Working Alone Won’t Get You Good Grades

Jan. 31, 2013 — Students who work together and interact online are more likely to be successful in their college classes, according to a study published Jan. 30 in the journal Nature Scientific Reports and co-authored by Manuel Cebrian, a computer scientist at the Jacobs School of Engineering at the University of California San Diego.

A graph showing interactions between 82 students during the last week of a course. High performing students are in dark blue and form a core where the highest density of persistent interactions can be observed. Mid-performing students are in red and low-performing student sin green. Persistent interactions are shown in thick blue edges, while dotted thin grey edges indicate transient interactions. (Credit: Image courtesy of University of California – San Diego)

Cebrian and colleagues analyzed 80,000 interactions between 290 students in a collaborative learning environment for college courses. The major finding was that a higher number of online interactions was usually an indicator of a higher score in the class. High achievers also were more likely to form strong connections with other students and to exchange information in more complex ways. High achievers tended to form cliques, shutting out low-performing students from their interactions. Students who found themselves shut out were not only more likely to have lower grades; they were also more likely to drop out of the class entirely.

“Elite groups of highly connected individuals formed in the first days of the course,” said Cebrian, who also is a Senior Researcher at National ICT Australia Ltd, Australia’s Information and Communications Technology Research Centre of Excellence. “For the first time, we showed that there is a very strong correspondence between social interaction and exchange of information — a 72 percent correlation,” he said “but almost equally interesting is the fact that these high-performing students form ‘rich-clubs’, which shield themselves from low-performing students, despite the significant efforts by these lower-ranking students to join them. The weaker students try hard to engage with the elite group intensively, but can’t. This ends up having a marked correlation with their dropout rates.”

This study co-authored by Luis M. Vaquero, based at Hewlett-Packard UK Labs, shows a way that we might better identify patterns in the classroom that can trigger early dropout alarms, allowing more time for educators to help the student and, ideally, reduce those rates through appropriate social network interventions.

Cebrian’s work is part of UC San Diego’s wider research effort at the intersection of the computer and social sciences, led by Prof. James H. Fowler, to enhance our understanding of the ways in which people share information and how this impacts areas of national significance, such as the spread of health-related or political behavior.


Story Source:

The above story is reprinted from materials provided byUniversity of California – San Diego.

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


Journal Reference:

  1. Luis M. Vaquero, Manuel Cebrian. The rich club phenomenon in the classroomScientific Reports, 2013; 3 DOI: 10.1038/srep01174
University of California – San Diego (2013, January 31). Working alone won’t get you good grades. ScienceDaily. Retrieved February 2, 2013, from http://www.sciencedaily.com/releases/2013/01/130131144454.htm
Advertisements

This Is What a Fish Thought Looks Like

Jan. 31, 2013 — For the first time, researchers have been able to see a thought “swim” through the brain of a living fish. The new technology is a useful tool for studies of perception. It might even find use in psychiatric drug discovery, according to authors of the study, appearing online on January 31 in Current Biology.

For the first time, researchers have been able to see a thought “swim” through the brain of a living fish. The new technology is a useful tool for studies of perception. It might even find use in psychiatric drug discovery, according to authors of the study, appearing online on Jan. 31 in Current Biology, a Cell Press publication. (Credit: Current Biology, Muto et al.)

 

“Our work is the first to show brain activities in real time in an intact animal during that animal’s natural behavior,” said Koichi Kawakami of Japan’s National Institute of Genetics. “We can make the invisible visible; that’s what is most important.”

The technical breakthrough included the development of a very sensitive fluorescent probe to detect neuronal activity. Kawakami, along with Junichi Nakai of Saitama University and their colleagues, also devised a genetic method for inserting that probe right into the neurons of interest. The two-part approach allowed the researchers to detect neuronal activity at single-cell resolution in the zebrafish brain.

Akira Muto, the study’s lead author from the Kawakami lab, used the new tool to map what happens when a zebrafish sees something good to eat, in this case a swimming paramecium. The researchers were also able to correlate brain activity with that prey’s capture.

