Beach weather at the ancient Arctic?
AI recruiting microbes can speed up staple crop resilience
A rapid test for beer malting barley
San STEM-related Cultural Knowledge & Virtual Reality
How ancient bowhunting technology developed focused human attention
Student teachers teaching VR avatars
UJ in Global Rankings
August 2024
The University of Johannesburg (UJ) is ranked among the top 500 universities worldwide in the Academic Rankings of World Universities (ARWU), also known as the Shanghai Ranking.
May 2024
UJ is ranked in the top 3% by the Center for World University Rankings (CWUR) for 2024 in its Global 2000 List.
May 2024
UJ is ranked number 1 in South Africa and on the African continent among universities that are younger than 50 years, according to the Times Higher Education (THE) Young University Rankings.
Dear Reader,
I am delighted to introduce to you the third issue of our Magazine, an exciting showcase of research and projects dedicated to the betterment of society.
We start off this issue with research indicating that our highly dynamic planet had weather suitable for beach vacations at its poles during Earth‘s middle age. That means the poles were not just free of ice, but also had tropical water temperatures. This startling result was published in Nature Communications by Prof Michiel de Kock from UJ Geology. The study is the culmination of years of research started by the late Prof Nic Beukes, a globally leading researcher during his long tenure at UJ.
Next, we look at UJ’s part in a global collaboration headed by the University of California at San Diego, published in Nature Microbiology. Dr Fidele Tugizimana, Director of the Centre for Plant Metabolomics at UJ Biochemistry, leads the UJ contributions to the growing microbeMASST database. The UJ researchers aim to find beneficial microbes for staple crop production much faster, to assist farmers in coming years with growing seasons expected to be far less predictable due to global warming.
While on the topic of growing seasons sensitive to weather disruptions, we present a UJ Technology Transfer Office (TTO) commercialisation project aimed at barley production. Barley farming, harvesting and delivery for beer malting are high-risk business activities. Prof Eduard Venter at UJ Botany and Plant Biotechnology is developing a rapid field test to assist farmers, silos and maltsters to better manage germination efficiency in barley batches.
Then we move on to learning from the traditional knowledge of the San people – using Virtual Reality (VR). Prof Umesh Ramnarain, the Director of the CALTSTEAM research centre at UJ’s Faculty of Education leads the CAVARS project that brings STEM-related cultural knowledge to school learners. Kalahari San still practise hunting with bows and arrows. Bowhunting in ancient times likely shaped the way humans learnt to focus on complex tasks, shows Prof Marlize Lombard, at the UJ Palaeo Research Institute.
We end this issue with a visit to a VR classroom at the UJ Soweto Campus. Here, student teachers learn how to ask good questions during lessons. The mixed reality simulation (MRS) project leader in UJ Childhood Education is Prof Sarah Gravett and the project manager is Dr Dean van der Merwe. The student teachers also get to practice managing naughty pupils, courtesy of an avatar puppeteer, before they head out to teach diverse pupils at real schools.
Happy reading!
Yours sincerely,
Prof Sarah Gravett
Deputy Vice-Chancellor: Research & Innovation (Acting)
Beach weather at the ancient Arctic?
Ancient magnetic clues in rocks from India indicate that the polar regions had most unexpected warm weather about 1,200 million years ago.
AI recruiting microbes can speed up staple crop resilience
If bacteria had ID cards, recruiting them into the protection of staple crops would be much faster. Instead, the AI-powered microbeMASST search tool presents a promising way to speed up development of agricultural products in the age of less predictable growing seasons.
A rapid field test for beer malting barley
Farmers, silo operators and import agents may soon be able to test barley for germination efficiency themselves with a simple, 30-minute test they can do while going about their business.
San STEM-related Cultural Knowledge and Virtual Reality
African cultures have ancient ways of solving everyday problems. However, traditional knowledge tends to be displaced or lost over time. The CAVARS project aims to preserve aspects of this knowledge using Virtual Reality (VR).
How ancient bowhunting technology developed focused human attention
Completing complex tasks requires focused attention. Boring and mundane ones do too. Also, when we engage with new technology, our minds start to think in new ways. The bow-and-arrow was first invented in Africa.
Student teachers teaching VR avatars
At the UJ Soweto Campus, student teachers enter a Mursion immersive Virtual Reality (VR) with 5 diverse primary school “avatars”.
They learned something crucial: How to ask good questions during a lesson while fielding the challenges of sometimes rowdy virtual pupils.
Beach weather at the ancient Arctic?
Ancient magnetic clues in rocks from India indicate that the polar regions had most unexpected warm weather about 1,200 million years ago.
Written by Prof Michiel de Kock
Image by Renide Peters at Shutterstock.com
Sub-editing by Therese van Wyk
The hot Indian air swirls in this quarry in central Andhra Pradesh, about 7 hours’ drive south of Hyderabad. Despite the heat and discomfort, a small cylinder of limestone is carefully removed from the quarry face. It was drilled using a handheld petrol drill resembling a chainsaw.
The thin beds of dark grey rock, known as Narji limestone, are mined for popular use as tiles or slabs, but we are interested in it for a very different reason. These were deposited at a time known as the Mesoproterozoic, 1200 million years ago, in a shallow sea that covered much of what is southern India today.
A different Earth
The cylindrical rock sample, together with similar samples collected by a team of researchers from South Africa and India over the last couple of days, is a treasure trove of clues about what our planet looked like back then.
It was a very different place. For one thing, the sun was less bright back then. A map of the world would also have looked very different.
Continents move 50 km per million years due to plate tectonic forces. Through time, continents coalesce and break up in an ever-changing dance across the planet’s surface. Since the Mesoproterozoic, India could have travelled around the globe 600,000 times!
Information held by tiny magnetic grains in the rock, once unlocked, will tell us exactly where India was located when the Narji limestone was deposited.
Was India near the pole?
Paleomagnetic data indicate that the Narji limestone was deposited at very high latitude, approximately 70 degrees from the equator. This is comparable to the northernmost point of Norway, or that of the Wendel Sea in the Antarctic today.
