Welcome To Matt Warren's Wiki!


First Bio PostLife is the ultimate example of complexity at work. An organism, whether it is a bacterium or a baboon, develops through an incredibly complex series of interactions involving a vast number of different components. These components, or subsystems, are themselves made up of smaller molecular components, which independently exhibit their own dynamic behavior, such as the ability to catalyze chemical reactions. Yet when they are combined into some larger functioning unit--such as a cell or tissue--utterly new and unpredictable properties emerge, including the ability to move, to change shape and to grow.

Although researchers have recognized this intriguing fact for some time, most discount it in their quest to explain life¿s fundamentals. For the past several decades, biologists have attempted to advance our understanding of how the human body works by defining the properties of life's critical materials and molecules, such as DNA, the stuff of genes. Indeed, biologists are now striving to identify every gene in the complete set, known as the genome, that every human being carries. Because genes are the "blueprints" for the key molecules of life, such as proteins, this Holy Grail of molecular biology will lead in the near future to a catalogue of essentially all the molecules from which a human is created. Understanding what the parts of a complex machine are made of, however, does little to explain how the whole system works, regardless of whether the complex system is a combustion engine or a cell. In other words, identifying and describing the molecular puzzle pieces will do little if we do not understand the rules for their assembly.
With understanding the natural pattern of construction from carbon models to tissue, we could fully put cloning and other cell research to full use. Perhaps to replicate it and produce an entirely synthetic species!Ingber. (1998, January 1). The architecture of life. Scientific American Magazine, Retrieved from http://www.sciamdigital.com/index.cfm?fa=Products.ViewIssuePreview&ARTICLEID_CHAR=E0933DE8-00FC-49CA-ABA0-E4EE1F88D0E
Post 2 - Apoptosis:
external image induction.jpg
There are a number of mechanisms through which apoptosis can be induced in cells. The sensitivity of cells to any of these stimuli can vary depending on a number of factors such as the expression of pro- and anti-apoptotic proteins (eg. the Bcl-2 proteins or the Inhibitor of Apoptosis Proteins), the severity of the stimulus and the stage of the cell cycle. Some of the major stimuli that can induce apoptosis are outlined in the illustration beside.
In some cases the apoptotic stimuli comprise extrinsic signals such as the binding of death inducing ligands to cell surface receptors called death receptors. These ligands can either be soluble factors or can be expressed on the surface of cells such as cytotoxic T lymphocytes. The latter occurs when T-cells recognise damaged or virus infected cells and initiate apoptosis in order to prevent damaged cells from becoming neoplastic (cancerous) or virus-infected cells from spreading the infection. Apoptosis can also be induced by cytotoxic T-lymphocytes using the enzyme granzyme.
In other cases apoptosis can be initiated following intrinsic signals that are produced following cellular stress. Cellular stress may occur from exposure to radiation or chemicals or to viral infection. It might also be a consequence of growth factor deprivation or oxidative stress caused by free radicals. In general intrinsic signals initiate apoptosis via the involvement of the mitochondria. The relative ratios of the various bcl-2 proteins can often determine how much cellular stress is necessary to induce apoptosis.

external image apoptosis.jpg

Post #3


Geneticist Richard Cawthon and colleagues at the University of Utah found shorter telomeres are associated with shorter lives. Among people older than 60, those with shorter telomeres were three times more likely to die from heart disease and eight times more likely to die from infectious disease.
Dr. Richard Cawthon
Dr. Richard Cawthon
Dr. Richard Cawthon

While telomere shortening has been linked to the aging process, it is not yet known whether shorter telomeres are just a sign of aging - like gray hair - or actually contribute to aging.
If telomerase makes cancer cells immortal, could it prevent normal cells from aging? Could we extend lifespan by preserving or restoring the length of telomeres with telomerase? If so, does that raise a risk the telomerase also will cause cancer?
Scientists are not yet sure. But they have been able to use telomerase to make human cells keep dividing far beyond their normal limit in laboratory experiments, and the cells do not become cancerous.
If telomerase could be used routinely to "immortalize" human cells, it would be theoretically possible to mass produce any human cell for transplantation, including insulin-producing cells to cure diabetes patients, muscle cells for muscular dystrophy, cartilage cells for people with certain kinds of arthritis, and skin cells for people with severe burns and wounds. Efforts to test new drugs and gene therapies also would be helped by an unlimited supply of normal human cells grown in the laboratory.

