The RNA Age: A Primer

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Cooperators Can Coexist With Cheaters, as Long as There Is Room to Grow

Feb. 1, 2013 — Microbes exhibit bewildering diversity even in relatively tight living quarters. But when a population is a mix of cooperators, microbes that share resources, and cheaters, those that selfishly take yet give nothing back, the natural outcome is perpetual war. A new model by a team of researchers from Princeton University in New Jersey and Ben-Gurion University in Israel reveals that even with never-ending battles, the exploiter and the exploited can survive, but only if they have room to expand and grow.


 

The researchers present their findings at the 57th Annual Meeting of the Biophysical Society (BPS), held Feb. 2-6, 2013, in Philadelphia, Pa.

“In a fixed population, cells that share can’t live together with cells that only take,” said David Bruce Borenstein, a researcher at Princeton. “But if the population repeatedly expands and contracts then such ‘cooperators’ and ‘cheaters’ can coexist.”

Our world and our bodies play host to a vast array of microbes. On our teeth alone, there are approximately a thousand different kinds of bacteria, all living in very close quarters. This is amazing, the researchers observe, because many of those species share resources with nearby neighbors, who might not be so cooperative or even related [1].

At the scale of cells, individuals cooperate mainly by exporting resources into the environment and letting them float away. “This is a deceptively complex process in which cells interact at long ranges, but compete only with nearby individuals,” explained Borenstein. “Our models predict that, even when this exploitation prevents any possibility of peaceful coexistence, the exploiter and the exploited can survive across generations in what is basically a perpetual war.” The researchers speculate that similar competition might occur between cancer cells and normal tissue.

Borenstein and his colleagues made their conclusions based on a computer model that considered two types of cells, cooperators and cheaters, and laid them out on a grid. Cooperators were given the ability, not uncommon in nature, to make a resource that speeds up growth in both kinds of cells. Producing this resource slowed down the growth of cooperators, because they have to divert some energy to resource production. This resource then spread out from the cooperator by diffusion, so that the cells closest to a producer have the greatest resource access. The model revealed that the producers tended to cluster, meaning that being a producer gave you greater access to resources. It also meant that even though cheaters are avoiding the cost of production, they pay for it with reduced resource access.

Within these basic constraints it was found that when the two populations must compete directly for survival, no coexistence is possible. “One type always wins out,” observed Borenstein. However, when the two populations can grow into empty space, the researchers found a strange and paradoxical interaction: cheaters may be outcompeting cooperators locally, even as cooperators grow better overall. These complex interactions may play an important role in the maintenance of diverse microbial communities, like those seen in the mouth.

“To our astonishment, we found that while cheaters can exploit cooperators, cooperators can isolate cheaters, just from cooperation and growth,” concludes Borenstein. “As a result, the community can persist in a sort of perpetual race from which a winner need not emerge.”

[1] J. M. ten Cate. “Biofilms, a new approach to the microbiology of dental plaque.” Odontolgy 2006(94):1-9.

 

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The above story is reprinted from materials provided byBiophysical Society, via Newswise.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.


Biophysical Society (2013, February 1). Cooperators can coexist with cheaters, as long as there is room to grow. ScienceDaily. Retrieved February 3, 2013, from http://www.sciencedaily.com/releases/2013/02/130201095947.htm

Note: If no author is given, the source is cited instead.

 

Vegetation Changes in Cradle of Humanity: Study Raises Questions About Impact On Human Evolution

Jan. 31, 2013 — What came first: the bipedal human ancestor or the grassland encroaching on the forest? A new analysis of the past 12 million years’ of vegetation change in the cradle of humanity is challenging long-held beliefs about the world in which our ancestors took shape — and, by extension, the impact it had on them.


 

The research combines sediment core studies of the waxy molecules from plant leaves with pollen analysis, yielding data of unprecedented scope and detail on what types of vegetation dominated the landscape surrounding the African Rift Valley (including present-day Kenya, Somalia and Ethiopia), where early hominin fossils trace the history of human evolution.