It is a highly unexpected result, because limestone is typically associated with tropical conditions. In addition, we cannot say whether the Narji limestone formed near the North Pole or the South Pole.
The reason is that in palaeomagnetism, we generally cannot distinguish between North or South Pole, because the magnetic field flipped multiple times in the geological past. However, we can say how far from the equator away a specific location was.
In rare instances our record is good enough to trace the drift of a continent back in time from its present locality. In such cases we do have hemispherical information. In this study hemispherical information is not needed because the Earth’s climate zones are symmetrical around the equator. So, what is true for one of the polar regions is also true for the other in terms of climate.
Modern limestone deposition
Today limestone is typically deposited in shallow tropical areas by marine algae and corals in places like the Bahamas about 25 degrees from the equator. Imagine clear aquamarine waters, white sand and palm trees.
Limestones do form in colder conditions but when they do, they are formed in much lower quantities and typically made up of shell fragments. Such shelly beds are often interbedded with glacial sediments near the poles. Cold-water limestones may also contain spiky pyramidal crystals of glendonite, the alteration product of metastable ikaite (a hexyhydrate of calcium carbonate mineral) that forms in the near-freezing polar water.
Narji puzzle
In contrast, the Narji limestone was produced by microbial communities and look like modern tropical marine limestones. They are devoid of glendonite and glacial interbeds. It also represents copious amounts of deposition. Remains of the Narji limestone occur across southern India and it once covered the whole subcontinent as a ~500- to 850-meter-thick layer. This finding presents a climate puzzle as it indicates that the ancient polar oceans were much warmer than today, potentially as warm as 15-20 degrees Celsius.
Reliable record
The magnetic record of limestones is notorious for being easily overprinted. The magnetic record in rocks, like the record in any other recording device (e.g., USBdrive) can be altered, overwritten, or even wiped clean. How can we be sure that the magnetic record of the Narji limestone is reliable? Is the paleolatitude of 70 degrees from the equator a record of where the limestone formed, or is it a record of the Earth’s magnetic field at a more recent time?
Magnetic minerals could for example have been altered when groundwater moved through the limestones many million years after the limestone’s formation. There are three arguments against this being the case.
Chemistry alibi
The first is the chemistry of the limestone, which argues against significant later interaction with groundwater. However, it is not only interaction with groundwater that can change the magnetic minerals of a rock. There are other ways in which this can happen, which would not alter the chemistry.
India not near Arctic recently
The paleogeography of India is well documented over the past 540 million years. Today India is welded to the rest of Asia along the Himalayas. In the past it formed part of the supercontinent Gondwana. When Gondwana broke up, India moved away from its former neighbors like Africa and Antarctica to reach its current location.
During this whole time, the Indian plate never reached a latitude and orientation as that recorded by the magnetic minerals of the Narji limestone.
This suggests that the high-latitude record must be older than 540 million years, but it leaves quite a long chunk of time between 1200 million years and 540 million years during which the high-latitude record could have been recorded.
Unfortunately, our knowledge of the paleogeography of India before 540 million years is fragmentary.
Dr Herve Wabo measuring the orientation of a palaeomagnetic limestone sample for the study.
Photo supplied by Herve Wabo.
Some of the Narji limestone samples analysed in the study. The arrows indicate the in-situ orientation of samples.
Photo by Therese van Wyk.
The Narji limestone quarry south of Hyderabad in central Andhra Pradesh, south-east India. This is one of several sites sampled for palaeomagnetic study.
Photo by Herve Wabo.
Prof Michiel de Kock sampling rocks of the Cuddapah basin in Andhra Pradesh in India. The rocks provide unique palaeomagnetic clues to mild, even tropical weather at the poles about 1,200 million years ago.
Photo supplied by Michiel de Kock.
Three researchers who made crucial contributions to earlier studies that culminated in this article. Sadly, they are no longer with us. On the left is Prof Dilip Saha and Prof Sarbani Patranabis-Deb from the Indian Statistical Institute in Kolkata, India. On the right is globally leading Prof Nic Beukes from the University of Johannesburg.
Photo by Herve Wabo.
Prof Michiel de Kock, the lead author of the study, at sedimentary rocks characteristic of the Witwatersrand Supergroup west of Johannesburg. Rock in this area is among the oldest well-preserved, accessible sedimentary rocks on Earth. Photo by Therese van Wyk.
Unlocking the ancient magnetic record of rocks
Written by Prof Michiel de Kock
Rocks can become magnetised and retain a record of the Earth’s magnetic field. This is known as remanence. A rock records and retains remanence for a long time if it contains minerals of the right chemical composition, and if those minerals are of the right size.
Magnetic minerals such as magnetite or hematite are needed, and crystals should not be too small or too big. Both size extremes would result in an unstable remanence that can easily be overwritten. Luckily for geologists, many rock types contain these and other magnetic minerals that are also of the desired grain-size to retain remanences for millions to billions of years.
Small crystals of magnetite or hematite present in the water column are caught up by the precipitation of calcium carbonate during the deposition of limestone.
These crystals act as tiny compass needles and rotate in the water column as to point north. This direction gets “frozen” in place when the crystals are captured during limestone deposition. The limestone will only lose this record if the magnetic minerals recrystallize to form new magnetic minerals through interaction with groundwater, or if the limestone is heated up to at least between 500-600 degrees Celsius.
To read the magnetic record in rocks, the collected samples are returned to the palaeomagnetic laboratory. Here, samples are slowly stripped of their magnetic record in a process known as demagnetisation to reveal the most stable kernel of the limestone’s remanence.
The laboratory is equipped with a sensitive superconducting rock magnetometer that can measure very weak magnetisations like those recorded in rocks.
Old-enough evidence
The magnetic record of the Narji limestone, however, is similar to rocks elsewhere from India that have been dated to 1192 million years. This can be seen as support for the limestone recording its high-latitude magnetic record either during or shortly after its deposition at around 1200 million years ago.
