Making Models -A Delicious Way to Learn

IB1 students were asked to construct an edible cell membrane model made from Oreo cookies and gummy candy. This tactile activity helped to solidify students understanding of the cell membrane structure and was deliciously enjoyable!

 

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Oldest human genome dug up in Spain’s pit of bones

A 400,000-year-old genome from ancient human bone could herald a missing link species – taking us closer than ever to our common ancestor with Neanderthals
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DEEP inside the Atapuerca cave system in northern Spain, 30 metres beneath the surface, lies the Sima de los Huesos, or the “pit of bones”. The remains of at least 28 ancient humans have been found at the bottom of this 12-metre-long vertical shaft. Now a thigh bone pulled out of the pit has yielded 400,000-year-old DNA – by far the oldest human DNA ever sequenced.

The results suggest the thigh bone belonged to a previously unknown human species – perhaps even a missing link between the Neanderthals and their mysterious cousins the Denisovans. This, say palaeontologists, brings us closer than ever before to understanding who our own common ancestor with the Neanderthals was.
Video: Pit of bones hides our oldest DNA

The bones at Sima de los Huesos pre-date the origin of Homo sapiens, who appeared around 200,000 years ago, and most closely resemble those of Neanderthals. Fred Spoor of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, calls them “Neanderthals in the making”.

Until now, it had only been possible to sequence the genomes of hominin fossils found in cold climates; DNA breaks down faster in warmer climates like Spain’s. But spurred by the successful sequencing of a 300,000-year-old cave bear genome from the same area, Matthias Meyer, also at the Max Planck Institute in Leipzig, and colleagues decided to give it a go.

They drilled into a hominin thigh bone from the cave and extracted 1.95 grams of material, processed it for DNA, and filtered out a large amount of modern human DNA – the bones had been heavily contaminated as they were removed and handled.

The end result was a near-complete mitochondrial genome – the DNA found inside the organelles that power cells. By comparing it with that of modern humans, chimpanzees and bonobos, plus Neanderthals and Denisovans, Meyer estimated its age at 400,000 years, twice as old as our own species and far older than any hominin genome previously sequenced (Nature, DOI: 10.1038/nature12788). The Neanderthal and Denisovan genomes sequenced in recent years are each around 40,000 years old.

“The genomes we have [up until now] are really very recent,” says Chris Stringer of the Natural History Museum in London. “This takes us at least a few hundred thousand years back, towards our common ancestor with other hominins.”

“This takes us back a few hundred thousand years, to our common ancestor with other hominins”
“This paper is the dream,” says David Reich of Harvard Medical School in Boston, Massachusetts. It is the latest in a series of breakthroughs in ancient DNA, coming just months after the sequencing of the oldest-ever genome, from a 700,000-year-old horse.

Since the Sima de los Huesos hominins look like Neanderthals, and lived in Europe where the Neanderthals would soon dominate, Meyer expected their DNA to look Neanderthal. But to his surprise, it proved quite distinct. It is most closely related to the Denisovans, a species known only from a finger bone and two molars found in a Siberian cave.

“We don’t quite know what to make of it,” says Meyer. “There’s no evidence the Denisovans ranged anywhere near Atapuerca,” says Stringer.

The biggest mystery is how and when our lineage diverged from that of the Neanderthals and Denisovans. Also unclear are the circumstances of the later split between Neanderthals and Denisovans. All we know is that both of these events happened around the time the Sima de los Huesos hominins were living in Spain.

One possibility is that the fossils belong to the common ancestor of Neanderthals and Denisovans, and some of their descendants later headed east and became the Denisovans. “I think that’s the most likely scenario,” says Meyer.

But that doesn’t explain why the Sima de los Huesos bones look so much like Neanderthals, says Stringer. He thinks they were Neanderthal ancestors, and came after the species split from Denisovans. The Neanderthals could easily have lost the mitochondrial genes they shared with Denisovans later on, he says, as mitochondrial DNA is only passed down the female line. “Mitochondrial DNA can be lost if a woman only has sons,” says Stringer.

That means the only way to settle exactly what happened is to sequence a full genome from the Sima de los Huesos fossils. Meyer is working on this now. “It is extremely difficult,” he says.

The Sima de los Huesos genome is particularly exciting because it is from a time that is very close to the origin of our human line. The archaeological evidence suggests these early humans were developing significant new behaviours. On the one hand, they were still using fairly primitive stone tools like a crafted hand axe – nicknamed Excalibur – that was found in the pit. But the bones also suggest more modern traits.