“It is the combination of evidence both molecular and pollen evidence that allows us to say just how long we’ve seen Serengeti-type open grasslands,” said Sarah J. Feakins, assistant professor of Earth sciences at the USC Dornsife College of Letters, Arts and Sciences and lead author of the study, which was published online in Geology on Jan. 17.

Feakins worked with USC graduate student Hannah M. Liddy, USC undergraduate student Alexa Sieracki, Naomi E. Levin of Johns Hopkins University, Timothy I. Eglinton of the Eidgenössische Technische Hochschule and Raymonde Bonnefille of the Université d’Aix-Marseille.

The role that the environment played in the evolution of hominins — the tribe of human and ape ancestors whose family tree split from the ancestors of chimpanzees and bonobos about 6 million years ago — has been the subject of a century-long debate.

Among other things, one theory dating back to 1925 posits that early human ancestors developed bipedalism as a response to savannas encroaching on shrinking forests in northeast Africa. With fewer trees to swing from, human ancestors began walking to get around.

While the shift to bipedalism appears to have occurred somewhere between 6 and 4 million years ago, Feakins’ study finds that thick rainforests had already disappeared by that point — replaced by grasslands and seasonally dry forests some time before 12 million years ago.

In addition, the tropical C4-type grasses and shrubs of the modern African savannah began to dominate the landscape earlier than thought, replacing C3-type grasses that were better suited to a wetter environment. (The classification of C4 versus C3 refers to the manner of photosynthesis each type of plant utilizes.)

While earlier studies on vegetation change through this period relied on the analysis of individual sites throughout the Rift Valley — offering narrow snapshots — Feakins took a look at the whole picture by using a sediment core taken in the Gulf of Aden, where winds funnel and deposit sediment from the entire region. She then cross-referenced her findings with Levin who compiled data from ancient soil samples collected throughout eastern Africa.

“The combination of marine and terrestrial data enable us to link the environmental record at specific fossil sites to regional ecological and climate change,” Levin said.

In addition to informing scientists about the environment that our ancestors took shape in, Feakins’ study provides insights into the landscape that herbivores (horses, hippos and antelopes) grazed, as well as how plants across the landscape reacted to periods of global and regional environmental change.

“The types of grasses appear to be sensitive to global carbon dioxide levels,” said Liddy, who is currently working to refine the data pertaining to the Pliocene, to provide an even clearer picture of a period that experienced similar atmospheric carbon dioxide levels to present day. “There might be lessons in here for the future viability of our C4-grain crops,” says Feakins.


Story Source:

The above story is reprinted from materials provided byUniversity of Southern California. The original article was written by Robert Perkins.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.


Journal Reference:

  1. S. J. Feakins, N. E. Levin, H. M. Liddy, A. Sieracki, T. I. Eglinton, R. Bonnefille. Northeast African vegetation change over 12 m.y.Geology, 2013; DOI:10.1130/G33845.1
University of Southern California (2013, January 31). Vegetation changes in cradle of humanity: Study raises questions about impact on human evolution. ScienceDaily. Retrieved February 1, 2013, from http://www.sciencedaily.com/releases/2013/01/130131121304.htm

Survival of the Prettiest: Sexual Selection Can Be Inferred from the Fossil Record

Jan. 29, 2013 — Detecting sexual selection in the fossil record is not impossible, according to scientists writing in Trends in Ecology and Evolution this month, co-authored by Dr Darren Naish of the University of Southampton.


 

The term “sexual selection” refers to the evolutionary pressures that relate to a species’ ability to repel rivals, meet mates and pass on genes. We can observe these processes happening in living animals but how do palaeontologists know that sexual selection operated in fossil ones?