A third line of evidence supports the early recording of the high-latitude position. This comes from results of a so-called field test. Field tests are designed to estimate the timing of magnetic recording against geological events that can be witnessed in the field.
For example, limestone that slumped down the slope near the edge of deposition along the continental shelf would be recorded in the rock record as a conglomerate layer made up of fragments or clasts of limestone.
The magnetic directions recorded in individual clasts would be random if the limestone recorded its magnetic record before the slump happened. While directions would be uniform if the magnetic record was locked-in only after the slump occurred.
This is known as a conglomerate test, and in the Narji limestone the test is positive. That is, lock-in of the high-latitude direction occurred before conglomerate formation and during deposition 1200 million years ago.
Unexpectedly warm Arctic
These Indian findings are similar to high-latitude limestone deposits of the same age from North China, but are otherwise seemingly unique when compared with other geological times where limestones are typically found at lower latitudes.
This suggests that there is something very special about the world’s climate in the Mesoproterozoic that would allow limestone to be deposited at the poles.
The polar regions had to be ice-free with relatively warm ocean temperatures, possibly as warm as 15-20 degrees Celsius, even though the sun was less bright 1200 million years ago compared to today.
Ancient greenhouse?
One way this could happen was through elevated levels of greenhouse gases like methane and nitrous oxide. Overall, the research highlights a major climatic anomaly in Earth’s history, where greenhouse conditions were far more intense than previously thought.
This would have allowed warm conditions to persist at high latitudes, challenging our understanding of ancient Earth’s climate dynamics and the factors that drove such extreme greenhouse warming.
It indicates a need for further research into the interactions between greenhouse gas concentrations, ocean temperatures, and limestone deposition. Understanding these dynamics is crucial for reconstructing ancient climate systems and the geological history of our planet, but also for understanding future greenhouse climatic conditions as our planet warms in response to anthropogenic activities.
Research Article
2024 Nature Communications
AI recruiting microbes can speed up staple crop resilience
If bacteria had ID cards, recruiting them into the protection of staple crops would be much faster. Instead, the AI-powered microbeMASST search tool presents a promising way to speed up development of agricultural products in the age of less predictable growing seasons.
Written by Therese van Wyk
At the 2024 International Metabolomics conference at Osaka ATC Hall in Japan, from left to right: Mrs Anza Ramabulana, UJ Biochemistry, PhD candidate in the Tugizimana Lab; Dr Fidele Tugizimana, incoming Co-Director of the UJ Research Centre for Plant Metabolomics and lead microbeMASST collaborator at UJ Biochemistry; Prof Pieter Dorrestein, Director of the Collaborative Mass Spectrometry Innovation Center and Co-Director of the Institute for Metabolomics Medicine at the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego; Dr Mosteoa Lephatsi, UJ Biochemistry, Postdoc in the Tugizimana Lab; Dr Claude Yasmin Hamany, UJ Biochemistry, Postdoc with Prof Dubery.
Photographed in the UJ Shimadzu Research Centre, from left to right: Dr Fidele Tugizimana, CoDirector for the UJ Research Centre for Plant Metabolomics, Dr Lerato Nephali, and Prof Ian Dubery, previous Director of the Centre. Photo by Therese van Wyk.
A search tool with data from researchers around the world is tracking down microbes and their metabolites in a game-changing new way. Uniquely, it can significantly speed up the identification of known and unknown bacteria, fungi and single-celled archaea, and their close relatives.
The tool can be used to improve the resilience of food crop production amidst changing climate; to analyze the human gut microbiome; and many other applications.
UJ researchers are contributing ‘fingerprinting and ancestry’ microbial metabolomic data to the project, says Dr Fidele Tugizimana from the UJ Department of Biochemistry. They are also testing the computational tool and workflows around it.
The global GNPS microbeMASST project is led by Prof Pieter C. Dorrestein at the University of California San Diego (UCSD). Curated data from 25 research teams, including the UJ Research Centre for Plant Metabolomics containing more than 60,000 microbial monocultures, forms the core of the search tool.
In a recent journal article in Nature Microbiology, Dorrestein and UCSD co-authors Dr Simone Zuffa, Dr Robin Schmid, and Dr Anelize Bauermeister introduce microbeMASST as part of a wider ecosystem of computational tools, facilities and equipment called GNPS.
Recruited via social media
For Tugizimana, the collaboration with Dorrestein started on Twitter, now known as X. Dorrestein tweeted that he was looking for collaborators around the world to compile a protocol for molecular networking in GNPS. The protocol was published in 2020 in Nature Protocols. Since then, the collaboration evolved and includes the microbeMASST journey.
There was a specific moment that triggered the idea for the GNPS ecosystem and microbeMASST, says Dorrestein via email.
“I realized that we could never understand microbial metabolism alone. We could not culture 60,000 microbes and obtain data on them. However, we realized if we work together with others in the scientific community, that it may be possible to build a large resource to understand microbes that are involved in microbe-host interactions, such as plants or humans.”
Typical in the online age of research, the Dorrestein and Tugizimana met in Japan in person, for the first time, after the Nature Microbiology research paper about microbeMASST had already been published.
Tugizimana is the incoming Co-Director for the UJ Research Centre for Plant Metabolomics. The Centre has published several research papers on bacterial metabolites. Their research analyses metabolites that can improve the resilience of tomatoes, sorghum, maize (corn) and barley.
In the first microbeMASST stage Dr Tugizimana, Prof Ian Dubery, Dr Lerato Nephali, and the UNIVEN collaborator Prof Edwin Madala, gathered metabolomic data from microbes. These microbes were bacterial and fungal monocultures, and the data was submitted to microbeMASST researchers. Nephali was a doctoral student at UJ at the time. Their data was then subjected to rigorous quality tests, before being imported into the system.
In the next stage, they were among the ‘alpha and beta testers’ of the microbeMASST tool, its Artificial Intelligence algorithms, and the associated workflows.