The new tool now makes it possible to ask which brain circuits are involved in complex behaviors, from perception to movement to decision making, the researchers say, noting that the basic design and function of a zebrafish brain is very much like our own.

“In the future, we can interpret an animal’s behavior, including learning and memory, fear, joy, or anger, based on the activity of particular combinations of neurons,” Kawakami said.

By monitoring neuronal activity in the zebrafish brain, Kawakami thinks that researchers may also be able to screen chemicals that affect neuronal activity in the brain. “This has the potential to shorten the long processes for the development of new psychiatric medications,” he said.


Story Source:

The above story is reprinted from materials provided byCell Press, via EurekAlert!, a service of AAAS.

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


Journal Reference:

  1. Akira Muto, Masamichi Ohkura, Gembu Abe, Junichi Nakai, Koichi Kawakami. Real-Time Visualization of Neuronal Activity during PerceptionCurrent Biology, 2013; DOI: 10.1016/j.cub.2012.12.040
Cell Press (2013, January 31). This is what a fish thought looks like. ScienceDaily. Retrieved February 2, 2013, from http://www.sciencedaily.com/releases/2013/01/130131144419.htm

Genome-Wide Atlas of Gene Enhancers in the Brain Online

Jan. 31, 2013 — Future research into the underlying causes of neurological disorders such as autism, epilepsy and schizophrenia, should greatly benefit from a first-of-its-kind atlas of gene-enhancers in the cerebrum (telencephalon). This new atlas, developed by a team led by researchers with the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) is a publicly accessible Web-based collection of data that identifies and locates thousands of gene-regulating elements in a region of the brain that is of critical importance for cognition, motor functions and emotion.

A new genome-wide digital atlas of gene enhancers in the brain will enable detailed scientific studies of gene regulation and the impacts of genetic mutations on neurological disorders. (Credit: Image courtesy of DOE/Lawrence Berkeley National Laboratory)

 

“Understanding how the brain develops and functions, and how it malfunctions in neurological disorders, remains one of the most daunting challenges in contemporary science,” says Axel Visel, a geneticist with Berkeley Lab’s Genomics Division. “We’ve created a genome-wide digital atlas of gene enhancers in the human brain — the switches that tell genes when and where they need to be switched on or off. This enhancer atlas will enable other scientists to study in more detail how individual genes are regulated during development of the brain, and how genetic mutations may impact human neurological disorders.”

Visel is the corresponding author of a paper in the journal Cell that describes this work. The paper is titled “A High-Resolution Enhancer Atlas of the Developing Telencephalon.” (See below for a list of co-authors.)

The cerebrum is the most highly developed region of the human brain. It houses the cerebral cortex, the so-called “gray matter” where complex information processing events take place, and the basal ganglia, a brain region that helps control movement throughout the body and is involved in certain types of learning. Many of the genes responsible for development of the cerebrum have been identified but most of the DNA elements responsible for expressing these genes — turning them on/off — have not. This is especially true for gene enhancers, sequences of DNA that act to amplify the expression of a specific gene. Characterizing gene enhancers tends to be difficult because an enhancer does not have to be located directly adjacent to the gene it is enhancing, but can in fact be located hundreds of thousands of DNA basepairs away.

“In addition to acting over long distances and being located upstream, downstream or in introns of protein-coding genes, the sequence features of gene enhancers are poorly understood,” Visel says. “However, gene-centric studies have provided strong evidence that gene enhancers are critical for normal embryonic development of the brain and have also linked human diseases to perturbed enhancer sequences.”

Visel and an international team of researchers met the challenges of systematic identification and functional characterization of gene enhancers in the cerebrum through a combination of ChIP-seq studies and large-scale histological analyses in transgenic mice, in which the activity patterns of human telencephalon enhancers can be studied. ChIP-seq, which stands for “chromatin immunoprecipitation followed by sequencing,” is a technique for genome-wide profiling of proteins that interact with DNA.