Could telomere research lead to an end to cancer and human aging? The future looks promising, but it will take many more years to put this theory into a tested product.

Genetic Science Learning Center (2011, January 24) Are Telomeres the Key to Aging and Cancer?. Learn.Genetics. Retrieved March 29, 2011, from http://learn.genetics.utah.edu/content/begin/traits/telomeres/

Post #4

Immune system actors map a perfect route in simple version of math dilemma external image 1552804.jpg

Forget GPS. With no fancy maps or even brains, immune system cells can solve a simple version of the traveling salesman problem, a computational conundrum that has vexed mathematicians for decades.

The new research, which simulates how a type of white blood cell seeks and destroys infectious particles, shows how living things — be they cells, sharks or bees — successfully find a target, with only limited information and even more limited cognitive skills.

“Some search strategies are perhaps not the best, but they make the whole exploration of a space very efficient,” says theoretical ecologist Frederic Bartumeus of the Spanish Council for Scientific Research’s Centre for Advanced Studies of Blanes.

While some of the best mathematical minds have been tackling the traveling salesman problem for decades and some have found efficient solutions, no one has figured out how to completely solve the puzzle: For a given number of cities, a traveling salesman must plan a route that visits each city once, covering the minimum possible overall distance. A pencil and paper and brute force can find the shortest route when there aren’t a lot of target cities. But fancy algorithms and serious computing power are usually needed when the number of targets reaches mere double digits. The new research, to appear in an upcoming Physical Review E, shows that when there aren’t a lot of targets, cells do a pretty good job of finding the shortest possible route that hits all the targets. These cells “search” by tuning into local concentrations of chemical signals and following the signals to the nearest target. Repeating that process allows immune cells to find and demolish numerous invaders.
“You can do pretty well by following your nose,” says mathematical biologist Andy Reynolds, who did the new work. “There’s no need to know where all of the other sites are or to have the means to figure out which one is the nearest one.”

Using the follow-your-nose-strategy, a process of moving in response to chemical gradients known as chemotaxis, an immune cell seeking five different targets will find a perfect traveling salesman route, show computer simulations by Reynolds, a scientist at the Biotechnology and Biological Sciences Research Council’s Rothamsted Research institute, in Harpenden, England. With 10 targets, the cells were still pretty efficient: on average, their routes were only 12 percent longer than the shortest possible path. These routes were comparable to the solutions calculated by a computer algorithm.

Currently, when there are many target cities, the best way to tackle the traveling salesman problem is a tool called linear programming, says William Cook, an expert in computational mathematics at Georgia Tech in Atlanta. This method finds a lower bound — a distance the minimum route can’t be shorter than — which can then guide the search for a short route. Routes that have 1,000 cities or fewer can be easily solved with this method. But when you add cities to your route, the number of calculations required to find the shortest path increases exponentially, and scientist still don’t have one clean algorithm that can crunch the numbers, no matter how many cities, and find the shortest route. In fact, researchers don’t even know if such a solution is out there. (The Clay Mathematics Institute in Cambridge, Mass., offers $1,000,000 to anyone who can come up with this solution or prove that it does not exist.)

Tackling the traveling salesman problem with chemotaxis is a nice example of when the suboptimal is optimal, says Bartumeus. Of course with all the information, time and resources in the world, thorough, systematic searches are ideal. But such situations rarely exist and perfect can’t be the enemy of good. Increasingly there are examples of organisms using suboptimal strategies, such as chemotaxis or a search pattern known as a Lévy walk (SN: 6/15/10, p. 15), or a combination of both strategies, which work best for the nonideal situations in which they exist.