Much faster microbial sleuthing
The unique strength of microbeMASST is finding the possible microbes that can produce a particular metabolite (example ‘X’) within its ‘search-engine’. The ‘search-engine’ is built from metabolomic data contributed by research groups from around the world.
MicrobeMASST can then ‘short-list’ X-producing microbes, taking into account the other metabolites (example R, S, T, V, W) also produced by the microbes. This is made possible by Artificial Intelligence which analyses the relationship between metabolites; the microbes which produce them; and the phylogenetic trees which trace the evolution of microbes and their extended families.
Which means that the tool can even suggest microbes that may be related to the ‘short-listed’ candidates.
From
microbes to improving yields
In laboratory and greenhouse tests, researchers may find a ‘soup’ of beneficial microbes that appear to help crop plants in some ways, says Tugizimana. But there is a lot to discover before the ‘soup’ can be ‘packaged’ in a liquid or carrier-material formulation and sold as an agricultural product.
Farmers are dealing with enough uncertainty already. The products they buy need to have a reliable and predictable effect on their crops.
“You need to know what type of chemistry those microbes in the formulation produce,” adds Tugizimana.
“I should be able to tell you that the formulation will help your specific crop resist a harsh environment, to produce a higher yield, and why that product would have that effect.”
Searchable metabolite data
The growing mountain of microbe metabolite data in microbeMASST is designed to be searchable in a specific way, explains Dorrestein.
“To make data ready for data science, including AI applications, is the key goal of microbeMASST. It was curated with around 100 scientists worldwide by taking metabolomic data from microbes grown in culture and curating the taxonomic information.
“Then each data piece is linked to a universal spectrum identifier – effectively a hyperlink to the raw data. This
How bacterial metabolites can defend food crops
To keep a field of corn (maize) plants going for an entire season and get a good harvest can be tough. Drought, heat, infertile soil, hail, floods, insects, diseases, weeds... the list of things that kill or stunt staple food plants is long.
Sometimes chemical fertilizers, insecticides, herbicides, and irrigation can be used. But these have their limits and can be too expensive for many farmers.
Farmers’ tiny helpers
For example, fertilizing a dryland field does not help if the corn variety cannot withstand much heat or water stress. Even a heat-and-water stress-resistant variety can use extra help. Especially on drought-prone fields where the weather fluctuates far more than in the past.
Recent research including UJ studies, has shown that significant help can come from microscopic helpers, available everywhere in planted fields. In particular, from beneficial microbes - tiny bacteria and fungi - in the soil next to plant roots, inside plant roots, and on the leaves and stems of crop plants.
Microbe partners
The relationship between crop plants and beneficial microbes is similar in some ways to the human gut microbiome, where bacteria in the human digestive tract help manage absorption of food nutrients, for example.
Beneficial microbes maintain two-way communications with the plants – even warning
can then be searched, and we report on the taxonomic distribution and, if available, any structural annotations.
“This will help understand the complex world of metabolites associated with the microbiome and will find applications in toxin research, agriculture, biotechnology and natural product discovery,” says Dorrestein
Future resilient agriculture
plants of impending insect attacks. The microbes also maintain an environment that works well for both microbes and plants.
Microbes like these are commercially available in biofertilizers which contain plant-growth promoting rhizobacteria (PGPR). Seeds can be coated with biofertilizers, and soil or plants can be sprayed with it.
Valuable metabolites in a haystack
However, there is a big catch. There can be thousands, even millions, of distinct types of microbes present in a planted field. Each of those can produce dozens of natural chemicals called metabolites.
Like humans, bacteria ‘eat’ materials in their environment, ‘digest’ them, and then either use the ‘digested’ chemicals as nutrients to survive, or ‘expel’ them as waste products – much like we breathe out carbon dioxide. These waste products are called microbial metabolites. The metabolites make it possible for the microbes and their partner crop plants to maintain two-way chemical communications.
The microbes also boost or defend their partner plants with these metabolites.
Beyond microbial soup to product development
When researchers find a group of microbes that could improve plant resilience in some way, they start asking questions. Which metabolites improve the plants’ ability to resist heat, drought, disease, or insects?
And which microbes do those metabolites come from? And why did those microbes produce those metabolites? And are there any ‘uncle, aunty and
Crops that could reliably be grown in the past are likely to have lower yields in future, due to global warming. Here the GNPS microbeMASST project can contribute to more resilient future agriculture.
“Climate change is a certainty,” says Prof Ian Dubery, from UJ Biochemistry. Dubery is the outgoing Director of the UJ Research Centre for Plant Metabolomics.
“What we know is that traditional phenotypes, for example disease resistance, are breaking down during secondary stress [created by climate change]. The combination of stresses – heat, drought, pathogens –is certain to have detrimental effects on agricultural production; not only in South Africa but worldwide.
“We need to look at alternative approaches to agricultural practices. That can include Plant Beneficial Rhizobacteria, known as plant growth-promoting rhizobacteria (PGPR) which interact with plants in the root zone. But there is also a microbial community of bacteria, fungi and more on the leaves and stems of crop plants, called the phyllosphere. That is also a possibility for resilience that can be manipulated.”
The phyllosphere is not as well-known as the rhizosphere around the roots.
“MicrobeMASST can certainly assist in enhancing future research globally. The tool can help speed up development of new microbial ‘cocktails’ or consortia to apply to seeds, soil or plants, to improve yield or resilience,” concludes Dubery.
Research Articles
2024 Nature Microbiology
2020 Nature Protocols
Use of Artificial Intelligence in this Article Google Gemini was used by Therese van Wyk to summarise the research article in plain English before interviewing the researchers, to help explain some research terms, and to find an article headline.
second cousin’ microbes that can also produce those helpful metabolites?
All these questions need to be answered before it is possible to develop a reliable, precise commercial product for farmers.
GNPS microbeMASST tool
But finding the answers to these types of questions is exceedingly difficult. For a start, identifying microbes with ‘DNA fingerprinting’ is often impossible, or very expensive and time-consuming.
