28th May 2020
The global demand and consumption of agricultural crops is increasing at a rapid pace. According to the 2019 Global Agricultural Productivity Report, global yield needs to increase at an average annual rate of 1.73 percent to sustainably produce food, feed, fiber and bioenergy for 10 billion people in 2050. In the US, however, agricultural productivity is struggling to keep pace with population growth, highlighting the importance of research into traditional practices as well as new ones.
In an effort to increase crop yield, scientists at Northern Arizona University’s Pathogen and Microbiome Institute (PMI) are working with Purdue University researchers to study the bacterial and fungal communities in soil to understand how microbiomes are impacting agricultural crops. They believe technological advances in microbiome science will ultimately help farmers around the world grow more food at a lower cost.
Nicholas Bokulich, a PMI assistant research professor, and Greg Caporaso, an associate professor of biological sciences and director of PMI’s Center for Applied Microbiome Science (CAMS), have been testing a long-held farming belief that phylogenetics—the study of the evolutionary relationship between organisms—should be used to define crop rotation schedules.
Please use the following link to access the rest of the article: ScienceX
Story by: Heather Tate
27th May 2020
The APOE ε4 gene variant that puts people at a greater risk of developing Alzheimer’s disease also has a link to COVID-19. According to a study published today (May 26) in The Journals of Gerontology, Series A, carrying two copies of the variant, often called APOE4, makes people twice as likely to develop a severe form of the disease, which is caused by the SARS-CoV-2 coronavirus currently spreading around the world.
David Melzer of Exeter University and colleagues used genetic and health data on volunteers in the UK Biobank to look at the role of the APOE4 variant, which affects cholesterol transport and inflammation. Of some 383,000 people of European descent included in the study, more than 9,000 carried two copies. The researchers cross-referenced this list with people who tested positive for COVID-19 between March 16 and April 26—the assumption being that most such cases were severe because testing at the time was largely limited to hospital settings. The analysis suggested that the APOE4 homozygous genotype was linked to a doubled risk of severe disease, compared with people who had two copies of another variant called ε3.
The result isn’t due to nursing home settings or to a greater likelihood of having a diagnosis of dementia, which none of the 37 people with two copies of APOE4 who tested positive for COVID-19 had. “It is pretty bulletproof—whatever associated disease we remove, the association is still there,” Melzer tells The Guardian. “So it looks as if it is the gene variant that is doing it.”
It is still possible that dementia itself is playing a roll, says David Curtis, an honorary professor at the University College London Genetics Institute, to The Guardian. Some of those 37 people who tested positive have or will develop cognitive issues, but just don’t have a diagnosis currently. “I’m afraid this study does not really convince me that the ApoE e4 allele [gene variant] is really an independent risk factor for severe Covid-19 infection. I would want to see this tested in a sample where dementia could be more confidently excluded, perhaps a younger cohort. I am sure additional data will soon emerge to illuminate this issue.”
If APOE4 is influencing the course of a SARS-CoV-2 infection, it wouldn’t be the first gene to be fingered as an important factor. Variants in the ACE2 gene that encodes the protein SARS-CoV-2 binds to on host cells, in the HLA genes, and in the genes encoding the ABO blood types have also been linked to COVID-19 susceptibility or severity in preliminary studies.
Tara Spires-Jones, neurodegeneration researcher at the University of Edinburgh who did not participate in the study, tells the publication, “It is possible that the role of ApoE in the immune system is important in the disease and future research may be able to harness this to develop effective treatments.”
Story by: Jef Akst for The Scientist
15th May 2020
An NC State researcher has developed a new way to get CRISPR/Cas9 into plant cells without inserting foreign DNA. This allows for precise genetic deletions or replacements, without inserting foreign DNA. Therefore, the end product is not a genetically modified organism, or GMO.
CRISPR/Cas9 is a tool that can be used to precisely cut and remove or replace a specific genetic sequence. The Cas9 protein serves as a pair of molecular scissors, guided to the specific genetic target by an easily swapped RNA guide. Basically, it seeks out a specific genetic sequence and, when it finds that sequence, cuts it out. Once the target DNA is snipped, it can be deleted or replaced.