This combination of approaches enabled Visel and his colleagues to identify over 4,600 candidate embryonic forebrain enhancers. Furthermore, studying mouse embryos they mapped the activity of 145 of these enhancers at high resolution to define where exactly in the developing brain they drive the expression of their respective target genes. The result is a comprehensive, electronically accessible database for investigating the gene regulatory mechanisms of cerebrum development, and for studying the roles of distant-acting enhancers in neurodevelopmental disorders.

“By mapping hundreds of gene enhancer sequences and defining where exactly in the developing brain they are active, our enhancer atlas provides important information to connect non-coding mutations to actual biological functions,” Visel says.

As an example of how the enhancer atlas could be used in this manner, Visel says that if through genetic studies a certain region of the human genome has been linked to a specific neurological disorder but that region does not contain any protein-coding genes, checking the atlas could reveal whether the region is home to any distant-acting gene enhancers.

“If there is a gene enhancer in the region,” Visel says, “researchers could determine exactly how the enhancer or a mutated form is related to the disorder. This encompasses a lot of territory in the human genome. More than half of all the disease-related DNA sequence changes discovered in genome-wide screens to date fall within the 98-percent of human genome sequences that do not code for proteins. These ‘non-coding’ sequences were once dismissed by many as ‘junk DNA’ but are now known to harbor critical gene regulatory functions.”

Visel says the enhancer atlas also provides a “molecular toolbox” that can be used to re-locate the expression of certain genes to specific regions of the brain in experimental applications. This could help researchers gain new insights into how the brain develops and how the human brain has evolved.

“The evolution of the gene regulatory architecture may have been one of the drivers of the extremely advanced brains that we see in primates in general and humans in particular,” he says.

While continuing to map and annotate additional enhancers, Visel and his colleagues are now also studying the biological mechanisms related to some of these enhancers in more detail.

“We still only partially understand how gene enhancers work in the context of a living brain, i.e., what proteins bind to them, how mutations change their function, and what exactly the role of these sequences is in the context of human neurological disorders,” Visel says. “Clearly, there is more work to do.”

Co-authoring the Cell paper with Visel were Leila Taher, Hani Girgis, Dalit May, Olga Golonzhka, Renee Hoch, Gabriel McKinsey, Kartik Pattabiraman, Shanni Silberberg, Matthew Blow, David Hansen, Alex S. Nord, Jennifer Akiyama, Amy Holt, Roya Hosseini, Sengthavy Phouanenavong, Ingrid Plajzer-Frick, Malak Shoukry, Veena Afzal, Tommy Kaplan, Arnold Kriegstein, Edward Rubin, Ivan Ovcharenko, Len Pennacchio and John Rubenstein.

This research was primarily supported by the National Institutes of Health. Studies were performed at all of the collaborating institutions.


Story Source:

The above story is reprinted from materials provided byDOE/Lawrence Berkeley National Laboratory.

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


Journal Reference:

  1. Axel Visel, Leila Taher, Hani Girgis, Dalit May, Olga Golonzhka, Renee V. Hoch, Gabriel L. McKinsey, Kartik Pattabiraman, Shanni N. Silberberg, Matthew J. Blow, David V. Hansen, Alex S. Nord, Jennifer A. Akiyama, Amy Holt, Roya Hosseini, Sengthavy Phouanenavong, Ingrid Plajzer-Frick, Malak Shoukry, Veena Afzal, Tommy Kaplan, Arnold R. Kriegstein, Edward M. Rubin, Ivan Ovcharenko, Len A. Pennacchio, John L.R. Rubenstein. A High-Resolution Enhancer Atlas of the Developing TelencephalonCell, 2013; DOI:10.1016/j.cell.2012.12.041
DOE/Lawrence Berkeley National Laboratory (2013, January 31). Genome-wide atlas of gene enhancers in the brain online.ScienceDaily. Retrieved February 2, 2013, from http://www.sciencedaily.com/releases/2013/01/130131144415.htm

Genome Shows Mutant Gene Gives Pigeons Fancy Hairdos

Jan. 31, 2013 — University of Utah researchers decoded the genetic blueprint of the rock pigeon, unlocking secrets about pigeons’ Middle East origins, feral pigeons’ kinship with escaped racing birds, and how mutations give pigeons traits like a fancy feather hairdo known as a head crest.