So going the ‘mass-spectrometry ancestry tracing route’ can be a more robust, versatile, and economical way of answering the questions. But it is still very time-consuming to identify the metabolites and which microbes produced them.
This is where the GNPS microbeMASST tool changes the game completely. MicrobeMASST can speed up the identification of known and unknown microbes by their metabolites by orders of magnitude.
As a result, the development of new agricultural products to protect crops can be speeded up also, in an era of far more unpredictable growing seasons.
More about UJ research on plantmicrobe communications https://www.eurekalert.org/newsreleases/915477
Image by Mike Flippo at Shutterstock.com
A rapid field test for beer malting barley
Farmers, silo operators and import agents may soon be able to test barley for germination efficiency themselves with a simple, 30-minute test they can do while going about their business.
Written by Therese van Wyk
C for Control line validates the test
T for Test line shows when germination efficiency is lower than 98%
Photos by Therese van Wyk
Comparing UJ test to existing tests
Brewing beer according to the German Reinheitsgebot (purity law) enacted in 1516 sounds simple. After all there are just four ingredients involved: water, hops, yeast and a barley malt.
However, when brewing on an industrial scale, that’s where the simplicity usually ends. One batch of beer could be multiple tanks of 10,000 liters each.
To produce a nearly perfect beer every time, all the ingredients must be virtually perfect also.
Every year a truly enormous amount of beer is brewed all over the world using malts made from barley. Without the fermented sugar of the barley malt, the beer would have hardly any alcohol content. The barley malt also makes a crucial contribution to the aroma, flavour, colour and mouth feel that aficionados expect.
But barley can be a very tricky ingredient for largescale malting, demanding very precise testing and processing.
A new test for malting barley
UJ researcher Prof Eduard Venter is developing a simple field test for the suitability of barley for beer malt. The test measures a critical property of barley –the germination efficiency.
Venter is a researcher and Head of Department at UJ Botany and Plant Biotechnology.
Related tests currently done in industry are called germinative or germination energy tests, and germinative capacity tests.
“Germinative energy” can be seen directly if one can wait three days to see how many in 100 grains germinate, says Venter. This visual, subjective test is done by maltsters.
Another test done by maltsters and some silos is a visual, subjective “germinative capacity” test which takes about 10 minutes. In this tetrazolium staining test, a hundred grains are cut along their length, stained, and inspected for dead grains that will never germinate. However, this test has limitations in that experienced staff are needed who can accurately interpret what they see, and controlled conditions.
In contrast, there is an objective test that also takes about 10 minutes. It requires sophisticated laboratory equipment and controlled conditions such as malting facilities. In this test, germination efficiency is ‘measured indirectly’ by estimating alpha-amylase, an enzyme present in barley grains very early in germination before sprouts are visible outside the grains. However, this test is only useful once germination has sufficiently progressed inside the grains.
A fast, objective, direct measurement in the field
The test being developed by Venter takes the tests currently done a step further.
It is designed to directly and objectively measure a plant growth hormone that is present in the grains, to indicate if germination has started. This also works at the very beginning of the germination process. The test is also designed to be accurate and robust, and to be used by farmers, silo operators, transporters and import agents as they go about their day-to-day business.
The goal is to produce a highly accurate test result within 30 minutes, in ambient temperatures from 15 to 35 degrees Celsius. The tests currently done at silos take about that long.
Simple procedure
The new barley test requires a small plastic Lateral Flow Device (LFD) about the size of a USB stick. The disposable LFDs are sealed individually in foil. Each LDF contains ‘dipstick paper’ that tests for the plant growth hormone.
LFD technology is widely used in COVID-19 and home pregnancy tests. It is considered accurate and reliable under a variety of conditions.
If the “T” for test line is visible on the LFD ‘dipstick paper’, it means that the germination efficiency of that sample from the batch is lower than 98%.
The other components of the test can be re-used to test several samples: a small plastic bottle with the first test liquid (also called a buffer), another tiny plastic bottle with a second test liquid, a small plastic test tube and a plastic eyedropper (or pipette in the laboratory).
The person doing the new barley test also needs a device to mill about a tablespoon of barley seeds to a fine powder. A home coffee grinder plugged into a small inverter would work almost anywhere. Measuring quantities and doing the test itself is simple.
Better informed expiry date management
When the barley test is ready for commercial use, it will be possible to test germination efficiency from harvest to malting, at every stage of the logistics along the way.
Currently most testing is done by silos and maltsters, and needs trained staff, specialised equipment or both, says Venter.
Accurate, objective tests from the very start of the value chain can then enable better informed business decisions. For example, much better ‘expiry date’ management of batches of barley becomes possible. It can also result in lower losses of barley batches unsuitable for beer; and help lower the risk of disruption to industrial-scale production.
Photo by Deyana Stefanova Robova at Shutterstock.com
Why sprout potential is such a beer deal
Brewing demands almost perfect barley. If a batch of barley is not suitable for beer production, its value can fall dramatically. Meanwhile, there is a lot that can happen to a harvest between the farm and the maltster. The value chain can be long and involve a lot of people on more than one continent.
There is possible rain, mist, humidity and other weather events during the growing season and the harvest. Add to that storage on the farm, transport to a silo or ship, storage in a silo, shipping across the seas, transport to another silo, another period of storage, and then delivery to the maltster, if exports and imports are involved.
Currently, silos and maltsters do a series of tests, to find out if a batch of barley is good enough to be turned into beer malt. Some of these are visual assessments by inspectors with many years of experience. Others require expensive laboratories and qualified staff.
However, even if a batch passes muster with all these tests for protein, starch and more, it could still be unsuitable for brewing.
The way barley grains germinate, and stringent beermaking requirements, are the reasons for this.
A barley seed needs just enough moisture and a high enough germination efficiency to start germinating. Then it must keep developing the barley sproutwithout any interruptions - until the desired stage for beer malting is reached. This is necessary to convert the stored starch into sugars necessary for fermentation. The entire process needs to happen in controlled conditions at the malting facility. Virtually all the grains need to sprout at roughly the same pace, to ensure a good beer.