By applying similar simple strategies, scientists are coming up with efficient ways to find all kinds of things, Bartumeus notes, like the source of a swirling plume of chemicals in a river, or even a child who has gone missing in a neighborhood of tangled, narrow streets.external image chemotaxis.jpgEhrenberg, Rachel,. (2011, April 18). Cells take on traveling salesman problem. Science News, Retrieved from http://www.sciencenews.org/view/generic/id/72472/title/Cells_take_on_traveling_salesman_problem

Post # 5 Bacterial Camera

A dense bed of light-sensitive bacteria has been developed as a unique kind of photographic film. Although it takes 4 hours to take a picture and only works in red light, it also delivers extremely high resolution.
The "living camera" uses light to switch on genes in a genetically modified bacterium that then cause an image-recording chemical to darken. The bacteria are tiny, allowing the sensor to deliver a resolution of 100 megapixels per square inch.external image dn8365-1_250.jpg
To make their novel biosensor, Chris Voigt's team at the University of California in San Francisco, US, chose E. Coli, the food-poisoning gut bacterium. One of the reasons for that choice is that E. Coli does not normally use light - photosynthesizing bacteria could have used light to prompt other, unwanted, biological processes.
The researchers used genetic engineering techniques to shuttle genes from photosynthesising blue-green algae into the cell membrane of the E. coli. One gene codes for a protein that reacts to red light. Once activated, that protein acts to shut down the action of a second gene. This switch-off turns an added indicator solution black.
external image bacteria3.jpgAs a result , a monochrome image permanently "printed" on a dense bed of the modified E. Coli.

The UCSF team are now working on expanding the colour range of their sensor, perhaps using retinol, a substance which helps the human retina to sense a wide range of colours.
As a method of nano-manufacturing, the biocamera is an "extremely exciting advance" says Harry Kroto, the Nobel prize-winning discoverer of buckminsterfullerene, or buckyballs. "I have always thought that the first major nanotechnology advances would involve some sort of chemical modification of biology."
Marks, P. (2005). Living camera uses bacteria to capture image. NewScientist, 438. Retrieved from http://www.newscientist.com/article/dn8365-living-camera-uses-bacteria-to-capture-image.html

Post #6

Un-likely Proteins are Found to be the Key in Artificial Chromosome Synthesis

CAMBRIDGE, Mass. (April 28, 2011) – Whitehead Institute scientists report that two proteins, once thought to have only supporting roles, are the true "stars" of the kinetochore assembly process in human cells.

The kinetochore is vital to proper DNA distribution during cell division. This finding suggests that scientists may be able to stimulate kinetochore assembly in a process that could lead to new genetic research tools, such as efficient creation of artificial human chromosomes. external image ANA_CentromerAK_HEp2.jpg

"When you understand a process really well, then it can become a tool. And I think this is a nice example of that," says Whitehead Member Iain Cheeseman. "We now fundamentally understand something about the way kinetochore specification and assembly works. And because we understand that, now one could imagine it being used as a tool."
For many years scientists have understood the kinetochore's role in cell division but did not know how its individual parts came together during this process. At the beginning of cell division, the kinetochore consists of a few proteins associated with a chromosome's centromere, which is the section where the arms of an X-shaped chromosome join. As cell division progresses, additional kinetochore proteins attach at the centromere, ultimately forming a complete kinetochore complex consisting of about 100 proteins. At this point, one kinetochore is partially integrated into each lengthwise half of the chromosome, called a sister chromatid; a chromosome's sister chromatids are identical copies of the same piece of DNA.

To distribute the sister chromatids between the two future cells, long protein filaments from opposite sides of the cell reach out, latch onto the chromatids' kinetochores, and begin pulling on them until the sister chromatids split apart. Then, the chromatids are dragged to opposite sides of the cell, ensuring that the future cells will each have a copy of this piece of DNA.

external image dellaval.jpgTo identify which proteins are necessary for a kinetochore to self-assemble, Karen Gascoigne, a postdoctoral researcher in the Cheeseman lab, positioned three of them on the chromatids' DNA and away from their normal location on the centromere. By moving the proteins away from their normal position, Gascoigne isolated the effects of each protein from potential interactions with the centromere and highlighted the capabilities attributable only to that protein.
The first protein, called CENP-A, is essential for identifying where the kinetochore should locate, and many scientists thought it was vital to kinetochore assembly. However, when Gascoigne moved CENP-A away from the centromere, only a few kinetochore components were recruited to attach onto CENP-A, showing that this protein is not responsible for assembling an entire kinetochore.

