Category: English

Source: The Conversation – Africa – By Victoria Gibbon, Professor in Biological Anthropology, Division of Clinical Anatomy and Biological Anthropology, University of Cape Town

Cape Town has consistently been one of the metropolitan regions in South Africa with the highest murder rates. It has more than double the national average, and is currently ranked second overall and 16th worldwide. Many victims are discovered only after their bodies have decomposed, burned, or been exposed to the elements. That makes identification difficult and delays justice.

Each year, more than 3,500 unnatural deaths, including murders and accidents, are handled by the city’s Observatory Forensic Pathology Institute. Around 9% remain unidentified. That’s hundreds of families left without answers. We asked Victoria Gibbon and colleagues about their work in forensic taphonomy.

What is the role of forensic taphonomists?

In death, we all decompose in the same general way. But understanding the nuances, especially those introduced by unnatural deaths, requires forensic taphonomy – the science of understanding how bodies break down. Every decomposition process is unique. It is shaped by everything around us: what we’re wearing, how we’re buried and what animals and insects might find us first.

Forensic taphonomists study all these variables and more, specialising in the recovery and analysis of human remains in the context of their environment. They play a vital role in death investigations involving unidentified persons, which requires specialised expertise in the human body and environment. There is a close working relationship with police and pathologists who hold the responsibility for identification and circumstances of death.

Imagine: a body is uncovered amid the sand and scrub of Cape Town’s coastline. By the time it’s found, the remains are in an advanced state of decomposition – identity unclear, the timeline murky. Understanding decomposition helps to determine how long someone has been dead, which can support identification, narrow down missing persons lists, or confirm (or contradict) witness accounts. It’s essential, delicate and some could say, grim work.

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Read more: Clothed pig carcasses are revealing the secrets of mummification – South African study provides insights for forensic scientists

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Forensic taphonomists’ expertise lies in understanding how bodies decompose under different conditions and how that process can reveal time-since-death, potential trauma, and ultimately, identity. Forensic taphonomists answer questions like: Who was this person? How long have they been there? And what happened to them? Their work sits at the intersection of science, justice and innovation. Because in the end, forensic science is about justice, not just science.

One of the main challenges in forensic taphonomy is that many of the global standards were developed in countries with very different climates and ecological systems. So, they are not representative of South Africa. Cape Town’s internationally unique microclimates, soil types and scavenger populations don’t align neatly with existing models.

To produce locally relevant data, researchers need to observe how decomposition actually happens in these settings. In South Africa, the legislation does not allow forensic taphonomists to study the decomposition of human bodies donated to medical science for research, as happens elsewhere in the world. Therefore they most frequently study the decomposition of adult domestic pigs as internationally accepted models for human decomposition. Pigs have numerous biological similarities to humans that are important for decomposition.

Initial decomposition studies in the Western Cape more than a decade ago began by examining unclothed bodies to establish baseline data. But as it turns out, that’s not what most cases look like. In reality, most deceased persons are clothed, and usually discovered alone. This mismatch prompted a shift.

What have you done differently in your research?

More realistic, single-body, clothed studies were needed. That meant smaller sample sizes, longer timelines, and greater data accuracy. But it leads to findings that are actually applicable in local forensic work.

We innovated, creating a world-first automated data collection machine to tackle the challenge of consistency and cost-effective, reliable long-term monitoring. It tracks decomposition in real-time, continuously and remotely. As bodies lose mass (due to water evaporation, insect activity, or tissue breakdown), the machine logs the weight changes, providing high-resolution data on the progression of decomposition. This removes the subjectivity of human observation. It allows researchers to collect standardised information across multiple cases and environments, simultaneously. It is solar-powered and transmits data remotely via cell phone networks, meaning it can be deployed anywhere we need to establish data for.

Our system has tracked in detail how tissues dry out beneath the skin. This can help reconstruct the time since death by linking drying patterns to environmental conditions and weather.

In addition to weighing decomposing bodies, our system provides continuous power to two motion-activated infrared trail cameras.

