Scientists create tiny RNA molecule with big implications for life’s origins

An extremely small RNA molecule created by a University of Colorado at Boulder team can catalyze a key reaction needed to synthesize proteins, the building blocks of life. The findings could be a substantial step toward understanding “the very origin of Earthly life,” the lead researcher contends.

The smallest RNA enzyme ever known to perform a cellular chemical reaction is described in a paper published this week in the Proceedings of the National Academy of Sciences. The paper was written by CU graduate student Rebecca Turk, research associate Nataliya Chumachenko and Professor Michael Yarus of the molecular, cellular and developmental biology department.

Cellular RNA can have hundreds or thousands of its basic structural units, called nucleotides. Yarus’ team focused on a ribozyme — a form of RNA that can catalyze chemical reactions — with only five nucleotides.

Tom Blumenthal, a professor and chair of the MCDB department, noted that Tom Cech, a Nobel laureate and distinguished professor of chemistry and biochemistry at CU, and Professor Norman Pace of MCDB, independently discovered that RNA can act as an enzyme, carrying out chemical reactions. That “pioneering work” has been carried on further by Yarus, Blumenthal said.

Because proteins are complex, one vexing question is where the first proteins came from, Blumenthal said. “It now appears that the first catalytic macromolecules could have been RNA molecules, since they are somewhat simpler, were likely to exist early in the formation of the first life forms, and are capable of catalyzing chemical reactions without proteins being present,” he said.

“In this paper the Yarus group has made the amazing discovery that even an extremely tiny RNA can by itself catalyze a key reaction that would be needed to synthesize proteins,” Blumenthal said. “Nobody expected an RNA molecule this small and simple to be able to do such a complicated thing as that.”

The finding adds weight to the “RNA World” hypothesis, which proposes that life on Earth evolved from early forms of RNA. “Mike Yarus has been one of the strongest proponents of this idea, and his lab has provided some of the strongest evidence for it over the past two decades,” Blumenthal said. …

via U. of Colorado scientists create tiny RNA molecule with big implications for life’s origins.

Remember Magnesium If You Want to Remember

…Begun at MIT, the research started as a part of a post-doctoral project by Dr. Inna Slutsky of TAU’s Sackler School of Medicine and evolved to become a multi-center experiment focused on a new magnesium supplement, magnesium-L-theronate (MgT), that effectively crosses the blood-brain barrier to inhibit calcium flux in brain neurons.

Published recently in the scientific journal Neuron, the new study found that the synthetic magnesium compound works on both young and aging animals to enhance memory or prevent its impairment. The research was carried out over a five-year period and has significant implications for the use of over-the-counter magnesium supplements. … “We are really pleased with the positive results of our studies,” says Dr. Slutsky. “But on the negative side, we’ve also been able to show that today’s over-the-counter magnesium supplements don’t really work. They do not get into the brain.

“We’ve developed a promising new compound which has now taken the first important step towards clinical trials by Prof. Guosong Liu, Director of the Center for Learning and Memory at Tsinghua University and cofounder of Magceutics company,” she says.

While the effects were not immediate, the researchers in the study — from Tel Aviv University, MIT, the University of Toronto, and Tsighua University in Beijing — were able to assess that the new compound shows improved permeability of the blood-brain barrier. After two weeks of oral administration of the compound in mice, magnesium levels in the cerebral-spinal fluid increased.

Toward a more “plastic” brain

“It seems counterintuitive to use magnesium for memory improvement because magnesium is a natural blocker of the NMDA receptor, a molecule critical for memory function. But our compound blocks the receptor only during background neuronal activity. As a result, it enhances the brain’s ‘plasticity’ and increases the number of brain synapses that can be switched on,” says Dr. Slutsky.

“Our results suggest that commercially available magnesium supplements are not effective in boosting magnesium in cerebro-spinal fluid,” she says. “Magnesium is the fourth most abundant mineral in the body, but today half of all people in industrialized countries are living with magnesium deficiencies that may generally impair human health, including cognitive functioning.”

Before the new compound becomes commercially available, Dr. Slutsky advises people to get their magnesium the old-fashioned way — by eating lots of green leaves, broccoli, almonds, cashews and fruit. The effects on memory won’t appear overnight, she cautions, but with this persistent change in diet, memory should improve, and the effects of dementia and other cognitive impairment diseases related to aging may be considerably delayed.

via American Friends of Tel Aviv University: Remember Magnesium If You Want to Remember.