The CRISPR/Cas9 system has tremendous potential for improving crops by changing their genetic code. That does not necessarily mean inserting foreign DNA, but the systems used to deliver CRISPR/Cas9 into a plant’s cells often do, which means the relevant crop is a GMO. GMOs undergo through a rigorous evaluation process and many consumers prefer non-GMO products.
Please use the following link to access the rest of the article: ScienceX
Story by: Mollie Rappe
23rd Apr 2020
Two South African entrepreneurs have developed a ground-breaking testing kit that promises to significantly speed up the process of identifying positive COVID-19 cases.
Allan Gray Orbis Foundation Fellows Daniel Ndima and Dineo Lioma have developed a testing kit that provides results in just 65 minutes, through their company CapeBio.
Testing is a pillar of any campaign against coronavirus, not only because it identifies infected individuals but because it also provides an idea of how the virus may be developing within the country. Once scientists potentially understand its spread, the government can plan resources accordingly.
This is why the qCPR kits developed by CapeBio are hailed as a massive breakthrough, with critical implications for the country’s ability to weather the current crisis
“The ability to obtain rapid test results allows us to gain a clearer picture of viral infections so that we are able to introduce interventions with greater effectiveness,” explains Daniel Ndima, CEO of CapeBio.
“This will remain important even after lockdown, as South Africa has a population of over 55 million people who will need to be monitored on an ongoing basis.”
A scientist with a special interest in structural biology, Ndima says that the development of the kits represents a spinoff of the work he has dedicated the past 12 years of his life to.
“Our kits help pathologists isolate and identify a virus’s DNA or genetic material from an infected person. This makes it possible to detect the virus accurately in a laboratory.”
As a locally manufactured product, the qCPR could mitigate the reliance on overseas imports, ensuring that testing reagents could be accessed quickly and without a wait. They are also more affordable than international products. Most importantly, CapeBio’s product makes it possible to obtain test results in just 65 minutes, compared to the usual three hours.
Collaboration for solutions
While efforts have been made to reduce the spread of the virus, Ndima points out that the impact of the crisis on our economy is just as concerning as the toll on our healthcare systems.
With this in mind, Ndima says that entrepreneurs would do well to consider their offerings and tactics, so they are better suited to a drastically changed ‘post coronavirus’ world. One of the hallmarks of this world is collaboration, he notes.
CapeBio has benefited from collaboration it with the Department of Science and Innovation’s COVID-19 response team, where experts from universities and R&D centres around the country have been given a platform to share ideas and capabilities in the search for viable solutions. But this is not the only mentorship Ndima has received – he has been guided along his entrepreneurial journey by the Allan Gray Orbis Foundation Fellowship Programme.
The Fellowship Programme is one of three programmes the Foundation offers in pursuit of creating a pipeline of responsible entrepreneurs. The Foundation provides Fellowship recipients, known as Allan Gray Candidate Fellows, funding for university studies as well as access to support and development to cultivate an entrepreneurial mindset. These programmes run throughout the academic year alongside the Candidate Fellow’s university studies.
The post-coronavirus world offers an opportunity for businesses to reimagine their offerings, believes Ndima.
“All of us need to go back to the drawing boards, rethink tactics, collaborate and rebuild, using the benefits offered by 4IR tools to create high impact businesses. This global pandemic is presenting us with serious health and economic threats, but I think it could present us with stimulated business mindsets going into the new world – so that, hopefully, we can build businesses rooted in kindness to all our people and a sense of responsibility and patriotism to our nation,” he concludes.
Story by: Tech Financials
9th Apr 2020
L. Jubair et al., “Systemic delivery of CRISPR/Cas9 targeting HPV oncogenes is effective at eliminating established tumors,” Mol Ther, 27:2091–99, 2019.
When the human papillomavirus enters a cervix, it doesn’t lyse cells or cause inflammation. While some strains can cause genital warts, in most cases the body clears the virus without much fuss. But “in an unfortunate number of people, the virus gets stuck,” says Nigel McMillan, a cancer researcher at Griffith University in Queensland, Australia. Even 15 or 20 years after infection with certain human pap-illomavirus (HPV) strains, cervical and other cancers can develop as a result.