Historically, palaeontologists have thought it challenging, even impossible, to recognise sexual selection in extinct animals. Many fossil animals have elaborate crests, horns, frills and other structures that look like they were used in sexual display but it can be difficult to distinguish these structures from those that might play a role in feeding behaviour, escaping predators, controlling body temperature and so on.

However in their review, the scientists argue that clues in the fossil record can indeed be used to infer sexual selection.

“We see much evidence from the fossil record suggesting that sexual selection played a major role in the evolution of many extinct groups,” says Dr Naish, of the University’s Vertebrate Palaeontology Research Group.

“Using observations of modern animal behaviour we can draw analogies with extinct animals and infer how certain features improve success during courtship and breeding.”

Modern examples of sexual selection, where species have evolved certain behaviours or ornamentation that repel rivals and attract members of the opposite sex, include the male peacock’s display of feathers, and the male moose’s antlers for use in clashes during mating season.

Dr Naish and co-authors state that the fossil record holds many clues that point to the existence of sexual selection in extinct species, for example weaponry for fighting, bone fractures from duels, and ornamentation for display, such as fan-shaped crests on dinosaurs. Distinct differences between males and females of a species, called ‘sexual dimorphism’, can also suggest the presence of sexual selection, and features observed in sexually mature adults, where absent from the young, indicate that their purpose might be linked to reproduction.

We can also make inferences from features that are ‘costly’ in terms of how much energy they take to maintain, if we assume that the reproductive advantages outweighed the costs.

Whilst these features might have had multiple uses, the authors conclude that sexual selection should not be ruled out.

“Some scientists argue that many of the elaborate features on dinosaurs were not sexually selected at all,” adds Dr Naish, who is based at the National Oceanography Centre, Southampton.

“But as observations show that sexual selection is the most common process shaping evolutionary traits in modern animals, there is every reason to assume that things were exactly the same in the distant geological past.”

 

Story Source:

The above story is reprinted from materials provided byUniversity of Southampton.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.


Journal Reference:

  1. Robert J. Knell, Darren Naish, Joseph L. Tomkins, David W.E. Hone. Sexual selection in prehistoric animals: detection and implicationsTrends in Ecology & Evolution, 2013; 28 (1): 38 DOI: 10.1016/j.tree.2012.07.015
University of Southampton (2013, January 29). Survival of the prettiest: Sexual selection can be inferred from the fossil record. ScienceDaily. Retrieved January 30, 2013, from http://www.sciencedaily.com/releases/2013/01/130129080217.htm

What Holds Chromosomes Together? Structure of DNA-Packaging Proteins Described

Jan. 28, 2013 — To ensure that the genetic material is equally and accurately distributed to the two daughter cells during cell division, the DNA fibers must have an ordered structure and be closely packed. At the Max Planck Institute of Biochemistry in Martinsried near Munich scientists have now elucidated the structure of a ring-shaped protein complex (SMC-kleisin), which ensures order in this packaging process. Together with their cooperation partners at the Korea Advanced Institute of Science and Technology, they studied these proteins in bacteria and found structural analogies to the human complex.

SMC-Kleisin-Complex. (Credit: Image courtesy of Max Planck Institute of Biochemistry)

 

The findings have now been published in the journal Nature Structural & Molecular Biology.

In each cell about two meters of DNA must fit into a cell nucleus that has a diameter of only a few thousandths of a millimeter. There the DNA is organized in individual chromosomes in the form of very long filaments. If they are not equally and accurately distributed to the daughter cells during cell division, this can result in cancer or genetic defects such as trisomy 21. Therefore, to ensure safe transport of DNA during cell division the long and coiled DNA fibers must be tightly packed.

Scientists have only a sketchy understanding of this step. The SMC-kleisin protein complexes play a key role in this process. They consist of two arms (SMC) and a bridge (kleisin). The arms wrap around the DNA like a ring and thus can connect duplicated chromosomes or two distant parts of the same chromosome with each other.