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Read more: How scavengers can help forensic scientists identify human corpses

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One camera trap is positioned directly above the body; the other is alongside the body. Together, these cameras record photos and videos of the decomposition process, giving us detailed insight into the activities of the animals that come to eat and otherwise interact with the decomposing body.

This machine offers precision, reliability and adaptability. It transforms how decomposition can be studied.

What’s next?

This technological innovation isn’t just a local solution. The team aims to provide a means by which researchers from different countries can share results that are directly comparable. These will form the basis for a global taphonomic data network: a collaborative platform for researchers to gain insights into decomposition as it plays out across geographies, environments and case types.

The hope is that this network will allow forensic anthropologists to adapt decomposition estimates to local contexts while contributing to an international evidence base.

Collectively, our research innovations may help produce more accurate case outcomes, that are admissible in court, and capable of providing justice for victims. Assistance with case resolution means restoring the identities of those who might otherwise have been lost to justice and history.

– How do bodies decompose? Cape Town forensic scientists are pushing frontiers of new detection methods
– https://theconversation.com/how-do-bodies-decompose-cape-town-forensic-scientists-are-pushing-frontiers-of-new-detection-methods-262832

Source: The Conversation – Africa – By Adeline Morez Jacobs, Postdoctoral researcher, University of Padova (Italy); visiting lecturer, Liverpool John Moores University (UK), University of Padua

A group of scientists has sequenced the genome of a man who was buried in Egypt around 4,500 years ago. The study offers rare insight into the genetic ancestry of early Egyptians and reveals links to both ancient north Africa and Mesopotamia, which includes modern day Iraq and parts of Syria, Turkey and Iran.

Egypt’s heat and terrain made it difficult for such studies to be conducted but lead researcher Adeline Morez Jacobs and team made a breakthrough. We spoke to her about the challenges of sequencing ancient remains, the scientific advances that made this discovery possible, and why this genome could reshape how we understand Egypt’s early dynastic history.

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What is genome sequencing? How does it work in your world?

Genome sequencing is the process of reading an organism’s entire genetic code. In humans, that’s about 3 billion chemical “letters” (A, C, T and G). The technology was first developed in the late 1970s, and by 2003 scientists had completed the first full human genome. But applying it to ancient remains came much later and has been far more difficult.

DNA breaks down over time. Heat, humidity and chemical reactions damage it, and ancient bones and teeth are filled with DNA from soil microbes rather than from the individual we want to study. In early attempts during the 1980s, scientists hoped mummified remains might still hold usable DNA. But the available sequencing methods weren’t suited to the tiny, fragmented molecules left after centuries or millennia.

To sequence DNA, scientists first need to make lots of copies of it, so there’s enough to read. Originally, this meant putting DNA into bacteria and waiting for the colonies to grow. It took days, demanded careful upkeep and yielded inconsistent results. Two breakthroughs changed this.

In the early 1990s, PCR (polymerase chain reaction) allowed millions of DNA copies to be made in hours, and by the mid-2000s, new sequencing machines could read thousands of fragments in parallel. These advances not only sped up the process but also made it more reliable, enabling even highly degraded DNA to be sequenced.

Since then, researchers have reconstructed the genomes of extinct human relatives like Neanderthals, and more than 10,000 ancient people who lived over the past 45,000 years. But the work is still challenging – success rates are low for very old remains, and tropical climates destroy DNA quickly.

What’s exceptional about the sequencing you did on these remains?

What made our study unusual is that we were able to sequence a surprisingly well-preserved genome from a region where ancient DNA rarely survives.

When we analysed the sample, we found that about 4%-5% of all DNA fragments came from the person himself (the rest came from bacteria and other organisms that colonised the remains after burial). The quantity of DNA of interest (here, human) is usually between 40% and 90% when working with living organisms. That 4%-5% might sound tiny, but in this part of the world, it’s a relatively high proportion, and enough to recover meaningful genetic information.

We think the individual’s unusual burial may have helped. He was placed inside a ceramic vessel within a rock-cut tomb, which could have shielded him from heat, moisture and other damaging elements for thousands of years.