When Gascoigne moved the proteins CENP-C and CENP-T away from the centromere, the two proteins attracted almost all of the kinetochore proteins to their location and fostered assembly of a makeshift kinetochore capable of separating sister chromatids.

"So that tells us that these two proteins are essential and sufficient to build the kinetochore even in the absence of CENP-A," says Gascoigne, who reports her findings in the April 29 issue of Cell. "Which is unexpected and very exciting. This tells us a lot about how kinetochores are put together in the cell."
This new ability to form a kinetochore anywhere on DNA may be particularly useful for creating artificial human chromosomes. These collections of genes could be used in research to insert new genes into a cell. Currently, scientists insert genes by infecting cells with a virus that haphazardly inserts the DNA into the cells' genomes, a process that can corrupt essential genes and possibly kill cells.

Artificial chromosomes circumvent this potential damage. But their widespread use is thwarted by scientists' current inability to outfit artificial chromosomes with kinetochores. Without kinetochore complexes for those long protein filaments to latch onto during cell division, the artificial chromosomes cannot be passed from the original cells to subsequent generations, meaning that the artificial chromosomes' traits are lost.

By perfecting kinetochore assembly using just CENP-C and CENP-T, Gascoigne is working to overcome this shortcoming in artificial human chromosomes. This is essential in many medical research fields for diseases like down-syndrome and stem cell research. Maybe these 2 little proteins will someday be the cause of a disease that will be forever cured. Giese, N. (2011). two unsuspected proteins may hold the key to creating artificial chromosomes. Whitehead Institute for Biomedical Research, Retrieved from http://www.wi.mit.edu/news/archives/2011/ic_0428.html
Post #7

Scientists at UCSB Discover 600 Million-Year-Old Origins of Vision
external image hydra-01.jpg
(Santa Barbara, Calif.) –– By studying the hydra, a member of an ancient group of sea creatures that is still flourishing, scientists at UC Santa Barbara have made a discovery in understanding the origins of human vision. The finding is published in this week's issue of the Proceedings of the Royal Society B, a British journal of biology.
Hydra are simple animals that, along with jellyfish, belong to the phylum cnidaria. Cnidarians first emerged 600 million years ago.

"We determined which genetic ‘gateway,' or ion channel, in the hydra is involved in light sensitivity," said senior author Todd H. Oakley, assistant professor in UCSB's Department of Ecology, Evolution and Marine Biology. "This is the same gateway that is used in human vision."
Oakley explained that there are many genes involved in vision, and that there is an ion channel gene responsible for starting the neural impulse of vision. This gene controls the entrance and exit of ions; i.e., it acts as a gateway.

The gene, called opsin, is present in vision among vertebrate animals, and is responsible for a different way of seeing than that of animals like flies. The vision of insects emerged later than the visual machinery found in hydra and vertebrate animals.

"This work picks up on earlier studies of the hydra in my lab, and continues to challenge the misunderstanding that evolution represents a ladder-like march of progress, with humans at the pinnacle," said Oakley. "Instead, it illustrates how all organisms –– humans included –– are a complex mix of ancient and new characteristics."
David Plachetzki, who received his Ph.D. for work done in the Oakley lab, is the first author. Plachetzki is now a postdoctoral fellow at UC Davis. UCSB undergraduate Caitlin R. Fong is the second author of the paper.

This mixture of old and new is present in almost every aspect of life. It's funny how a n almost microscopic Hydrazoan can reveal wonders of nature such as sight.