Looking for a new way to treat these cancers, McMillan focused on two oncogenes, E6 and E7, that HPV delivers to host cells. If E6 and E7 are turned off, cancer cells will not survive—a phenomenon known as oncogene addiction. In the early 2000s, McMillan and others used short interfering RNAs (siRNAs) to reduce levels of the mRNA products of these two oncogenes. This treatment killed cancer cells in vitro, but there was no effective and commercially available way to get the siRNA to tumors in a live animal.
So in 2009, McMillan and his colleagues began working with something called stealth liposomes. Unlike regular liposomes, which are spherical phospholipid containers that researchers can use to deliver drugs into cells but which are often targeted by the immune system to be removed from the body, these liposomes are coated with a polyethylene glycol (PEG) layer that’s nontoxic and non-immunogenic. In a mouse model that had been injected with cancer cells, tumors shrank considerably when the animals were treated with siRNA-loaded stealth liposomes. But the tumors never completely disappeared.
In 2013, CRISPR-Cas9 gene editing burst onto the scientific scene, and by 2016 McMillan decided to try deploying it against the HPV oncogenes. With CRISPR, “we were actually attacking the very gene, the absolute primary cause of this cancer,” rather than its products, as siRNAs did, says McMillan. His team made guide RNAs targeting the E7 gene and put them into PEGylated liposomes along with the other components needed for CRISPR-Cas9 editing. They then injected the liposomes into the bloodstreams of mice with tumors
The PEG coating falls off within 24 hours of injection, allowing the liposome to merge with tumor cells and release the CRISPR-Cas9 system, shutting down E7. McMillan and graduate student Luqman Jubair gave some of the mice three injections, which caused the tumors’ growth to slow, but still, it didn’t stop. In a separate group of mice given seven injections, the tumors disappeared altogether. “It was like, ‘Holy moly! This is amazing,’” says McMillan. “We kept being amazed each time we did a measurement.”
McMillan says the study is the first example he knows of wiping out cancer in vivo using CRISPR. Edward Stadtmauer, a clinical oncologist and researcher at the University of Pennsylvania who was not involved in this study but recently demonstrated the safe use of CRISPR-edited cells in cancer patients, writes in an email that the work is “certainly innovative” and demonstrates “really interesting delivery of CRISPR technology to tumors in a mouse model.”
McMillan hopes to launch a clinical trial of liposomes delivered via a patch placed on the cervix, rather than intravenously, in the next couple of years, working with Kevin Morris, a gene therapy researcher at City of Hope Hospital in California who wasn’t involved in the current study. “It’s the whole package,” Morris says of McMillan’s study. “He’s shown here that you can obliterate the cancer itself.”
1st Apr 2020
In recent years, laboratories on the continent have ramped up genomic sequencing capabilities, offering in-country analyses rather than outsourcing the job.
Three days after the confirmation of Nigeria’s first COVID-19 case, the genome sequencing results of the SARS-CoV-2 specimen were announced on March 1. The sputum samples, taken from an Italian consultant who entered Nigeria through Lagos on February 27 before traveling to the neighboring Ogun State, were analyzed at the African Center of Excellence for Genomics of Infectious Diseases (ACEGID) at Redeemer University. They became the first analysis of SARS-CoV-2 in Africa, signaling the continent’s contribution to the growing global body of evidence to understand the virus’s behavior outside China.
“We have moved from being spectators to contributors and players in the field of infectious disease genomics,” Christian Happi, ACEGID director in Ede, Nigeria, who led the sequencing effort, tells The Scientist.
Whether the tool is used for disease outbreaks or routine surveillance, we now have the capacity to perform in-country sequencing, which has traditionally been done through collaborations with laboratories outside the countries.—Chikwe Ihekweazu, Nigeria Centre for Disease Control
Nigeria’s demonstration of rapid sequencing during a health emergency shows that African countries have capacities to monitor the progression of an infectious disease outbreak in real time to understand transmission patterns, says Chikwe Ihekweazu, the director general of the Nigeria Centre for Disease Control based in Abuja.
Africa’s ability to sequence its own COVID-19 cases demonstrates that countries in the region have invested in diagnostic capabilities, says Ihekweazu. “Whether the tool is used for disease outbreaks or routine surveillance, we now have the capacity to perform in-country sequencing, which has traditionally been done through collaborations with laboratories outside the countries,” he tells The Scientist.