To make the most of this rare preservation, we filtered out the very shortest fragments, which are too damaged to be useful. The sequencing machines could then focus on higher-quality pieces. Thanks to advanced facilities at the Francis Crick Institute, we were able to read the DNA over and over, generating about eight billion sequences in total. This gave us enough data to reconstruct the genome of what we call the Nuwayrat individual, making him the oldest genome from Egypt to date.

Does this open new frontiers?

We did not develop entirely new techniques for this study but we combined some of the most effective methods currently available into a single optimised pipeline. This is what palaeogeneticists (scientists who study the DNA of ancient organisms) often do: we adapt and refine existing methods to push the limits of what can be recovered from fragile remains.

That’s why this result matters. It shows that, with the right combination of methods, we can sometimes retrieve genomes even from places where DNA usually doesn’t survive well, like Egypt.

Egypt is also a treasure trove for archaeology, with remains that could answer major questions about human history, migration and cultural change.

Our success suggests that other ancient Egyptian remains might still hold genetic secrets, opening the door to discoveries we couldn’t have imagined just a decade ago.

What was your biggest takeaway from the sequencing?

The most exciting result was uncovering this man’s genetic ancestry. By comparing his DNA to ancient genomes from Africa, western Asia and Europe, we found that about 80% of his ancestry was shared with earlier north African populations, suggesting shared roots within the earlier local population. The remaining 20% was more similar to groups from the eastern Fertile Crescent, particularly Neolithic Mesopotamia (present-day Iraq).

This might sound expected, but until now we had no direct genetic data from an Old Kingdom (2686–2125 BCE) Egyptian individual. The results support earlier studies of skeletal features from this period, which suggested close links to predynastic populations, but the genome gives a far more precise and conclusive picture.

This genetic profile fits with archaeological evidence of long-standing connections between Egypt and the eastern Fertile Crescent, dating back at least 10,000 years with the spread of farming, domesticated animals and new crops into Egypt. Both regions also developed some of the world’s first writing systems, hieroglyphs in Egypt and cuneiform in Mesopotamia. Our finding adds genetic evidence to the picture, suggesting that along with goods and ideas, people themselves were moving between these regions.

Of course, one person can’t represent the full diversity of the ancient Egyptian society, which was likely complex and cosmopolitan, but this successful sequencing opens the door for future studies, building a richer and more nuanced picture of the people who lived there over thousands of years.

– We decoded the oldest genetic data from an Egyptian, a man buried around 4,500 years ago – what it told us
– https://theconversation.com/we-decoded-the-oldest-genetic-data-from-an-egyptian-a-man-buried-around-4-500-years-ago-what-it-told-us-262061

Source: The Conversation – Africa – By Claudia Christowitz, Postdoctoral Research Fellow, Stellenbosch University

Cancer treatment is becoming more personalised. By considering a patient’s unique genetic and molecular profile, along with their lifestyle and environmental factors, doctors can make more accurate treatment decisions. This approach, known as personalised or precision medicine, has been increasingly used in South Africa and has expanded to other African countries in recent decades. It requires doctors to rely more on genetic tests to guide decisions. But these tests don’t always give clear answers. Functional genomics may offer a way to improve the interpretation of unclear genetic test results. We spoke to physiological scientist Claudia Christowitz about it.

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Is cancer a genetic disease and what is personalised medicine?

Cancer is fundamentally a genetic disease. It arises when changes in a person’s DNA (referred to as variants or mutations) disrupt normal cell functions such as cell growth and division. It eventually leads to tumour formation. These changes can be inherited from families or acquired during a person’s lifetime. This can be due to lifestyle and environmental risk factors such as smoking, ultraviolet radiation and infectious agents, among others.

Over the past few decades, we’ve entered the era of personalised medicine. As a result, the role of genetics in cancer treatment has become more prominent. Personalised medicine involves tailoring cancer treatment to each patient’s unique characteristics.

For example, even if two people are diagnosed with the same type and stage of cancer, their treatment outcomes may differ. This is because factors such as their genetic and molecular make-up, overall health status, age, body composition, lifestyle habits, and use of other medication can all influence how well a treatment works for them.