Prof Eduard Venter is developing a simple field test for the suitability of barley for beer malt. The patented test measures a critical property of barley – the germination efficiency.
But barley grains have only one chance at germination. If too many don’t get far enough along with their sprouting the first time, there is no next time. That batch cannot be turned into malt.
In addition, if some grains start germinating for any reason before delivery to the maltster – that batch could be unusable for beer malt as well.
As an example, pre-germination, also called chitting, happens when there is prolonged rain or mist before a harvest, and the grains start sprouting while still attached to the plant.
Yield versus pre-germination
Farmers plant a variety of barley cultivars for beer malting, says Venter.
“Some of these cultivars are more prone to pregermination than others. If you have a cultivar that is high yielding, has all the best characteristics for making beer, but also has an inherent pre-disposition to pregermination, that would be a cultivar that needs more testing for germination efficiency. Especially during adverse weather conditions, which could be anything that provides enough moisture for the barley to pregerminate – such as a sea mist during harvest or drying.”
When 98% is a pass
Currently, a farmer could harvest some barley, visually inspect it, and transport it to a silo. The silo inspectors would assess the barley on the truck. Depending on their skills and facilities, they may not know that the batch has a germination efficiency of ‘only’ 98%.
That germination efficiency means that 98 out of every 100 barley grains would germinate and keep going under optimal conditions until they reach the correct stage for malting. To most people this sounds good enough.
But in the UK brewing industry, 98% is the bare minimum. In Canada, 95% is the norm.
Worse, germination efficiency is reduced during longterm storage, even under controlled conditions in silos. That 98% batch that just arrived could be a 96% batch in a few weeks or months, and unsuitable for UK beer.
Expiry
date decisions
If the farmer and the silo staff could know that it is a 98% batch before the grain is decanted at the silo, they would likely make a new decision. They would not store the grain in the silo but fast-track it to the maltster, while the barley is still suitable for beer.
If they could test the batch in the truck parked at the silo, and find out that it is a 99% batch, their decision could also be different. They could then know that the germination efficiency ‘expiry date’ of that batch could be a few months or even a year out.
The 99% batch could then be stored in the silo, to be dispatched later.
The germination efficiency information from the new test being developed by Prof Venter can help manage the ‘expiry dates’ of barley batches in a whole new way.
PATENTS
The barley test is patented in several countries with significant beer production.
Photo by Therese van Wyk
San STEMrelated Cultural Knowledge & Virtual Reality
This picture is from the CAVARS Virtual Reality (VR) experience called ‘Phases of the Moon’. In this VR, school learners can explore how San people of the Kalahari Desert in Southern Africa observe the moon.
The San people use this information to guide their way of life in maintaining harmony with the natural world.
CAVARS – Culturally Anchored Virtual and Augmented Reality
Simulations – is a VR project of UJ’s Faculty of Education CALTSTEAM research centre. Prof Umesh Ramnarain heads CALTSTEAM.
More about CALTSTEAM.
African cultures have ancient ways of solving everyday problems. However, traditional knowledge tends to be displaced or lost over time. The CAVARS project aims to preserve aspects of this knowledge using Virtual Reality (VR). School learners (students) can interact with the VRs and learn about the STEM (Science, Technology, Engineering and Mathematics) knowledge related to these cultures.
The project is located in the CALTSTEAM (Centre for Advanced Learning Technologies in Science. Technology, Engineering, Arts and Mathematics) research centre of UJ’s Faculty of Education.
Written by Therese van Wyk and Umesh Ramnarain
Photos by Nokuthula Mbatha
Virtual Reality headset kit
The CAVARS simulations are implemented on three different Virtual Reality headsets. Ms Linda Mapaseka (left) experiences the San ‘Phases of the Moon’ VR with the most economical option, the mobile VR headset.
The kit is easily assembled by a layperson, and then a smartphone running a VR app is added. This option does not include interaction with the VR, so there are no hand controls.
Ms Mapaseka is a Research Assistant and studying towards a Bachelor of Education Honours (BEdHons) at the CALTSTEAM research centre of UJ’s Faculty of Education.
Coding VR applications
Developing a VR understanding of with ‘virtual objects’ Mr Izak Potgieter
Oculus Quest 2
Teacher casting Virtual Reality
A teacher with an Oculus Quest Pro headset ‘casts’ the VR onto a screen so that all learners can see what happens within the VR. The teacher can also direct learners to a particular area within Virtual Reality, almost like a real-world classroom. The teacher navigates the learners’ VR experience by drawing their attention to important elements within the VR environment, such as specific objects, phenomena, or scenarios.
Ms Thato Mashishi (right) demonstrates the use of the dual hand controls. She is a Research Assistant and a Master of Philosophy (MPhil) student at the CALTSTEAM research centre of UJ’s Faculty of Education.
applications for immersive experiences
VR application involves coding complex 3D environments and interactions, requiring a deep of both software development and immersive user experience design. In VR, users interact objects’ using hand controllers and experience a sense of presence and immersion. Potgieter coded the San ‘Phases of the Moon’ VR. Here he demonstrates the application using an headset. Mr Potgieter is from the UJ Metaverse Research Unit sponsored by Meta.
Cultural STEM practices in Virtual Reality
Prof Umesh Ramnarain (right) and Mr Izak Potgieter (2nd from right) travelled to the San people at Andriesvale, a community in the Northern Cape province of South Africa, just south of the Kalahari Desert, to observe their cultural practices firsthand. They also interviewed the San about their knowledge of the phases of the moon, and how they use that information.
Prof Ramnarain heads the UJ CALTSTEAM research centre within UJ Faculty of Education, which is developing the CAVARS VRs. More about Prof Ramnarain’s research in Science and Technology Education.
Mr Potgieter coded the VR for CAVARS ‘Phases of the Moon’. Dr Pieter Myburgh (left) heads the UJ Metaverse Research Unit sponsored by Meta, where Mr Potgieter is a staff member.