The Africa Center for Disease Control (CDC) is encouraging countries that have the ability to sequence their own samples to do so, while those that cannot should send their samples to institutions such as ACEGID, Sofonias Kifle Tessema, the head of the genomic sequencing program at Africa CDC, tells The Scientist.
Africa CDC says 4,871 total COVID-19 cases have been reported in 46 African countries with a total of 152 deaths and 340 recoveries as of March 30. ACEGID has enough expertise and equipment to sequence all confirmed cases from Africa so far, but would need more reagents and additional staff to support bigger outbreaks, says Happi. Each sequencing costs about $600 US.
The center got its first equipment and staff in January 2014 from a World Bank investment of $8 million US that was part of a $165 million package for 19 higher education institutions specializing in STEM initiatives in eight West African nations.
The need to enable Africa to contribute to the genomics revolution, and to reduce the knowledge and economic gaps between the rest of the world and Africa, prompted this investment, Happi says. “I wanted to use genomics technologies and to address health problems in Africa, especially infectious disease and facilitate outbreak response,” he says.
Long before the coronavirus epidemic struck, in 2014, ACEGID sequencing gave the first accurate diagnosis of the Ebola virus in Nigeria.
The ability to conduct genomic sequencing locally will contribute to the global fight against COVID-19, says Denis Chopera, the program executive manager of the Sub-Saharan African Network for TB/HIV Research Excellence at the Africa Research Institute (SANTHE) in KwaZulu-Natal in South Africa. “Viruses can easily change form to adapt to the environment and evade recognition by the immune system and drugs so it is crucial to understand all these aspects of this virus,” says Chopera. “Remember, it is a new virus and very little is known about it,” he adds. SANTHE has the expertise and resources for sequencing, but is not actively working on coronavirus samples as all laboratory tests are being conducted by the South Africa’s National Institute for Communicable Diseases.
The World Health Organization has been supporting African governments with early detection by providing thousands of COVID-19 testing kits to countries, training dozens of health workers, and strengthening surveillance in communities, resulting in 46 countries being able test for COVID-19. So far, the number of cases in Africa is dwarfed by those on other continents.
The initial cases detected in Africa were from travelers coming from countries with widespread outbreaks. “The Nigeria virus is similar to the viruses recently circulating in Europe, which is consistent with the travel history of the COVID-19 patient,” Ihekweazu says of the first case.
“I do not think that the sequence can tell us why there are few cases in Africa at this point as it is highly likely that the climate in Africa is the reason. However, we will know whether the virus is changing to adapt to the climate, which is a possibility and this could result in more cases on the African continent,” Chopera tells The Scientist.
Ihekweazu says a number of different factors can be contributing to the limited number of cases detected, and sequencing will provide evidence to show if SARS-CoV-2 is changing, if it’s acquired during hospitalization, and if importations from other countries are still causing outbreaks or if community transmission is driving numbers upward.
For Akebe Luther King Abia, a Cameroonian environmental microbiologist at the University of KwaZulu-Natal in South Africa, the biggest contribution African scientists can bring are their experiences with previous outbreaks such as Ebola. After the first SARS-CoV outbreak of 2003, scientists within the continent started looking for other members of the coronavirus family in bats and developing methods to detect them, for instance. Medical personnel were trained and health infrastructure was improved to handle future emergencies. Following the previous SARS and Ebola outbreaks, Nigeria created the Nigerian Center for Disease Control and established a network of laboratories within the country for rapid identification of cases.
“It is no doubt that most countries on the continent do not have sophisticated equipment, but the fact that they have been exposed to numerous diseases outbreaks has made most of them to be ready with what they have,” Abia tells The Scientist.
26th Mar 2020
Modified gene editing machinery enables targeted disruptions of mitochondrial genes in rice and rapeseed plants.
Gene editing technologies have revolutionized the field of genetics, allowing researchers to make targeted changes to the DNA of various animal and plant nuclei, animal mitochondria, plant chloroplasts, and more. Missing from this list until recently, however, was plant mitochondrial DNA. The tools for delivering the necessary editing enzymes to plant mitochondria simply hadn’t been built.