How have advances in genetic testing helped in treating cancer?

Advances in DNA sequencing technologies have made it possible to detect genetic variants more quickly and accurately. The tests can look for just a few genes linked to certain medical conditions, or they can describe the entire genome of an individual, or just the protein-coding regions of the genome (the exome).

DNA sequencing has revolutionised cancer care. Doctors can use it to improve prevention in people who are at risk of cancer, detect cancer early, and select the most appropriate treatment.

Africa’s first high-throughput Genomics Centre was launched in 2019 by the South African Medical Research Council. Cancer patients can now undergo whole exome sequencing and whole genome sequencing locally for around R10,000 (about US$566) to R20,000 (about US$1,132). This is sometimes covered by medical insurance. These services are also available at research facilities like the Centre for Proteomic and Genomic Research or the Centre for Epidemiological Research and Innovation at Stellenbosch University.

These facilities strengthen the capacity to sequence, analyse and store human genomes, particularly for the diverse gene pool in Africa. But routine genome sequencing, especially in the public health sector, remains limited due to high costs, limited awareness and the need for trained personnel.

What are the shortcomings of genetic testing?

Genetic testing doesn’t provide all the answers. Unfortunately, not all genetic results are clear-cut. In many cases, patients receive results showing changes in their DNA that cannot be confidently classified as either harmful (pathogenic variants or mutations) or harmless (benign variants). These unclassified variants are known as variants of uncertain significance. The uncertainty often leaves both patients and their oncologists (cancer doctors) unsure of the way forward.

With the advancement of sequencing technologies, rare or novel variants are more frequently detected. But without a clear understanding of whether the variant affects gene function, clinicians are often forced to wait – sometimes for years – until more information emerges.

When patients undergo genetic testing – often as part of a hereditary cancer screening or in response to early-onset or familial cancers – the hope is to find a variant that clearly explains their condition. But sequencing may yield variants of uncertain significance, raising questions about its usefulness in patient care and whether the tests are worth the cost.

What is functional genomics and how can it make genetic test results clearer?

Functional genomics is a growing field that could transform how we interpret these unresolved genetic results and make it possible to improve clinical care for cancer patients.

Functional genomics goes beyond simply reading the DNA code. It investigates how genetic variants behave in biological systems. By examining how a variant alters gene expression, protein function, cell behaviour, or response to treatments, scientists can determine whether it is likely to be benign or pathogenic.

This information is crucial for making timely medical decisions. Importantly, cells derived from patients can be used to mimic real biological conditions more accurately. By using cells carrying such a variant and comparing them to cells without the variant, scientists can determine whether the variant is influencing the response of cells to certain treatments or not.

In short: genetic testing is like reading the “instruction manual” of a cell. Functional genomics is like testing the effects of changes to these instructions.

My study, using patient-derived cells, investigated the effects of a rare TP53 variant that was identified for the first time in germline (inherited) DNA through whole exome sequencing in a South African family with multiple cancers. I found that this variant made cells resistant to the chemotherapy drug doxorubicin. Instead of undergoing cell death as expected, the cells went into a kind of “sleep mode” called senescence, where damaged cells stop dividing.

Although this prevents the growth of damaged cells, senescent cells can release signals that may inflame and harm nearby healthy cells. The variant also reduced how well immune cells can move, which may affect their ability to go to cancer cells and attack them. This study, supervised by Prof Anna-Mart Engelbrecht, Prof Maritha Kotze, and Dr Daniel Olivier from Stellenbosch University, highlighted how functional genomics can unravel the impact of a variant of uncertain significance, which may guide medical decisions.

In a world where personalised medicine is rapidly evolving, functional genomics represents a critical step forward, offering more clarity, better care, and renewed hope to those facing cancer.

– Genetic tests for cancer can give uncertain results: new science is making the picture clearer to guide treatment
– https://theconversation.com/genetic-tests-for-cancer-can-give-uncertain-results-new-science-is-making-the-picture-clearer-to-guide-treatment-262545