Culturally-anchored VR
While inside the VR, a person can turn around physically to see the landscape, look up to see the virtual stars or down to the virtual ground. They can also ‘click’ and interact with cultural objects about the narrative on ‘Phases of the Moon.’
At this stage of development, each person can see the VR, but not the other ‘players’. Up to four learners and a teacher can experience the VR at the same time.
In this photo (left), all three types of headsets can be seen. Prof Ramnarain (left) wears an Oculus Quest Pro, Dr Pieter Myburgh (2nd from left) wears the mobile VR headset, Ms Thato Mashishi (centre) wears an Oculus Quest Pro, and Ms Linda Mapaseka (2nd from right) and Mr Izak Potgieter wear Oculus Quest 2 headsets.
Dr Mafor Penn (second from left) an expert in science education made an invaluable contribution in conceptualising the project, and then working with the developers to ensure that the VR simulation effectively supported the teaching and learning of ‘Phases of the Moon.’ Dr Penn, together with Ms Noluthando Mdlalose (centre), a researcher at CALTSTEAM, also managed the piloting of the simulation at schools.
The project is funded by the Technology Innovation Agency (TIA) of South Africa.
How ancient bowhunting technology developed focused human attention
Completing complex tasks requires focused attention. Boring and mundane ones do too. Also, when we engage with new technology, our minds start to think in new ways. The bow-andarrow was first invented in Africa. The earliest evidence comes from South Africa, dating to between 80,000 and 60,000 years ago. Using bowhunting technology so long ago likely helped to shape how we can pay attention today, surrounded by mobile devices.
Image by 2630ben at Shutterstock.com
GRASHOEK, NAMIBIA – CIRCA MAY 2016 – A San man demonstrate how to make hunt with a bow. The San shows their skills in Living Museums which helps preserve their culture and skills.
Written by Prof Marlize Lombard (Research Professor, UJ Palaeo-Research Institute) Editing and subediting by Therese van Wyk
Today, the pings, alerts, rings, and notifications of our computers, phones and tablets impact the way we think and behave. Researchers from France and the United Kingdom found that it can even cause long-lasting difficulties with paying attention. It may also contribute to diminished grey matter in brain areas that control our attention span.
Using technology, however, can also help us to develop our attentional range. One technology able to do so, is the bow-and-arrow, whether using it for subsistence hunting in the past or for archery in sporting competitions today.
Ancient bowhunting
San trackers of the Kalahari are acutely aware. They pay close attention to animal spoor and other signs. Yet, they avoid focussing all their attention on the tracks. Instead, they maintain a keen consciousness of everything else around them.
Tracking wild animals during the hunt thus requires both selective and intermittent attention. It means a constant refocussing between changes in the minute details of the spoor and the greater environment. When stalking an animal, the most important thing is not to attract attention with sudden movements. Hunters thus take their time, moving slowly when the prey animal is not looking, and not moving when the animal is looking in their direction. They are also careful not to disturb other animals that may alarm the intended prey.
Finally, they aim with quiet-eye precision to bring down their prey – not unlike Olympic archers today.
Archery driving neuroplasticity
To hit a target, the archer uses both hands at the same time, in different ways, and aims at a distance. For this, modern sports archers need high levels of focus, precision, and emotional control. They need to coordinate their physical movements with visual processing and sustained attention. As their brains adapt through practice, their accuracy improves –reflecting high levels of neuroplasticity.
Brain regions for accuracy
In neuroimaging studies, Korean researchers compared the brain responses of expert Olympic archers to those of novice archers.
The studies showed that expert archers’ brains exhibit more efficient neural networks, particularly in regions associated with visuospatial attention and motor planning.
This efficiency allows them to reach an alert state quicker, use environmental information better, and suppress distractions more effectively than novices. In this way, expert archers can better meet the high cognitive demands of the sport.
Evolving human ‘software’ and ‘hardware’ for attention
Nowadays, it is possible to study brain activity and human behaviour in real time – thus, to study the human mind (cognition) in action.
However, cognitive archaeologists and palaeo-neurologists cannot excavate ancient human minds or observe early humans going about their business.
Instead, we use fossil skulls and Stone Age technologies (the ‘mental hardware’) as well as ancient DNA (the ‘software’) to indirectly explore developments in the cognition and behaviour of humans in the past.
Earliest complex machine
For our species, Homo sapiens (which means wise human), there are fossil skulls and some ancient DNA that can be studied: both stretching back to 300,000 years ago in Africa where all living humans originated from.
The fossil record shows that human brain regions needed for paying attention in complex ways, changed and expanded at roughly the same time as changes in ancient hunting technologies. One of those technologies was the bow-and-arrow. It is the earliest complex ‘machine’ we know of that requires using both hands in different ways and aiming at a target over a distance.
A brain region that facilitates the use of such technologies, and that showed change and expansion in humans, is the precuneus, which also caused changes in the parietal lobe.
Brain region needed for bowhunting
The parietal lobe is one of five major lobes in the brain and sits at the top back of the head. The precuneus is tucked inside the parietal lobe, closer to the centre of the skull.
In modern humans, the precuneus is involved in visuospatial integration and attention. This helps you understand what you see around you, and what you need to pay attention to, to interact effectively with your environment. The precuneus is crucial in for modern archery today and was probably key to the success of ancient bowhunters.
Brain development from ancient times
Fossil evidence shows that the human skull gradually became more spherical, from prehistory to the present day. This suggests that the human parietal lobe and Photo
precuneus continued to develop and specialize over the past 600,000 years or more. They reached their modern size ranges by about 100,000 years ago and continued to develop until about 35,000 years ago.
Such sustained modification suggests that neuronal and cognitive adaptations associated with these areas were ongoing in the sapient brain when people started to use bows and arrows in southern Africa since about 80,000 years ago.
The gradual development of the parietal lobe and precuneus in early humans suggest that the practice of bow hunting could have driven the evolution of advanced cognitive abilities.