Learning from bacteria Simple organisms like bacteria also use this method of DNA packaging. The scientists, in collaboration with colleagues from South Korea, have now elucidated the structure of a precursor of human SMC-kleisin complexes of the bacterium Bacillus subtilis. The researchers showed that the bacterial SMC-kleisin complex has two arms made of identical SMC proteins that form a ring. The arms differ in their function only through the different ends of the kleisin protein with which they are connected.

In humans the DNA packaging machinery is similarly organized. “We suspect that this asymmetric structure plays an important role in the opening and closing of the ring around the DNA,” explains Frank Bürmann, PhD student in the research group ‘Chromosome Organization and Dynamics’ of Stephan Gruber. In addition, the scientists discovered how the ends of the kleisin can distinguish between correct and wrong binding sites on one pair of arms.

The cohesion of chromosomes is of critical importance for reproduction as well. In human eggs this cohesion must be maintained for decades to ensure error-free meiosis of the egg cell. Failure of cohesion is a likely cause for decreased fertility due to age or the occurrence of genetic defects such as trisomy 21. “The elucidation of the structure of SMC-kleisin protein complexes is an important milestone in understanding the intricate organization of chromosomes,” says group leader Stephan Gruber.

 

Story Source:

The above story is reprinted from materials provided byMax Planck Institute of Biochemistry.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.


Journal Reference:

  1. Frank Bürmann, Ho-Chul Shin, Jérôme Basquin, Young-Min Soh, Victor Giménez-Oya, Yeon-Gil Kim, Byung-Ha Oh, Stephan Gruber. An asymmetric SMC–kleisin bridge in prokaryotic condensinNature Structural & Molecular Biology, 2013; DOI: 10.1038/nsmb.2488
Max Planck Institute of Biochemistry (2013, January 28). What holds chromosomes together? Structure of DNA-packaging proteins described. ScienceDaily. Retrieved January 30, 2013, from http://www.sciencedaily.com/releases/2013/01/130128081522.htm

New Insights Into Cell Division from Simplified Model: Artificial Minimal Actin Cortex Developed

Jan. 14, 2013 — All living organisms consist of cells that have arisen from other living cells by the process of cell division. However, it is not yet fully understood just how this important process takes place. Scientists at the Max Planck Institute (MPI) of Biochemistry in Martinsried near Munich have now developed a minimal biological system, which brings together key components of the cell division apparatus. With the aid of this minimal model, the researchers were able to take a closer look at the biophysical mechanisms involved.

Researchers have constructed an artificial minimal actin cortex (MAC). (Credit: Image courtesy of Max Planck Institute of Biochemistry)

 

“Our model may help to develop and test new treatments for diseases caused by errors in cell division,” said Sven Vogel, scientist at the MPI of Biochemistry. The results of the study have now been published in the new journal eLife.

The researchers of the department “Cellular and Molecular Biophysics” try to remodel the structures of a cell with the help of a modular approach. Their aim is to observe and visualize step by step the underlying mechanisms of living systems. “Our vision is to assemble more and more building blocks of natural and synthetic biomolecules until we finally have the minimal version of a cell in front of us,” said Petra Schwille, director at the MPI of Biochemistry. Using such an approach, the scientists have now succeeded in investigating the process of cell division in greater detail.

Making two out of one

During cell division both the genetic information and the cell plasma must be distributed correctly to the two daughter cells. Moreover, the two newly created cells must be separated physically from each other. An important component of this cell division machinery is the cell cortex. This layer is located directly below the cell membrane and consists of a thin layer of thread-like protein chains, so-called actin filaments. During the actual division process, myosin motors from the interior of the cell exert force on the actin filaments, causing the cell cortex to constrict in the middle and ultimately to divide.

The Max Planck researchers have now constructed an artificial minimal actin cortex (MAC) on which they can study the physical phenomena more precisely. The researchers combined only the most essential components of the cell division machinery, thus creating a synthetic minimal system. Such a system is a very simplified model for complex processes. In nature, by contrast, cells took several million years to develop and were not precisely planned and constructed. “For that reason some of the processes may be more complex than they theoretically need to be,” the biophysicist Sven Vogel said. “This complexity often makes it almost impossible to study the basic mechanisms in detail.”