Gallessich, G. (2011, 05 10). Scientists at ucsb discover 600 million-year-old origins of vision . Royal Society B, Retrieved from http://insciences.org/article.php?article_id=8513

Post #8
Parasitic Wasps

There are certains species of wasps with an unusual reproductive methods. They're in the class hymenoptera and they bring chills to my spine. Adults of many species are very small (ranging from 1/100 to 3/4 inch long) and often go unnoticed. They vary in shape and coloration but usually have long, thread-like (filiform) antennae or they may appear elbowed, clear or colored wings with characteristic venation and a narrow "waist" between the thorax and abdomen. Females of many species have a spine-like egg-laying structure (ovipositor) at the tip of the abdomen. Larval stages are usually not observed unless they are dissected from hosts (internal parasites) or detected on the host (external parasites). They are usually cream colored, legless and tapered at both ends. Occasionally, caterpillars are observed with white silken cocoons of parasites (Braconidae) attached to their bodies.

They use their ovipositor to inject zygotes into the host caterpiller and for 2 weeks, they grow and eat tissues in the caterpillar until they use their newly developed jaws to eat their way out. While doing so they release chemicals that paralyze the host and then spin a silken cocoon around themselves to undergo their final life stage.

The caterpillar than protects the cocoons by weaving a silken blanket around it and protecting it from predators until it dies of starvation.

Jackman, John. Feild Guide To Texas Insects. Houston, Texas: Gulf Publishing Company, 1999. Print.

Post #9

Deadly bacteria may be evolving antibiotic resistance by mimicking human proteins, according to a new study by the Translational Genomics Research Institute (TGen).

This process of "molecular mimicry" may help explain why bacterial human pathogens, many of which were at one time easily treatable with antibiotics, have re-emerged in recent years as highly infectious public health threats, according to the study published May 26 in the journal Public Library of Science (PLoS) One.

"This mimicry allows the bacteria to evade its host's defense responses, side-stepping our immune system," said Dr. Mia Champion, an Assistant Professor in TGen's Pathogen Genomics Division, and the study's author.

Using genomic sequencing, the spelling out of billions of genetic instructions stored in DNA, the study identified several methyltransferase protein families that are very similar in otherwise very distantly related human bacterial pathogens. These proteins also were found in hosts such as humans, mouse and rat.

Researchers found methyltransferase in the pathogen Francisella tularensis subspecies tularensis, the most virulent form ofexternal image Histamine_n-methyltransferase.png Francisella. Just one cell can be lethal. Methyltransferase is a potential virulence factor in this pathogen, which causes Tularemia, an infection common in wild rodents, especially rabbits, that can be transmitted to humans though bites, touch, eating or drinking contaminated food or water, or even breathing in the bacteria. It is severely debilitating and even fatal, if not treated.

external image MTBCDC.jpgSimilar methyltransferase proteins are found in other highly infectious bacteria, including the pathogen Mycobacterium tuberculosis that causes Tuberculosis, a disease that results in more than 1 million deaths annually. The study also identified distinct methyltransferase subtypes in human pathogens such as Coxiella, Legionella, and Pseudomonas.

In general, these bacterial pathogens are considered "highly clonal," meaning that the overall gene content of each species is very similar. However, the study said, "The evolution of pathogenic bacterial species from nonpathogenic ancestors is … marked by relatively small changes in the overall gene content."

Genomic comparisons were made with several strains of the bacteria, as well as with plants and animals, including humans. The methyltransferase protein also was found to have an ortholog, or similar counterpart, in human DNA. Although the overall sequence of the orthologs is highly similar, the study identifies a protein domain carrying distinct amino acid variations present in the different organisms.

"Altogether, evidence suggests a role of the Francisella tularensis protein in a mechanism of molecular mimicry. Upon infection, bacterial pathogens dump more than 200 proteins into human macrophage cells called 'effector proteins.' Because these proteins are so similar to the human proteins, it mimics them and enables them to interfere with the body's immunity response, thereby protecting the pathogen,'' Dr. Champion said.

