health and Medical Research Council of Australia, the Sylvia and Charles Viertel Foundation, the German Academic Exchange Service, Pfizer Australia Research, the Australian Research Council and the Victorian Government. Editor's Note: Original news release can be found here.

New breast cancer gene found

The discovery was made using new genetic sequencing technology, which could help scientists to find other cancer genes. Image: cosmin4000/iStockphoto An international team of researchers led by the University of Melbourne has used new technology to fast track the discovery of a breast cancer risk gene which could assist in the discovery of other cancer genes. Professor Melissa Southey of the Genetic Epidemiology Laboratory, Department of Pathology at the University of Melbourne, who led the study, said it was a significant discovery and the first breast cancer risk gene to be discovered using the latest genetic sequencing technology. “The mutations in the newly identified gene XRCC2, although rare, explain another proportion of breast cancers that run in families where there is no known genetic cause and that particularly occur at an early age,” she said. “We identified this gene quite quickly using genetic technology called massively parallel sequencing, which enables sequencing of large amounts of human DNA at high speed.’ “Due to these results and our methodology we believe that further breast cancer risk genes will be identified at a faster rate than before and potentially for other cancers such as colorectal and prostate cancers,” she said. Professor Southey said the discovery could help manage the risk of breast cancer for families with a strong history of the disease and no known genetic cause. “This discovery will assist some families to determine individual risk and which family members are at high risk of contracting the disease,” Professor Southey said. “Unaffected relatives of people with a mutation in this gene could also be offered predictive testing, subsequent genetic counselling and ongoing clinical management on the basis of their mutation status.’ “People whose breast cancer is associated with XRCC2 mutations could also benefit from specific treatments that target the genetic fault,” she said. Currently, only about 30 per cent of the familial risk for breast cancer has been explained, leaving the substantial majority still unaccounted for. “Research indicates that no single gene is likely to account for a large proportion of the remaining unexplained genetic susceptibility to breast cancer,” Professor Southey said. “Although mutations in XRCC2 are rare, it is most likely that the remaining unknown breast cancer susceptibility genes will account for similar small proportions of the disease.” Initially, using massively parallel sequencing, researchers identified XRCC2 mutations in two families (in Melbourne and the Netherlands). This was followed by a larger series of studies using DNA from blood samples of 689 families with multiple members affected by breast cancer, and from 1308 women who were affected at an early age by breast cancer and recruited from the general population, as well as 1120 controls. More XRCC2 mutations were detected in the breast cancer cases but not in the controls. These additional studies were conducted in Melbourne and at the International Agency for Research on Cancer (IARC) in France. Co-first author Dr Daniel Park of the University’s Department of Pathology (with Dr Fabienne Lesueur of IARC) said the study demonstrated the power of massively parallel sequencing for discovering susceptibility genes for common, complex diseases like breast cancer. “Our study approach could be applied to many other common, complex diseases with components of unexplained heritability, such as colorectal and prostate cancers,” he said. Professor Southey oversaw this work with two long-standing collaborators and experts in the field of breast cancer genetics, Associate Professor Sean Tavtigian and Professor David Goldgar at the University of Utah. The research was conducted in a large collaborative network including researchers from the Huntsman Cancer Institute, The University of Utah, USA, The Breast Cancer Family Registry, Australia, the Victorian Life Sciences Computation Initiative, hosted by The University of Melbourne, The International Agency for Research on Cancer, France, The Kathleen Cuningham Foundation Consortium for Research into Familial Breast Cancer and The Cancer Council Victoria, Australia. The work was supported by The Cancer Council Victoria, The National Institutes of Health (USA) and the National Health and Medical Research Council of Australia. The study was published in the American Journal of Human Genetics. For information about counselling and genetic testing in Australia contact Cancer Council Helpline on 13 11 20. Editor's Note: Original news release can be found here.

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