Today we chat to SCI member Luca Steel about her life as a plant pathology PhD student in 2020.
Zymoseptoria tritici is a fungal pathogen of wheat which can cause yield losses of up to 50%. We’re investigating an effector protein secreted by Z. tritici which acts as a ‘mask’, hiding the pathogen from host immune receptors and avoiding immune response.
What does a day in the life of a plant pathology PhD Student look like?
My days are very varied – from sowing wheat seeds to swabbing pathogenic spores onto their leaves, imaging symptoms, discussing results with my supervisor and lab team, and of course lots of reading. It doesn’t always go to plan - I recently attempted to make some wheat leaf broth, which involved lots of messy blending and ended up turning into a swampy mess in the autoclave!
Wheat in the incubator!
How did your education prepare you for this experience?
The most valuable preparation was my placement year at GSK and my final year project at university. Being in the lab and having my own project to work on made me confident that I wanted to do a PhD – even if it was a totally different research area (I studied epigenetics/immunoinflammation at GSK!).
What are some of the highlights so far?
My highlight was probably attending the European Conference on Fungal Genetics in Rome earlier this year. It was great to hear about so much exciting work going on – and it was an added bonus that we got to explore Rome. I’ve also loved getting to know my colleagues and being able to do science every day.
What is one of the biggest challenges faced in a PhD?
My biggest challenge so far has probably been working from home during lockdown. Although I am very privileged to have a distraction-free space and good internet connection, it was difficult to adjust to working from my kitchen! It was sad abandoning unfinished experiments, and I missed being in the lab – so I’m glad to be back now.
What advice would you give to someone considering a PhD?
If you’re sure you want to do one, then absolutely go for it and don’t be afraid to sell yourself! If not, I’d recommend spending some time working in a lab before you apply and chatting to any prospective labs. If you don’t get a reply from the PI, existing students/post-docs in the group are often very happy to talk and give honest opinions.
How have things been different for you because of the global pandemic?
I was lucky that the pandemic came early on in my PhD, so I had a lot of flexibility to change what I was working on. I switched from lab work involving lots of bioimaging, towards a more bioinformatic approach. My poor laptop will be glad when I’m back to using my computer at work!
Organised by the National Human Genome Research Institute each year, National DNA Day in the US on 25 April celebrates the discovery of DNA’s double helix in 1953 and the completion of the Human Genome Project in 2003. Here, we explore the history of DNA and its discovery’s unparalleled effect on science, medicine and the way we now understand the human body.
Discovering DNA’s structure
Using the pictures that she had taken, Franklin was able to calculate the dimensions of the strands and found the phosphates were on the outside of the DNA helix.
Rosalind Franklin working in her lab. Image: Wikimedia Commons
Meanwhile, at the University of Cambridge, James Watson and Francis Crick deduced the double-helix structure of DNA, describing it as ‘two helical chains each coiled round the same axis’ following a right-handed helix containing phosphate diester groups joining β-D-deoxyribofuranose residues with 3’,5’ linkages.
The discoveries made by these scientists would propel the study of genetics into the modern science we know today. Crick and Watson were awarded the Nobel Prize for Physiology or Medicine alongside Maurice Wilkins, who worked with Rosalind Franklin, in 1962. You can read their original paper here.
Dolly the sheep
Dolly on display at the National Museum of Scotland, UK.
Dolly is arguably the most famous sheep in the world, having been the first mammal to be cloned from an adult cell. Born in 1996, Dolly was part of a series of experiments at the Roslin Institute in Edinburgh to create GM livestock that could be used in scientific experiments.
She was cloned using a technique called somatic cell nuclear transfer, where a cell nucleus from one adult is transferred into an unfertilised developing egg cell of another that has had its nucleus removed, which is then implanted into a surrogate mother.
The scientific legacy of Dolly the sheep. Video: Al Jazeera English
Dolly lived until 2003 when she was euthanised after contracting a form of lung cancer. Many speculated that Dolly’s early death was related to the cloning experiment but extensive health screening throughout Dolly’s life by the Roslin Institute suggest otherwise.