Now, plant molecular biologist Shin-ichi Arimura of the University of Tokyo and colleagues have filled this gap, creating plant-friendly mitoTALENs—mitochondria-targeting gene editing tools based on transcription activator-like editing nucleases (TALENs).“This is an important paper—it’s the first demonstration that we can make targeted and heritable changes to mitochondrial DNA” in plants, Ian Small, a plant scientist at the University of Western Australia who was not involved in the research, writes in an email to The Scientist
Regular TALENs are composed of a DNA binding domain that can be readily engineered to recognize practically any DNA sequence, and a nuclease domain that chops up the DNA at that site, causing deletions. To target a mitochondrial gene, the team modified a plant-adapted TALEN such that it also included a mitochondrial homing signal, and engineered DNA binding domains to recognize particular genes of interest. The researchers then transferred a plasmid encoding a mitoTALEN into plants via agrobacteria—a common strategy used by plant geneticists.
In proof-of-principle experiments, the researchers designed two mitoTALENs, each targeting a particular mitochondrial gene: orf79 in rice and orf125 in rapeseed (canola). The resulting deletions enabled the researchers to confirm the genes’ hitherto suspected roles in male sterility—a natural phenomenon that prevents self-fertilization in certain hermaphroditic plants, thus promoting hybrid seed development. Indeed, disabling the genes reinstated self-fertilization in the two types of plants, the team showed.
Such male sterility genes, which are encoded in the maternally inherited mitochondria of certain plants, are desirable for agriculturalists wishing to produce hybrid crops that “grow faster, produce more, and are more resistant to disease,” explains Small. Thus, generally speaking, the goal is to activate such genes or introduce them into crop plants that lack them, rather than delete them, as Arimura’s team did.
While the plant mitoTALENs can’t yet deliver the “holy grail” of plant mitochondrial gene editing, this study is “an important first step,” says plant physiologist Ralph Bock of the Max Planck Institute of Molecular Plant Physiology who did not participate in the research. In the meantime, he adds, “one could use [the technology] to ask questions about the functions of mitochondrial genes.” (Nat Plants, 5:722–30, 2019)
Story by: Ruth Williams, for The Scientist, March 2020
19th Mar 2020
Following the call by the Government to practice social distancing in order to curb the spread of COVID-19, the ACGT staff will be working remotely and will be reachable via emails (please see our Contact Us page for our email addresses).
The ACGT is looking into ways to continue with its activities through the means of Webinars. More information on the Webinars will follow in the next few weeks.
12th Dec 2019
The African Centre for Gene Technologies (ACGT) partnered with the Council for Scientific and Industrial Research (CSIR), the University of Cape Town (UCT) and the Centre for Proteomic and Genomic Research (CPGR) to host the 2019 proteomics advanced workshop and symposium. The advanced workshop, which took place from the 18th to the 21st of November 2019, focused on the analysis of targeted proteomic and metabolomic data, using the open-source software package Skyline. The workshop was immediately followed by a national proteomics symposium, on the 22nd of November 2019, which provided emerging scientists in the field an ideal platform to showcase their work.
The four-day workshop was facilitated by Mr Brendan MacLean (MacCoss lab, University of Washington), Dr Birgit Schilling (Buck Institute for Research in Aging), Dr Ben Collins (Queen’s University Belfast and formerly Aebersold lab, ETH Zurich) and Dr Lindsay Pino (Garcia Lab, University of Pennsylvania and formerly MacCoss lab, University of Washington). The workshop had theory and practical sessions and covered a number of topics including:
- Brief introduction to targeted analysis;
- Skyline overview;
- Targeted Selected Reaction Monitoring: Method development and Data analysis;
- Targeted SWATH/ Data-Independent Acquisition: Introduction, Suitability (QC) test, library generation, data processing;
- Panaroma and AutoQC;
- Statistical group comparisons in Skyline; and
- Small molecule applications in Skyline.
The participants represented various research institutions from across the country, including the Universities of Pretoria (UP), the Witwatersrand (Wits), Johannesburg (UJ), Stellenbosch, Cape Town, the CSIR and CPGR. The participants were also given an opportunity to engage with the experts on a one-to-one basis to discuss their projects.
The symposium, which followed the workshop, had the workshop facilitators as keynote speakers as well as local researchers presenting their work. Local speakers hailed from a number of South African institutions including UP, Wits, CSIR and UCT. The symposium was a great platform to showcase what has been transpiring in the field since the last national meeting, which took place at Wits in 2018. The symposium also gave emerging scientists the opportunity to network with established researchers in the field.