Related: MIT: Magnesium may reverse middle-age memory loss (2004)

Humans to launch genetic attack on insects: Flightless mosquitoes to help control dengue fever

A new strain of mosquitoes in which females cannot fly may help curb the transmission of dengue fever, according to UC Irvine and British scientists.

Dengue fever causes severe flulike symptoms and is among the world’s most pressing public health issues. There are 50 million to 100 million cases per year, and nearly 40 percent of the global population is at risk. The dengue virus is spread through the bite of infected female Aedes aegypti mosquitoes, and there is no vaccine or treatment.

UCI researchers and colleagues from Oxitec Ltd. and the University of Oxford created the new breed. Flightless females are expected to die quickly in the wild, curtailing the number of mosquitoes and reducing – or even eliminating – dengue transmission. Males of the strain can fly but do not bite or convey disease.

When genetically altered male mosquitoes mate with wild females and pass on their genes, females of the next generation are unable to fly. Scientists estimate that if released, the new breed could sustainably suppress the native mosquito population in six to nine months. The approach offers a safe, efficient alternative to harmful insecticides.

Study results appear in the early online edition of the Proceedings of the National Academy of Sciences for the week of Feb. 22. The research is receiving funding support from the Foundation for the National Institutes of Health through the Grand Challenges in Global Health initiative, which was launched to support breakthrough advances for health challenges in the developing world.

“Current dengue control methods are not sufficiently effective, and new ones are urgently needed,” said Anthony James, Distinguished Professor of microbiology & molecular genetics and molecular biology & biochemistry at UCI and an internationally recognized vector biologist. “Controlling the mosquito that transmits this virus could significantly reduce human morbidity and mortality.”

Using concepts developed by Oxitec’s Luke Alphey, the study’s senior author, researchers made a genetic alteration in the mosquitoes that disrupts wing muscle development in female offspring, rendering them incapable of flight. Males’ ability to fly is unaffected, and they show no ill effects from carrying the gene.

“The technology is completely species-specific, as the released males will mate only with females of the same species,” Alphey said. “It’s far more targeted and environmentally friendly than approaches dependent upon the use of chemical spray insecticides, which leave toxic residue.”

“Another attractive feature of this method is that it’s egalitarian: All people in the treated areas are equally protected, regardless of their wealth, power or education,” he added.

James and Alphey have pioneered the creation of genetically altered mosquitoes to limit transmission of vector-borne illnesses. While their current work is focused on the dengue fever vector, they noted that this approach could be adapted to other mosquito species that spread such diseases as malaria and West Nile fever.

via Flightless mosquitoes developed to help control dengue fever.

If we can do this with insects, I wonder if aliens altered the DNA of our early ancestors. Sci Fi ideas: Two different alien factions fought a war on this planet long ago and we are the remains of biological weapons designed by one side.

A midday nap markedly boosts the brain’s learning capacity

If you see a student dozing in the library or a co-worker catching 40 winks in her cubicle, don’t roll your eyes. New research from the University of California, Berkeley, shows that an hour’s nap can dramatically boost and restore your brain power. Indeed, the findings suggest that a biphasic sleep schedule not only refreshes the mind, but can make you smarter.

Conversely, the more hours we spend awake, the more sluggish our minds become, according to the findings. The results support previous data from the same research team that pulling an all-nighter – a common practice at college during midterms and finals –- decreases the ability to cram in new facts by nearly 40 percent, due to a shutdown of brain regions during sleep deprivation.

“Sleep not only rights the wrong of prolonged wakefulness but, at a neurocognitive level, it moves you beyond where you were before you took a nap,” said Matthew Walker, an assistant professor of psychology at UC Berkeley and the lead investigator of these studies.

In the recent UC Berkeley sleep study, 39 healthy young adults were divided into two groups – nap and no-nap. At noon, all the participants were subjected to a rigorous learning task intended to tax the hippocampus, a region of the brain that helps store fact-based memories. Both groups performed at comparable levels.

At 2 p.m., the nap group took a 90-minute siesta while the no-nap group stayed awake. Later that day, at 6 p.m., participants performed a new round of learning exercises. Those who remained awake throughout the day became worse at learning. In contrast, those who napped did markedly better and actually improved in their capacity to learn.