One research finding the minimal system revealed was that the addition of myosin motors to the MAC induces actin pattern formation. Moreover, the myosin motors break individual actin filaments into fragments and compact them. The Martinsried researchers are certain that artificial minimal systems will contribute to a detailed understanding of cell division. Vogel added: “Our findings and minimal systems may help to develop and test new treatments for diseases that are caused by errors in cell division.”

 

Story Source:

The above story is reprinted from materials provided byMax Planck Institute of Biochemistry.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.


Journal Reference:

  1. Sven K Vogel, Zdenek Petrasek, Fabian Heinemann, Petra Schwille. Myosin motors fragment and compact membrane-bound actin filamentseLife, 2013; 2 DOI:10.7554/eLife.00116
Max Planck Institute of Biochemistry (2013, January 14). New insights into cell division from simplified model: Artificial minimal actin cortex developed. ScienceDaily. Retrieved January 16, 2013, from http://www.sciencedaily.com/releases/2013/01/130114092557.htm

Organisms Cope With Environmental Uncertainty by Guessing the Future

ScienceDaily (Aug. 16, 2012) — In uncertain environments, organisms not only react to signals, but also use molecular processes to make guesses about the future, according to a study by Markus Arnoldini et al. from ETH Zurich and Eawag, the Swiss Federal Institute of Aquatic Science and Technology. The authors report in PLoS Computational Biology that if environmental signals are unreliable, organisms are expected to evolve the ability to take random decisions about adapting to cope with adverse situations.

Most organisms live in ever-changing environments, and are at times exposed to adverse conditions that are not preceded by any signal. Examples for such conditions include exposure to chemicals or UV light, sudden weather changes or infections by pathogens. Organisms can adapt to withstand the harmful effects of these stresses. Previous experimental work with microorganisms has reported variability in stress responses between genetically identical individuals. The results of the present study suggest that this variation emerges because individual organisms take random decisions, and such variation is beneficial because it helps organisms to reduce the metabolic costs of protection without compromising the overall benefits.

The theoretical results of this study can help to understand why genetically identical organisms often express different traits, an observation that is not explained by the conventional notion of nature and nurture. Future experiments will reveal whether the predictions made by the mathematical model are met in natural systems.

 


Story Source:

The above story is reprinted from materials provided byPublic Library of Science.


Journal Reference:

  1. Markus Arnoldini, Rafal Mostowy, Sebastian Bonhoeffer, Martin Ackermann. Evolution of Stress Response in the Face of Unreliable Environmental SignalsPLoS Computational Biology, 2012; 8 (8): e1002627 DOI:10.1371/journal.pcbi.1002627
Citation:

Public Library of Science (2012, August 16). Organisms cope with environmental uncertainty by guessing the future.ScienceDaily. Retrieved August 19, 2012, from http://www.sciencedaily.com/releases/2012/08/120816201616.htm

Shedding New Light On How Jaws Evolve

ScienceDaily (Aug. 7, 2012) — If you’re looking for information on the evolution and function of jaws, University of Notre Dame researcher Matt Ravosa is your man.

Matt Ravosa with a llama. (Credit: Image courtesy of University of Notre Dame)


His integrative research program investigates major adaptive and morphological transformations in the mammalian musculoskeletal system during development and across higher-level groups. In mammals, the greater diversification and increasingly central role of the chewing complex in food procurement and processing has drawn considerable attention to the biomechanics and evolution of this system. Being among the most highly mineralized, and thus well-preserved, tissues in the body, craniodental remains have long been used to offer novel insights into the behavior and affinities of extinct organisms.