Dr Ben Collins (Queen’s University Belfast) – Keynote speaker
Parallel accumulation – serial fragmentation combined with data-independent acquisition (diaPASEF): Bottom-up proteomics with near optimal ion usage
Dr Previn Naicker (CSIR)
Development of sample preparation workflows and application to Clinical Proteomics
Mr Matthys Potgieter (UCT)
MetaNovo: a probabilistic pipeline for peptide and polymorphism discovery in complex metaproteomic datasets
Mr Brendan MacLean (University of Washington) – Keynote speaker
Growth in the software ecosystem for targeted quantitative proteomics
Dr Tracy Hurrell (CSIR)
Contextualizing the proteome of hepatocyte models
Mr Andea Ellero (UP)
Time course convergence of hepatocellular proteomic phenotypes seen in HepG2 spheroid cultures
Mr Emmanuel Nweke (Wits)
Deciphering the proteomic landscape of Pancreatic Ductal Adenocarcinoma in South African patients using SWATH mass spectrometry
Dr Birgit Schilling (Buck Institute for Research in Aging) – Keynote speaker
Proteomic tools to decipher mechanisms of senescence in aging and age-related diseases
Dr Shaun Garnett (UCT)
Generating a proteomic profile of neurogenesis, through the use of human foetal neural stem cells
Mr Daniel Mutithu (UCT)
Metabolic profiling for biomarker discovery to understand pathogenesis of rheumatic heart disease
Dr Lindsay Pino (University of Washington) – Keynote speaker
Using an external reference material to harmonize and calibrate quantitative mass
spectrometry data at scale
Establishing a community of practice for the proteomics society came up during the welcome address and closing remarks given by Prof Jonathan Blackburn from UCT and Mr Thabo Khoza from the ACGT. Mr Khoza highlighted that an informal platform (Google Groups) has been set up by the ACGT to encourage the researchers in the field to communicate more effectively. This platform is open to any researcher who wishes to join it.
The workshop and symposium would have not been possible without the generous financial support from Anatech, Bruker, Inqaba Biotec, Microsep and The Scientific Group.
The ACGT will engage with the community to plan and organise the next national proteomics workshop and national symposium for the year 2020.
For any queries related to this, or other proteomics capacity-building and networking events, contact Mr Thabo Khoza, Liaison Scientist at:
To see more photos, please visit our ACGT Facebook page.
Story by: ACGT, December 2019
5th Nov 2019
Life science researchers from and around Gauteng, gathered at the University of Pretoria for a Bioprospecting Regulations Forum on the 23rd of October 2019. This information sharing day was intended give the life science community an overview of the national legislative provisions on bioprospecting and biodiversity in South Africa and to address the concerns of the researchers on how these relate to their work. For context, “Bioprospecting economy is based on searching for, collecting, harvesting and extracting living or dead indigenous species or derivatives and genetic material thereof for commercial or industrial purposes.”
There was a clear need for these discussions between the Department of Environment, Forestry and Fisheries (DEFF) personnel and Life Science researchers on the bioprospecting regulations. The meeting consisted of presentations that provided definitions and clarifications on different aspects of bioprospecting and biodiversity regulations in South Africa. The attendees were guided through key regulatory frameworks for bioprospecting, the Nagoya protocol, permits, compliance and benefits sharing. Healthy discussions and debates occurred throughout and after the presentations. Some of the discussion points were on how long the permit applications take, differences between bioprospecting vs scientific/basic research permits, amendments to the Biodiversity Act, the importance of the Nagoya Protocol and provincial level capacity and limitations.
The African Centre for Gene Technologies (ACGT) believes that the forum will improve the communication between the DEFF and the researchers applying for permits and also believes that interests are now more aligned. This event raised significant awareness on national bioprospecting regulations and addressed the concerns of the researchers in attendance. The ACGT is looking forward to working with the DEFF on other future initiatives such as this one. We would like to thank Ms Natalie Feltman and Mrs Lactitia Tshitwamulomoni from the DEFF and the delegates that were in attendance, for their contributions to the success of this event.
For more info on the event; visit our Facebook page: link or contact Mr Molati Nonyane for further information at