These findings reinforce the researchers’ hypothesis that sleep is needed to clear the brain’s short-term memory storage and make room for new information, said Walker, who is presenting his preliminary findings on Sunday, Feb. 21, at the annual meeting of the American Association of the Advancement of Science (AAAS) in San Diego, Calif. …

- EA

New tool illuminates connections between stem cells and cancer

Researchers have a new tool to understand how cancers grow — and with it a new opportunity to identify novel cancer drugs. They’ve been able to break apart human prostate tissue, extract the stem cells in that tissue, and alter those cells genetically so that they spur cancer.

Owen Witte, a Howard Hughes Medical Institute investigator at the University of California, Los Angeles, will present the findings on February 20, 2010, at the annual meeting of the American Association for the Advancement of Science.

Many tissues contain pools of stem cells that replenish the tissue when it’s damaged or when changes take place. For instance, stem cells in the skin produce new cells to replace those irreparably damaged by the sun, and stem cells in the breast create milk-producing cells when a woman is pregnant. The hallmark of these stem cells is that they self-renew. This means that in addition to making cells with a specific function, they also make many new stem cells.

Mounting evidence suggests that these self-renewing cells are also tied to cancer. They tend to collect mutations, says Witte, and not much separates tumor cells, with their capacity for unchecked growth, from healthy, tissue-forming stem cells. “These cells have a huge capacity for self-renewal, and when the pathways that control self-renewal are augmented or changed, they can form tumors,” says Witte.

Many scientists suspect that although tumors are made up of many cells, only the tumor cells derived from stem cells contribute to the growth of the tumor. For certain cancers, such as breast cancer and leukemia, that idea is well established. For others, such as prostate cancer, which Witte studies, the data are not conclusive.

Witte’s group has been analyzing the relationship between tissue stem cells and cancer stem cells in the prostate. They have been attacking this problem by dividing mouse prostate tissue into its component cell types, culturing those cells, and then reassembling them to understand how they interact. Now, for the first time, they’ve accomplished that feat with human tissue. Importantly, they’ve also engineered specific genetic changes into human prostate stem cells to transform them into cancer cells.

The group is in the early stages of putting the technique to use, but Witte says it offers some distinct advantages for developing new cancer drugs. Cells can be grown directly from a prostate tumor for use in experiments, but without knowing the precise genetics of those cells, scientists may never know why they became cancerous. Drugs that are effective in stopping their growth may not have the same impact on prostate tumors driven by different gene mutations. Starting from prostate stem cells, Witte knows exactly which genetic changes have made a cell cancerous.

“Here you can preprogram the genetic buffet, and then evaluate a compound in the face of those specific changes,” says Witte.

That precision should speed the development of a new generation of fine-tuned cancer therapies. The new system should give scientists a firmer grasp of the genetic makeup of cells that are affected by particular compounds, and by extension, help clinicians identify the drugs that will best help particular patients. “The field of cancer research has produced a significant number of major new targeted therapies,” says Witte. “Now we have to understand how best to use those therapies.”

via New tool illuminates connections between stem cells and cancer.

Somewhat related and interesting:

Dalhousie Medical School cancer researcher Dr. Patrick Lee has proven that a common virus can infect and kill breast cancer stem cells. This breakthrough finding is published in the current issue of Molecular Therapy, the journal of the American Society of Gene Therapy.

It is only within the past few years that the scientific community has understood the full significance of cancer stem cells and the urgent need to find a means of eliminating them.

“Cancer stem cells are essentially mother cells,” explains Dr. Lee, Cameron Chair in Basic Cancer Research at Dalhousie Medical School. “They continuously produce new cancer cells, aggressively forming tumours even when there are only a few of them.”

Cancer stem cells are difficult to kill as they respond poorly to chemotherapy and radiation. As Dr. Lee notes, “You can kill all the regular cancer cells in a tumour, but as long as there are cancer stem cells present, disease will recur.”

Dr. Lee is optimistic that his team has found the key to destroying cancer stem cells. The researchers have recently shown that human reovirus, a common virus that does not cause disease, effectively targets and kills cancer stem cells in breast cancer tissue.