This is a rock pigeon of the breed old Dutch capuchine, which has a kind of head crest known as a mane. More than 80 breeds out of some 350 breeds of rock pigeon have head crests, which form when head and neck feathers grow upward instead of downward. Scientists from the University of Utah, BGI-Shenzen in China and other institutions decoded the genome or genetic blueprint of the rock pigeon, then found that a single gene mutation linked to the head crest trait. (Credit: Michael D. Shapiro, University of Utah.)

 

“Birds are a huge part of life on Earth, and we know surprisingly little about their genetics,” especially compared with mammals and fish, says Michael D. Shapiro, one of the study’s two principal authors and an assistant professor of biology at the University of Utah. “There are more than 10,000 species of birds, yet we know very little about what makes them so diverse genetically and developmentally.”

He adds that in the new study, “we’ve shown a way forward to find the genetic basis of traits — the molecular mechanisms controlling animal diversity in pigeons. Using this approach, we expect to be able to do this for other traits in pigeons, and it can be applied to other birds and many other animals as well.”

The study appears Jan. 31 onScience Express, the website of the journal Science. Shapiro led the research with Jun Wang of China’s BGI-Shenzhen (formerly Beijing Genomics Institute) and other scientists from BGI, the University of Utah, Denmark’s University of Copenhagen and the University of Texas M.D. Anderson Cancer Center in Houston.

Key findings of the study of pigeons, which first were domesticated some 5,000 years ago in the Mediterranean region:

“The researchers sequenced the genome, or genetic blueprint, of the rock pigeon, Columba livia, among the most common and varied bird species on Earth. There are some 350 breeds with different sizes, shapes, colors, color patterns, beaks, bone structure, vocalizations and arrangements of feathers on the feet and head — including head crests that come in shapes known as hoods, manes, shells and peaks.

“The pigeon is among the few bird genomes sequenced so far, along with those of the chicken, turkey, zebra finch and a common parakeet known as a budgerigar or budgie, so “this will give us new insights into bird evolution,” Shapiro says.

Using innovative software developed by study co-author Mark Yandell, a University of Utah professor of human genetics, the scientists revealed that a single mutation in a gene named EphB2 causes head and neck feathers to grow upward instead of downward, creating head crests.

“This same gene in humans has been implicated as a contributor to Alzheimer’s disease as well as prostate cancer and possibly other cancers,” Shapiro says, noting that more than 80 of the 350 pigeon breeds have head crests, which play a role in attracting mates in many bird species.

The researchers compared the pigeon genome to those of chickens, turkeys and zebra finches. “Despite 100 million years of evolution since these bird species diverged, their genomes are very similar,” Shapiro says.

The study turned up more conclusive evidence that major pigeon breed groups originated in the Middle East, and that North American feral pigeons — which are free-living but not wild — are close relatives of racing pigeons, named racing homers.

A Genome for the Birds, a Gene for Head Crests

The study assembled 1.1 billion base pairs of DNA in the rock pigeon genome, and the researchers believe there are about 1.3 billion total, compared with 3 billion base pairs in the human genome. The rock pigeon’s 17,300 genes compare with about 21,000 genes in people.

The researchers first constructed a “reference genome” — a full genetic blueprint — from a male of the pigeon breed named the Danish tumbler. They did less complete sequencing of two feral pigeons and 38 other pigeons from 36 breeds.

Shapiro says his team’s study is the first to pinpoint a gene mutation responsible for a pigeon trait, in this case, head crests.

“A head crest is a series of feathers on the back of the head and neck that point up instead of down,” Shapiro says. “Some are small and pointed. Others look like a shell behind the head; some people think they look like mullets. They can be as extreme as an Elizabethan collar.”

The study found strong evidence that the EphB2 (Ephrin receptor B2) gene acts like an on-off switch to create a head crest when mutant, and no head crest when normal. It also showed the mutation and related changes in nearby DNA are shared by all crested pigeons, so the trait evolved just once and was spread to numerous pigeon breeds by breeders. They ruled out the alternate possibility the mutation arose several times independently in different breeds.