Ravosa feels that the study of mandibular symphysis, which is the midline joint between the left and right lower jaws, is one of the most interesting and complex articulations in the bodies of mammals. This is due to the remarkable evolutionary and postnatal variation in the degree of fusion, or the amount of hard versus soft tissue, in this joint. For instance, humans, apes and monkeys all have a bony symphysis, which differs from the condition observed in most other living and fossil primates.

In two papers about adaptive and non-adaptive influences on mandibular evolution with his postdoctoral fellow Jeremiah Scott, Ravosa and his colleagues present analyses based on more than 300 species and 2,900 individual mandibles from highly diverse mammal groups where the feeding behavior of living species is well-documented.

Ravosa is particularly interested in determining if there is a relationship between the properties of food being consumed and the degree of fusion of the jaw. His recent paper in the Journal of Evolutionary Biology is the most broad-based examination to date relating dietary properties of mammals to the degree of fusion. His research reveals that in the case of marsupials, carnivorans and strepsirrhine primates that eat harder, tougher and bigger foods have a lesser degree of fusion. By contrast, animals that consume softer, smaller foods do not have as great a degree of fusion. This supports biomechanical arguments that fusion strengthens the symphyseal joint during postcanine chewing and biting.

In another paper appearing in the journal Evolution, Ravosa reports that in some bat lineages, the fusing of the jaw can be evolutionarily constrained as its morphology does not vary as a function of dietary products. Such evidence about limits on musculoskeletal variation is typically rare in mammals, with these findings having important implications regarding the evolution of the feeding apparatus in humans and other anthropoids. Though dietarily diverse, all members of this primate group exhibit a fused symphysis that also does not vary with diet.

Ravosa notes that similar analysis of other species would further help our understanding of the evolution and development of the mammalian skull, which includes his lab’s ongoing anatomical, imaging, cellular, molecular and engineering approaches to determinants of jaw-joint formation, aging and pathology.

 

Link:

http://newsinfo.nd.edu/news/32425-notre-dame-researcher-sheds-light-on-how-jaws-evolve/

Journal Reference:

  1. J. E. SCOTT, A. S. HOGUE, M. J. RAVOSA. The adaptive significance of mandibular symphyseal fusion in mammals. Journal of Evolutionary Biology, 2012; 25 (4): 661 DOI: 10.1111/j.1420-9101.2012.02457.x

Citation:

University of Notre Dame (2012, August 7). Shedding new light on how jaws evolve. ScienceDaily. Retrieved August 9, 2012, from http://www.sciencedaily.com­ /releases/2012/08/120807151316.htm

Division of Labor Offers Insight Into the Evolution of Multicellular Life

ScienceDaily (Aug. 7, 2012) — Dividing tasks among different individuals is a more efficient way to get things done, whether you are an ant, a honeybee or a human.

(Credit: Adele Conover)


A new study by researchers at Michigan State University’s BEACON Center for the Study of Evolution in Action suggests that this efficiency may also explain a key transition in evolutionary history, from single-celled to multi-celled organisms.

The results, which can be found in the current issue of the Proceedings of the National Academy of Sciences, demonstrate that the cost of switching between different tasks gives rise to the evolution of division of labor in digital organisms. In human economies, these costs could be the mental shift or the travel time required to change from activity to another.

Using the digital evolution platform Avida, self-replicating computer programs, a the team imposed a time cost on the organisms that had to perform different computational tasks to get rewards, said Heather Goldsby, who led the study and is now a postdoctoral researcher at the University of Washington.

“More complex tasks received more rewards,” she said. “They evolved to perform these more efficiently by using the results of simpler tasks solved by neighboring organisms and sent to them in messages.”

In this way, the organisms were breaking the tasks down into smaller computational problems and dividing them up among each other.

The division of labor did not come about by bringing together individuals with different abilities — each member of a community was genetically identical, in the same way that all of the cells in a human body contain the same genetic material. Instead, the organisms had to have flexible behavior and a communication system that allowed them to coordinate tasks.