“We suspected that reovirus might be effective against cancer stem cells, because we have shown time and again how well it destroys regular cancer cells,” remarks Dr. Lee, who was the first in the world to discover that a benign and naturally occurring virus could selectively infect and kill cancer cells without harming healthy cells. A Calgary-based company, Oncolytics Biotech Inc., is testing reovirus in clinical trials to prove the treatments are safe and effective. … – sciencedaily (Apr. 9, 2009)

Neuroscientist: Think twice about cutting music in schools

… “People’s hearing systems are fine-tuned by the experiences they’ve had with sound throughout their lives,” says Kraus. “Music training is not only beneficial for processing music stimuli. We’ve found that years of music training may also improve how sounds are processed for language and emotion.”

Researchers in the Kraus lab provided the first concrete evidence that playing a musical instrument significantly enhances the brainstem’s sensitivity to speech sounds. The findings are consistent with other studies they have conducted revealing that anomalies in brainstem sound encoding in some learning disabled children can be improved with auditory training.

The Kraus lab has a unique approach for demonstrating how the nervous system responds to the acoustic properties of speech and music sounds with sub-millisecond precision. The fidelity with which they can access the transformation of the sound waves into brain waves in individual people is a powerful new development.

The neural enhancements seen in individuals with musical training is not just an amplifying or volume knob effect,” says Kraus. “Individuals with music training show a selective fine-tuning of relevant aspects of auditory signals.”

By comparing brain responses to predictable versus variable sound sequences, Kraus and her colleagues found that an effective or well-tuned sensory system takes advantage of stimulus regularities, such as the sound patterns that distinguish a teacher’s voice from competing sounds in a noisy classroom.

They previously found that the ability of the nervous system to utilize acoustic patterns correlates with reading ability and the ability to hear speech in noise. Now they have discovered that the effectiveness of the nervous system to utilize sound patterns is linked to musical ability.

“Playing music engages the ability to extract relevant patterns, such as the sound of one’s own instrument, harmonies and rhythms, from the ‘soundscape,’” Kraus says. “Not surprisingly, musicians’ nervous systems are more effective at utilizing the patterns in music and speech alike.” …

via Neuroscientist: Think twice about cutting music in schools.

Right. Music is essential. It is vitamin M.

PS. I re-posted a few of my older songs tonight (box.net on the left) with some new tweaks.

Genome analysis of marine microbe reveals a metabolic minimalist

Flightless birds, blind cave shrimp, and other oddities suggest a “use it or lose it” tendency in evolution. In the microbial world, an unusual marine microorganism appears to have ditched several major metabolic pathways, leaving it with a remarkably reduced set of genes.

This metabolic minimalist is a specialist uniquely suited to performing one very important function: taking nitrogen gas from the atmosphere and “fixing” it into a form that makes this essential nutrient available to other organisms. Nitrogen fixation fertilizes the oceans, controlling overall biological productivity and thereby affecting how much carbon dioxide the oceans absorb from the atmosphere.

Jonathan Zehr, the marine microbiologist who discovered the microbe, said it has stubbornly resisted efforts to grow it in the laboratory. But that hasn’t stopped his team from determining the complete DNA sequence of its genome. Genome analysis enabled the researchers to reconstruct the organism’s unusual metabolic lifestyle. They published their findings in Nature in a paper available online February 21.

Zehr, a professor of ocean sciences at the University of California, Santa Cruz, characterized the microbe as an atypical member of the cyanobacteria, a group of photosynthetic bacteria formerly known as blue-green algae. Still lacking a formal taxonomic classification, it is known only as UCYN-A. First detected in the open ocean near Hawaii in 1998, it is now known to be periodically abundant in tropical and subtropical waters throughout the world.

“Biogeochemists have never been able to balance the nitrogen budget of the oceans–there seems to be more nitrogen produced than we can account for from known organisms. So this organism may be an important part of the overall nitrogen budget,” Zehr said.

In a 2008 paper in Science, Zehr’s team reported that UCYN-A is completely lacking the genes for a key component of the photosynthetic apparatus <http://press.ucsc.edu/text.asp?pid=2555>. The missing parts, known as photosystem II, carry out the stage in photosynthesis that generates oxygen by splitting water molecules. This is significant because oxygen inhibits nitrogen fixation. Most nitrogen-fixing cyanobacteria carry out photosynthesis during the day and nitrogen fixation at night, but UCYN-A can fix nitrogen all day long.

The new paper extends the list of UCYN-A’s missing metabolic pathways to include, among other things, a process central to aerobic metabolism known as the TCA cycle or Krebs cycle. It also lacks the Calvin cycle, which uses the carbon from carbon dioxide to build sugars, and it is unable to synthesize about half of the 20 essential amino acids.