For instance, some believe the pit might have been an early burial site, part of a simple funeral rite. Excalibur could be a tribute to the dead, suggests Stringer.

And the deformed skull of a girl who lived to be around 12 years old, also found in the pit, suggests that the tribe cared for her. “There’s a hint of something human – caring for the disabled,” says Stringer.

Elsewhere in Atapuerca, archaeologists have discovered the remains of an elderly man with severe back problems, who couldn’t have fended for himself. Here, too, the man’s age suggests a community must have protected him.

The possibility of peering into the Sima people’s genes as well as their bones is a huge step forward. A full genome would be invaluable, says Reich. We could find out which of our modern genes were already in place, and which ones had to change to produce modern humans. As Reich puts it: “It’s about what makes us human.”

“A full genome from these bones would tell us which genes had to change to produce modern humans”

A brief history of human fossils

The fossil remains found in Sima de los Huesos, Spain, offer important clues to unravelling the origins of our species (see main story). Here are five other key ancestors.

Lucy Modern humans are descended from the ape-like Australopithecus, which lived in Africa. The most famous specimen is Lucy, a 3.2-million-year-old Australopithecus afarensis found in Ethiopia in 1974. She got her name from The Beatles’ song Lucy in the Sky with Diamonds.

Karabo This 1.9-million-year-old boy was found in South Africa in 2008, alongside an adult female. He belongs to the species Australopithecus sediba, has a mix of ape-like and human-like features, and was named “Answer” by a 17-year-old South African student in a competition.

Turkana Boy An almost complete 1.5-million-year-old Homo erectus fossil was found by Kenya’s Lake Turkana in 1984. The species spread as far as Java, and may be our direct ancestors.

Neanderthal 1 The first recognised Neanderthal was found in 1856 in Germany’s Neander valley. It didn’t get a snappy name, but was the first primitive human identified, and in 1997 became the first to yield DNA.

X-Woman A female finger bone from the Denisova cave in Siberia turned out to belong to a new species when its genome was sequenced in 2010. The Denisovans are most closely related to Neanderthals. Genetics show they roamed as far as Indonesia, where they interbred with modern humans.

This article appeared in print under the headline “Pit of bones hides our oldest DNA”

By Michael MarshallMagazine issue 2946 published 7 December 2013

https://www.newscientist.com/article/mg22029462-600-oldest-human-genome-dug-up-in-spains-pit-of-bones

iPad Digital Bioengineering and GMO Science Stories

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Year 12 Biology HL students were asked to create digital stories using the Book Creator app on their iPads. The stories needed to be linked to their learning objective applications from the Bioengineering and Genetic Modification Unit ( See the topics below).  It is no surprise that the stories that were created were unique, interesting and educational. I am so proud of their creations. There are two samples below. Enjoy!

TOPICS
 
TOPIC 1: Application: Use of DNA profiling in paternity and/or forensic investigations 
 
TOPIC 2: Gene transfer to bacteria using plasmids makes use of restriction endonucleases and DNA ligase 
 
TOPIC 3: Assessment of potential risks and benefits associated with genetic modification of crops (
 
TOPIC 4: Production of cloned embryos produced by somatic-cell nuclear transfer 

 

iBook:The Cloning Zoo: Maria Alba: CGB 2015

The secret of purple hood

Amazing DNA Models : Year 12 Biology HL

Year 12 Biology HL students were asked to create DNA models that illustrated their knowledge of the DNA structure. Here is the criteria that was given to the class:

Construct a model of the DNA molecule. Your final model must meet the following criteria:

1. It must be self-supporting, stand at least 30 cm high and have a diameter of at least 12 cm

2. It must clearly model the double helix structure of the DNA molecule

3. Each of the major components of the molecule (bases, sugar, phosphate) must be clearly recognizable using labeling, colour coding, shape, size, material or any combination of the above. Purines must be distinguished from pyrimidines.

4. 3’ and 5’ ends are shown

5. A minimum of six base pairs must be represented

6. Correct number of hydrogen bonds between base pairs must be demonstrated in the model

The models were a great success!

See images below.

DNA Models 1 DNA Models 2 Stephy DNA Model Year 12 DNA Models Group Pic

Article: Controlling Genes with your thoughts

Controlling genes with your thoughts

Date:
November 11, 2014
Source:
ETH Zurich
Summary:
Researchers have constructed the first gene network that can be controlled by our thoughts. Scientists have developed a novel gene regulation method that enables thought-specific brainwaves to control the conversion of genes into proteins (gene expression). The inspiration was a game that picks up brainwaves in order to guide a ball through an obstacle course.