The most surprising result was that the organisms evolved to become dependent on each other.

“The organisms started expecting each other to be there, and we tested them in isolation, they could no longer make copies of themselves,” said Charles Ofria, MSU associate professor of computer science and engineering.

Ben Kerr at the University of Washington and Ann Dornhaus with the University of Arizona contributed to this study. The research was funded by the National Science Foundation.

 

Link:

http://news.msu.edu/story/division-of-labor-offers-insight-into-the-evolution-cells/

Journal Reference:

  1. Heather J. Goldsby, Anna Dornhaus, Benjamin Kerr, and Charles Ofria. Task-switching costs promote the evolution of division of labor and shifts in individuality. PNAS, August 7, 2012 DOI: 10.1073/pnas.1202233109

Citation:

Michigan State University (2012, August 7). Division of labor offers insight into the evolution of multicellular life. ScienceDaily. Retrieved August 9, 2012, from http://www.sciencedaily.com­ /releases/2012/08/120807132211.htm

Actinobacteria as the Base of the Evolutionary Tree

ScienceDaily (July 26, 2012) — Ever since Darwin first published The Origin of the Species, scientists have been striving to identify a last universal common ancestor of all living species. Paleontological, biochemical, and genomic studies have produced conflicting versions of the evolutionary tree. Now a team of researchers, led by a professor at the State University of New York at Buffalo and including area high school students, has developed a novel method to search the vast archives of known gene sequences to identify and compare similar proteins across the many kingdoms of life. Using the comparisons to quantify the evolutionary closeness of different species, the researchers have identified Actinobacteria, a group of single membrane bacteria that include common soil and water life forms, as the base of the evolutionary tree.


 

They will present their findings at the annual meeting of the American Crystallographic Association (ACA), held July 28 — Aug. 1 in Boston, Mass.

“Today the gene banks are enormous. They contain more than 600,000 genes from the genomes of more than 6,000 species,” says William Duax, a physical chemist and lead researcher on the team. However, many of the gene sequences, and the proteins they encode, are not systematically identified. Proteins that are structurally similar and perform the same function could be labeled with different numbers that obscure the fact that they belong to the same protein family. “Our first challenge is to make sure that we are comparing apples to apples and oranges to oranges,” says Duax.

Duax and his team have developed efficient ways to search through the gene banks looking for all copies of the same family of protein. They concentrated their efforts on proteins that are found on the surface of cell components called ribosomes. The ribosomal proteins are among the most accurately identified proteins, and because they are not transferred between individuals independent of reproduction, are good candidates for tracing the evolution of all species.

Ribosomal proteins in the same family twist into the same shape. The sequence of amino acids in a protein determines what 3D structure it folds into and Duax and his colleagues identified patterns that marked specific types of turns. They used these marker sequences to identify and almost perfectly align the proteins, similar to the way you could use five points to identify the shape of a star and align its orientation to match other star shapes.

Structurally aligning the proteins allowed the researchers to easily spot small differences that indicate organisms belong on different branches of the evolutionary tree. For example, a single amino acid difference in one ribosomal protein separates bacteria with one cell membrane from those with two.

At the ACA meeting, the researchers will present the results from the analysis of two different ribosomal protein families, called S19 and S13. Duax will present the analysis of protein S19, while high school student Alexander Merriman will present analysis of protein S13. Merriman joined Duax’s lab through a scientific mentorship program designed to give teenagers hands-on experience with cutting-edge research. “They are enthusiastic researchers and do great work,” Duax says of the students he welcomes into his lab each Friday.

Both analyses point to Actinobacteria as the last universal common ancestor. This agrees with previous work done by the group on proteins named S9 and S12. The researchers will continue to search for more evidence to add to their developing picture of the evolutionary tree. The group plans to analyze additional proteins, as well as DNA and RNA. “We are applying a systematic approach to make sense of a sometimes messy gene bank,” says Duax.