“This thing is really stripped down,” said James Tripp, a bioinformatics specialist at UCSC and lead author of the Nature paper. “My analysis indicates it has to have an outside source to obtain sugars, amino acids, and two out of the four bases needed to make DNA.” …

via Genome analysis of marine microbe reveals a metabolic minimalist.

It seems I’m Descended from Kings of England

Interesting surprise:  If not for King Henry I of England 32 generations ago, I would not exist.  I do partly have his nose … and his chin according to the Illustration of King Henry I from Cassell’s History of England.

I have a new interest in history now.  My line to him is through “Elizabeth, Princess of England” whose father was King Henry I of England, whose father was also a king. I like the fact that King Henry I had scholarly interests and that he managed to curb abuses of power.

Henry I (c. 1068/1069 – 1 December 1135) was the fourth son of William I the Conqueror. He succeeded his elder brother William II as King of England in 1100 and defeated his eldest brother, Robert Curthose, to become Duke of Normandy in 1106. He was called Beauclerc for his scholarly interests and Lion of Justice for refinements which he brought about in the administrative and legislative machinery of the time.

Henry’s reign is noted for its political opportunism. His succession was confirmed while his brother Robert was away on the First Crusade and the beginning of his reign was occupied by wars with Robert for control of England and Normandy. He successfully reunited the two realms again after their separation on his father’s death in 1087. Upon his succession he granted the baronage a Charter of Liberties, which formed a basis for subsequent challenges to rights of kings and presaged Magna Carta, which subjected the King to law.

The rest of Henry’s reign was filled with judicial and financial reforms. He established the biannual Exchequer to reform the treasury. He used itinerant officials to curb abuses of power at the local and regional level, garnering the praise of the people. The differences between the English and Norman populations began to break down during his reign and he himself married a daughter of the old English royal house. He made peace with the church after the disputes of his brother’s reign, but he could not smooth out his succession after the disastrous loss of his eldest son William in the wreck of the White Ship. His will stipulated that he was to be succeeded by his daughter, the Empress Matilda, but his stern rule was followed by a period of civil war known as the Anarchy.

- wikipedia

I’m also related to the last person to ever to conquer England (Henry I’s father).

“To press his claim to the English crown, William invaded England in 1066, leading an army of Normans, Bretons, Flemish people, and Frenchmen (from Paris and Île-de-France) to victory over the English forces of King Harold Godwinson (who died in the conflict) at the Battle of Hastings, and suppressed subsequent English revolts in what has become known as the Norman Conquest.^[2]

….William’s invasion was the last time that England was successfully conquered by a foreign power.”

I wonder if my late grandfather, a 33rd Degree Freemason, ever knew he was descended from kings. He may have known, but he never mentioned it. He also never mentioned being a Freemason. Not once. I only found out after he passed away.  The only thing he ever said was, “If a man tells you the Freemasons asked him to join them, he is lying. If you have to ask join them, you have to go to them.” I wasn’t even sure why he said it at the time, but it made sense years later.

Myotonic Goats

A fainting goat is a breed of domestic goat whose muscles freeze for roughly 10 seconds when the goat is startled. Though painless, this generally results in the animal collapsing on its side. The characteristic is caused by a hereditary genetic disorder called myotonia congenita. When startled, younger goats will stiffen and fall over. Older goats learn to spread their legs or lean against something when startled, and often they continue to run about in an awkward, stiff-legged shuffle – wikipedia

Tracy, California Residents Now Have To Pay For 911 Calls – cbs13.com

Tracy residents will now have to pay every time they call 9-1-1 for a medical emergency.

But there are a couple of options. Residents can pay a $48 voluntary fee for the year which allows them to call 9-1-1 as many times as necessary.

Or, there’s the option of not signing up for the annual fee. Instead, they will be charged $300 if they make a call for help.

“A $300 fee and you don’t even want to be thinking about that when somebody is in need of assistance,” said Tracy resident Greg Bidlack.

Residents will soon receive the form in the mail where they’ll be able to make their selection. No date has been set for when the charges will go into effect

via Tracy Residents Now Have To Pay For 911 Calls – cbs13.com.

How many people in Tracy, California will die now because they are afraid to make the call?  Tracy City Council: Make your budget cuts elsewhere. File for emergency assistance. Hold a bake sale. You are failing public service.