Her creation has led to further cloning projects and could be used in the future to preserve the populations of endangered or extinct species, and has led to significant developments in stem cell research.
In 2009, Spanish researchers announced the cloning of a Pyrenean ibex, which has been extinct since 2000, and was the first cloning of an extinct animal. Unfortunately, the ibex died shortly after birth but there have been a few successful stories since then.
The Human Genome Project
Beginning in 1990 and finishing in 2003, the Human Genome Project was an international research initiative that aimed to write the entire sequence of nucleotide base pairs that make up the human genome, including the mapping of all its genes that determine our physical and functional attributes.
The publicly funded $3bn project was able to map 99% of the human genome with 99.99% accuracy, which included its 3.2bn Mega-base pairs, 20,000 genes and 23 chromosome pairs, and has led to advancements in bioinformatics, personalised medicine and a deeper understanding of human evolution.
In honour of World Health Day, held on 7 April 2019 annually, we have collated the five most innovative healthcare projects we have featured on SCI’s website over the past year.
Using 2D imaging techniques to diagnose problems with the heart can be challenging due to the constant movement of the cardiac system. Currently, when a patient undergoes a cardiac MRI scan they have to hold their breath while the scan takes snapshots in time with their heartbeat.
Still images are difficult to obtain with this traditional technique as a beating heart and blood flow can blur the picture. This method becomes trickier if the individual has existing breathing problems or an irregular heartbeat.
An innovative new screening method using cell aggregates shaped like spheres may lead to the discovery of smarter cancer drugs, a team from the Scripps Research Institute, California, US, has reported.
The 3D aggregates, called spheroids, can be used to obtain data from potentially thousands of compounds using high throughput screening (HTS). HTS can quickly identify active compounds and genes in a specific biomolecular pathway using robotics and data processing.
Several thousand antibiotic combinations have been found to be more effective in treating bacterial infections than first thought.
Antibiotic combination therapies are usually avoided when treating bacterial infections, with scientists believing combinations are likely to reduce the efficacy of the drugs used. Now, a group at UCLA, USA, have identified over 8,000 antibiotic combinations that work more effectively than predicted.
Researchers at the University of Copenhagen, Denmark, have identified a mechanism that prevents natural DNA errors in our cells. These errors can lead to permanent damage to our genetic code and potentially diseases such as cancer.
Mutations occurring in human DNA can lead to fatal diseases like cancer. It is well documented that DNA-damaging processes, such as smoking tobacco or being exposed to high levels of ultraviolet (UV) light through sunburn, can lead to increased risk of developing certain forms of cancer.
Treatments for Alzheimer’s disease can be expensive to produce, but by using novel cultivation of daffodils one small Welsh company has managed to find a cost-effective production method of one pharmaceutical drug, galanthamine.
Alzheimer’s disease is a neurodegenerative disease with a range of symptoms, including language problems, memory loss, disorientation and mood swings. Despite this, the cause of Alzheimer’s is very understood. The Alzheimer’s disease drug market is currently worth an estimated US$8bn.
For British Science Week 2019, we are looking back at how Great Britain has shaped different scientific fields through its research and innovation. First, we are delving into genetics and molecular biology – from Darwin’s legacy, to the structure of DNA and now modern molecular techniques.
The theory of evolution by natural selection is one of the most famous scientific theories in biology to come from Britain. Before Charles Darwin famously published this theory, several classical philosophers considered how some traits may have occurred and survived, including works where Aristotle pondered the shape of teeth.
These ideas were forgotten until the 18th century, when they were re-introduced by philosophers and scientists including Darwin’s own grandfather, Erasmus Darwin.
Darwin used birds, particularly pigeons and finches to demonstrate his theories. Image: Pixabay
In 1859, Darwin first set out his theory of evolution by natural selection to explain adaptation and speciation. He was inspired by observations made on his second voyage of HM Beagle, along with the work of political economist Thomas Robert Malthus on population.