"These findings not only provide insights into the evolution of virulence in Francisella, but have broader implications regarding the molecular mechanisms that mediate host-pathogen relationships," she added.
Identifying small differences between the pathogen and human proteins through Next Generation genome-wide datasets could help develop molecular targets in the development of new drug treatments, she said.

TGen, . "http://www.biologynews.net/archiDeadly bacteria may mimic human proteins to evolve antibiotic resistance." Biology News Net (2011): n. pag. Web. 9 Jun 2011. <http://www.biologynews.net/archives/2011/06/01/deadly_bacteria_may_mimic_human_proteins_to_evolve_antibiotic_resistance.html>.

Post #10

Researchers have discovered that the ultraviolet (UV) light that causes the temporary but painful condition of snow blindness in humans is life-saving for reindeer in the arctic.

A BBSRC-funded team at UCL has published a paper today (12 May) in the Journal of Experimental Biology that shows that this remarkable visual ability is part of the reindeer's unique adaptation to the extreme arctic environment where they live. It allows them to take in live-saving information in conditions where normal mammalian vision would make them vulnerable to starvation, predators and territorial conflict. It also raises the question of how reindeer protect their eyes from being damaged by UV, which is thought to be harmful to human vision.

Lead researcher Professor Glen Jeffery said "We discovered that reindeer can not only see ultraviolet light but they can also make sense of the image to find food and stay safe. Humans and almost all other mammals could never do this as our lenses just don't let UV through into the eye.external image 070313-reindeer-eyes_170.jpg

"In conditions where there is a lot of UV – when surrounded by snow, for example – it can be damaging to our eyes. In the process of blocking UV light from reaching the retina, our cornea and lens absorb its damaging energy and can be temporarily burned. The front of the eye becomes cloudy and so we call this snow blindness. Although this is normally reversible and plays a vital role to protect our sensitive retinas from potential damage, it is very painful."

Human beings are able to see light with wavelengths ranging from around 700nm, which corresponds to the colour red, right through all the colours of the rainbow in sequence to 400nm, which corresponds to violet. Professor Jeffery and his team tested the reindeer's vision to see what wavelengths they could see and found that they can handle wavelengths down to around 350-320nm, which is termed ultraviolet, or UV, because it exceeds the extreme of the so-called visible spectrum of colours.

The winter conditions in the arctic are very severe; the ground is covered in snow and the sun is very low on the horizon. At times the sun barely rises in the middle of the day, making it dark for most of the time. Under these conditions light is scattered such that the majority of light that reaches objects is blue or UV. In addition to this, snow can reflect up to 90% of the UV light that falls on it.
Professor Jeffery continued "When we used cameras that could pick up UV, we noticed that there are some very important things that absorb UV light and therefore appear black, contrasting strongly with the snow. This includes urine - a sign of predators or competitors; lichens - a major food source in winter; and fur, making predators such as wolves very easy to see despite being camouflaged to other animals that can't see UV."

external image 20080916121750!Jupiter.Aurora.HST.UV.jpg research raises some interesting questions about the effect of UV on eye health. It had always been assumed that human eyes don't let UV in because of the potential that it will cause damage, just as it does to our skin. In our eyes, UV could damage our sensitive photoreceptors that cannot be replaced. This would lead to irreversible damage to our vision. Arctic reindeer are able to let UV into their eyes and use the information effectively in their environment without suffering any consequences.

Professor Jeffery added "The question remains as to why the reindeer's eyes don't seem to be damaged by UV. Perhaps it's not as bad for eyes as we first thought? Or maybe they have a unique way of protecting themselves, which we could learn from and perhaps develop new strategies to prevent or treat the damage the UV can cause to humans."

Professor Douglas Kell, Chief Executive, BBSRC said "We can learn a lot from studying the fundamental biology of animals and other organisms that live in extreme environments. Understanding their cell and molecular biology, neuroscience, and other aspects of how they work can uncover the biological mechanism that meant they can cope with severe conditions. This knowledge can have an impact on animal welfare and has the potential to be taken forward to new developments that underpin human health and wellbeing."