It sounds like something from the scene in Star Wars where Master Yoda instructs the young Luke Skywalker to use the force to release his stricken X-Wing from the swamp: Marc Folcher and other researchers from the group led by Martin Fussenegger, Professor of Biotechnology and Bioengineering at the Department of Biosystems (D-BSSE) in Basel, have developed a novel gene regulation method that enables thought-specific brainwaves to control the conversion of genes into proteins — called gene expression in technical terms.

“For the first time, we have been able to tap into human brainwaves, transfer them wirelessly to a gene network and regulate the expression of a gene depending on the type of thought. Being able to control gene expression via the power of thought is a dream that we’ve been chasing for over a decade,” says Fussenegger.

A source of inspiration for the new thought-controlled gene regulation system was the game Mindflex, where the player wears a special headset with a sensor on the forehead that records brainwaves. The registered electroencephalogram (EEG) is then transferred into the playing environment. The EEG controls a fan that enables a small ball to be thought-guided through an obstacle course.

Wireless Transmission to Implant

The system, which the Basel-based bioengineers recently presented in the journalNature Communications, also makes use of an EEG headset. The recorded brainwaves are analysed and wirelessly transmitted via Bluetooth to a controller, which in turn controls a field generator that generates an electromagnetic field; this supplies an implant with an induction current.

A light then literally goes on in the implant: an integrated LED lamp that emits light in the near-infrared range turns on and illuminates a culture chamber containing genetically modified cells. When the near-infrared light illuminates the cells, they start to produce the desired protein.

Thoughts Control Protein Quantity

The implant was initially tested in cell cultures and mice, and controlled by the thoughts of various test subjects. The researchers used SEAP for the tests, an easy-to-detect human model protein which diffuses from the culture chamber of the implant into the mouse’s bloodstream.

To regulate the quantity of released protein, the test subjects were categorised according to three states of mind: bio-feedback, meditation and concentration. Test subjects who played Minecraft on the computer, i.e. who were concentrating, induced average SEAP values in the bloodstream of the mice. When completely relaxed (meditation), the researchers recorded very high SEAP values in the test animals. For bio-feedback, the test subjects observed the LED light of the implant in the body of the mouse and were able to consciously switch the LED light on or off via the visual feedback. This in turn was reflected by the varying amounts of SEAP in the bloodstream of the mice.

New Light-sensitive Gene Construct

“Controlling genes in this way is completely new and is unique in its simplicity,” explains Fussenegger. The light-sensitive optogenetic module that reacts to near-infrared light is a particular advancement. The light shines on a modified light-sensitive protein within the gene-modified cells and triggers an artificial signal cascade, resulting in the production of SEAP. Near-infrared light was used because it is generally not harmful to human cells, can penetrate deep into the tissue and enables the function of the implant to be visually tracked.

The system functions efficiently and effectively in the human-cell culture and human-mouse system. Fussenegger hopes that a thought-controlled implant could one day help to combat neurological diseases, such as chronic headaches, back pain and epilepsy, by detecting specific brainwaves at an early stage and triggering and controlling the creation of certain agents in the implant at exactly the right time.


Story Source:

The above story is based on materials provided by ETH Zurich. Note: Materials may be edited for content and length.


Journal Reference:

  1. Marc Folcher, Sabine Oesterle, Katharina Zwicky, Thushara Thekkottil, Julie Heymoz, Muriel Hohmann, Matthias Christen, Marie Daoud El-Baba, Peter Buchmann, Martin Fussenegger. Mind-controlled transgene expression by a wireless-powered optogenetic designer cell implant. Nature Communications, 2014; 5: 5392 DOI: 10.1038/ncomms6392

A New Way to Take Notes: Graphic Notes on iPad

One of my Year 12 Biology HL students uses this APP for creating her graphic notes during lessons.  GoodNotes 4 – Notes & PDF by Time Base Technology Limited allows students to take notes and annotate PDF documents. They will be synced to all your iOS devices automatically, thanks to iCloud. Mac client is coming soon.

Below is an example of my student’s work on our DNA topic – they are colorfully fantastic! Screen Shot 2014-11-10 at 2.48.21 PM Screen Shot 2014-11-10 at 2.48.28 PM Screen Shot 2014-11-10 at 2.48.35 PM Screen Shot 2014-11-10 at 2.48.42 PM Screen Shot 2014-11-10 at 2.48.48 PM Screen Shot 2014-11-10 at 2.48.56 PM Screen Shot 2014-11-10 at 2.49.02 PM