In particular, the ability to focus attention selectively and maintain it under challenging conditions, as well
as focussing on both hands doing different things simultaneously, are dependent on the precuneus.
Feedback between the use of technology and the brain
For developing the ability to pay attention in the way we do today, a co-evolutionary feedback loop was probably required. That feedback loop probably started 600,000 years ago, continuing into the present day.
Each small improvement in the Homo sapiens brain, our or DNA, or in the ways we use technology – from a bowan-arrow to our cell phones – drives small changes in one or all, of the other factors.
Eventually, the attention-paying Homo sapiens brain would not only direct accurate bowhunting, but also the development of electronic technology that pervades the lives of so many people today.
Parietal lobe and Precuneus
Brain region developed for archery
Images by Alexander Supertramp and Chrystal Light at Shutterstock.com
Prof Marlize Lombard in Sibudu Cave, KwaZulu-Natal, South Africa, during an archaeological excavation. Evidence of bow hunting in southern Africa going back to more than 60,000 years has been found in the cave by Lombard and her colleagues.
Image by Celso Pupo at Shutterstock.com
Rio de Janeiro, Brazil – August 05, 2016: Saori NAGAMINE (JPN) during the Archery Rio Olympics 2016 held at the Sambadrome in the qualifying Round.
Research Articles
2024 Phenomenology and the Cognitive Sciences
2023 Oxford Handbook of Cognitive Archaeology
2023 Biological Theory
2021 Quaternary Science Reviews
2021 Journal of Archaeological Method and Theory
2020 Biology and Philosophy
Migration of ancient tech out of Africa
The oldest evidence for bow hunting worldwide, dating to about 80 000 to 60 000 years ago, currently comes from South African Stone Age sites. Some of the best examples are Sibudu Cave and Umhlatuzana Cave in KwaZulu-Natal; and Klasies River and Pinnacle Point in the Western Cape.
Some of the small stone artefacts from these sites show damage consistent with use as arrow tips and still contain blood and other residues. Also, bone arrowheads may preserve traces of arrow poison. By about 54 000 years ago, bow hunting arrived with early Homo sapiens settlers in France.
Human species and tech use
In the Phenomenology and the Cognitive Sciences study, genetic differences between modern humans and their extinct relatives such as the Neanderthals and Denisovans, are highlighted.
These two early human species lived in Eurasia more than 40,000 years ago. Our African ancestors had offspring with them once they left Africa.
DNA data shows that certain genes associated with attention and cognitive flexibility are found exclusively in modern humans, and that the ability to pay attention in the way we do today, evolved uniquely in Homo sapiens.
Photo by Owlie Productions at Shutterstock.com
Student teachers teaching VR avatars
At the UJ Soweto Campus, student teachers enter a Mursion immersive Virtual Reality (VR) with 5 diverse primary school “avatars”.
The student teachers learn something crucial: How to ask good questions during a lesson while fielding the challenges of sometimes rowdy virtual pupils.
Here, lecturer and coach Ms Pamela Tshabalala (front, blue shirt) reviews how student teacher Ms Mashudu Mokhatshelwa (front, red jacket) taught the ‘avatars’ displayed on the screen in front of the classroom during a micro lesson.
The other student teachers provide peer coaching and discuss how the micro lesson went. Each student teacher gets an opportunity to interactively teach a micro lesson to the avatars displayed on the screen.
Each avatar has a distinct personality. The Mursion avatars challenge the student teachers in real time - by asking hard questions, not understanding the teacher’s explanations, demanding things, refusing to cooperate, or needing attention in other ways.
From left to right, Ms Luyanda Brown (headband), Ms Noko Hlahla (glasses), Ms Tannika Bhaga (black jacket), Ms Chanice Marais (white & black skirt) and Ms Promise Khoza (pink pleated jacket).
Avatar puppeteer
The student teachers teach five primary school pupil avatars at the same time. Each avatar has a distinct appearance, voice and personality. The avatars react in real time to the student teachers’ actions – giving them instant feedback on how effective their microlesson is.
Here, ‘avatar puppeteer’ Ms Pumzile Mello is both voicing and acting the five avatars. She invents - on the spot - the questions the avatar kids ask the student teacher. She also improvises all the ways they can make the student teacher’s life difficult, and how they respond to the questions asked by the student teacher.
Ms Mello reckons her years of computer gaming were excellent preparation for this role.
She uses an Xbox gaming controller to move the avatars around. The Mursion technology turns her voice into the voice of the pupil she is acting. Becoming an avatar puppeteer (officially a simulation specialist at UJ) requires training.
Student teachers say the way the avatars test their teaching and classroom management skills is really valuable. In a private and controlled environment, they get to practice asking questions during a lesson and managing diverse learners before going out to schools to teach real kids.
Prof Sarah Gravett (left) is the founder and leader of the Mixed Reality Simulation (MRS) project at UJ. She says she saw the potential of MRS, which is a blend of artificial intelligence and live actors, to replicate the dynamics of real classrooms to support pre-service teacher preparation for the teaching profession.
Gravett is the previous Executive Dean of the Faculty of Education. Currently she is the Acting Deputy Vice-Chancellor Research and Innovation.
Dr Dean van der Merwe (2nd from left) manages the project. He envisions the next steps as scaling the project and permanently integrating the mixed reality simulations into the foundation and intermediate phase programmes in the Department of Childhood Education, thereby enhancing the preparation of pre-service teachers for the profession.
Prof Sarita Ramsaroop (2nd from right) is the former Head of Department at UJ Childhood Education. She played a crucial role from the beginning of the project and acted as one of the coaches for student teachers during the pilot phase.
Dr Kathleen Fonseca (right) is the Head of the Department of Childhood Education. She believes the MRS provides a safe space for student teachers to develop their mathematical pedagogical content knowledge and to build their confidence in teaching a subject like mathematics.
Written by Therese van Wyk
Photos by Nokuthula Mbatha
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