The researchers analyzed full or partial genetic sequences for 69 crested birds from 22 breeds, and 95 uncrested birds from 57 breeds. They found a perfect association between the mutant gene and the presence of head crests.

“The way we tracked this trait was innovative,” Shapiro says. “We used gene-finding software from Mark Yandell’s group that was developed to find mutations that control human diseases. We adapted this software to find mutations that control interesting traits in pigeons. This should be extendable to other animals as well.”

The scientists also showed that while the head crest trait becomes apparent in juvenile pigeons, the mutant gene affects pigeon embryos by reversing the direction of feather buds — from which feathers later grow — at a molecular level.

Other genetic factors — not identified in the new study — determine what kind of head crest east pigeon develops: shell, peak, mane or hood, according to Shapiro.

Tracking the Origins of Pigeons

A 2012 by Shapiro study provided limited evidence of pigeons’ origins in the Middle East and some breeds’ origins in India, and indicated kinship between common feral or free-living city pigeons and escaped racing pigeons.

In the new study, “we included some different breeds that we didn’t include in the last analysis,” Shapiro says. “Some of those breeds only left the Middle East in the last few decades. They’ve probably been there for hundreds if not thousands of years. If we find that other breeds are closely related to them, then we can infer those other breeds probably also came from the Middle East. That’s what we did.”

“We found that the owl breeds — which are pigeon breeds with very short beaks and that are very popular with breeders — likely came from the Middle East,” he says. “They are very closely related to breeds we know came from Syria, Lebanon and Egypt.”

Shapiro says the study also “found a lot of shared genetic heritage between breeds from Iran and breeds we suspect are from India, consistent with historical records of trade routes between those regions. People were not only trading goods along those routes, but probably also interbreeding their pigeons.”

As for the idea that free-living pigeons descended from escaped racing pigeons, Shapiro says his 2012 study was based on “relatively few genetic markers scattered throughout the genome. We now have stronger evidence based on 1.5 million markers, confirming the previous result with much better data.”

The scientists analyzed partial genomes of two feral pigeons: one from a U.S. Interstate-15 overpass in the Salt Lake Valley, and the other from Lake Anna in Virginia.

“Despite being separated by 1,000 miles, they are genetically very similar to each other and to the racing homer breed,” Shapiro says.

He notes that pigeons were one of evolutionist Charles Darwin’s “favorite examples of how selection works. He used this striking example of artificial selection [by breeding] to communicate how natural selection works. Now we can get to the DNA-level changes that are responsible for some of the diversity that intrigued Darwin 150 years ago.”

The study’s University of Utah co-authors were Yandell; Eric Domyan, biology postdoctoral fellow; Zev Kronenberg and Michael Campbell, Ph.D. students in human genetics; Anna Vickery, biology undergraduate student; Sydney Stringham, Ph.D. student in biology; and Chad Huff, a former postdoctoral fellow in human genetics now at the University of Texas.

The study was funded by the Burroughs Wellcome Fund, the National Science Foundation, the University of Utah Research Foundation, the National Institutes of Health and the Danish National Research Foundation.

 

Story Source:

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

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


Journal Reference:

  1. Michael D. Shapiro, Zev Kronenberg, Cai Li, Eric T. Domyan, Hailin Pan, Michael Campbell, Hao Tan, Chad D. Huff, Haofu Hu, Anna I. Vickrey, Sandra C. A. Nielsen, Sydney A. Stringham, Hao Hu, Eske Willerslev, M. Thomas P. Gilbert, Mark Yandell, Guojie Zhang, Jun Wang. Genomic Diversity and Evolution of the Head Crest in the Rock PigeonScience, 2013 DOI:10.1126/science.1230422
University of Utah (2013, January 31). Genome shows mutant gene gives pigeons fancy hairdos. ScienceDaily. Retrieved February 1, 2013, from http://www.sciencedaily.com/releases/2013/01/130131144059.htm

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