Darwin coined the term ‘natural selection’, thinking of it as like the artificial selection imposed by farmers and breeders. After publishing a series of papers with Alfred Russel Wallace, followed by On the Origin of Species, the concept of evolution was widely accepted.
Although many initially contested the idea of natural selection, Darwin was ahead of his time, and further evidence was yet to come in the form of genetics.
Gregor Mendel first discovered genetics whilst working on peas and inheritance in the late 19th century. The unraveling of the molecular processes that were involved in this inheritance, however, allowed scientists to study inheritance and genetics in a high level of detail, ultimately advancing the field dramatically.
A major discovery in the history of genetics was the determination of the structure of deoxyribose nucleic acid (DNA).
DNA was first isolated by Swiss scientists, and it’s general structure – four bases, a sugar and a phosphate chain – was elucidated by researchers from the United States. It was a British team that managed to make the leap to the three-dimensional (3D)structure of DNA.
Using x-ray diffraction techniques, Rosalind Franklin, a British chemist, discovered that the bases of DNA were paired. This lead to the first accurate model of DNA’s molecular structure by James Watson and Francis Crick. The work was initially published in Nature in 1953, and would later win them a Nobel Prize.
The age of genetic wonder. Source: TED
By understanding the structure of DNA, further advances in the field were made. This has lead to a wide range of innovations, from Crispr/CAS9 gene editing to targeted gene therapies. The British-born science has been utilised by British pharmaceutical companies – pharma-giants GlaxoSmithKline (GSK) and AstraZeneca use this science today in driving new innovations.
Coeliac disease is caused by an autoimmune response to gluten and affects approximately 1 in 100 people worldwide. Those affected must eat a gluten-free diet, or they may experience uncomfortable digestive symptoms, mouth ulcers, fatigue and anaemia.
What’s the big deal with gluten? Video: TED-Ed
Problems occur for coeliac disease patients when they are exposed to gluten – a protein found in wheat and other grains – and the immune system is triggered to attack the body. This results in inflammation, mainly in the intestines, and causes the subsequent acute symptoms related to the condition.
Over 90% of coeliac disease patients carry immune recognition genes known as HLA-DQ2.5. These genes are human leukocyte antigen (HLA) genes, which usually relate to specific diseases.
ImmusanT, a leader in the development of therapies for autoimmune disorders, has developed a vaccine that targets patients carrying the HLA-DQ2.5 genes. This novel therapeutic vaccine, known as Nexvax2, works by reprogramming specific T cells that are responsible for triggering an inflammatory response when gluten is consumed.
Plant breeders are increasingly using techniques to produce new varieties they say are indistinguishable from those developed through traditional breeding methods. New genome editing technologies can introduce new traits more quickly and precisely.
However, in July, 2018, the European Court of Justice decreed they alter the genetic material of an organism in a way that does not occur naturally, so they should fall under the GMO Directive. This went against the opinion of the Advocate General.
In October 2018, leading scientists representing 85 European research institutions endorsed a position paper warning that the ruling could lead to a de facto ban of innovative crop breeding.
The paper argues for an urgent review of European legislation, and, in the short term, for crops with small DNA adaptations obtained through genome editing to fall under the regulations for classically bred varieties.
‘As European leaders in the field of plant sciences […] we are hindered by an outdated regulatory framework that is not in line with recent scientific evidence,’ says one of the signatories, Dirk Inzé, Scientific Director at Life Sciences Institute VIB in Belgium.
Stem cells with shared genetic information aid in the study of human disease. Image: Kyoto University/Knut WoltjenSingle nucleotide polymorphisms (SNPs) are the most common form of genetic mutation, with more than ten million currently identified, and are often found in hereditary diseases – from Alzheimer’s to diabetes.
Due to the precise nature of SNPs, researchers need to compare genetic differences with isogenic twins – two cells which differ in their makeup by only a single gene.
To do this, scientists in Japan have used induced pluripotent stem (iPS) cells to create a novel gene editing technique that can modify DNA to a single gene.
iPS cells are unique in that they retain the genetic makeup of a donor and can be converted into any cell type. These characteristics mean the cells are perfect for testing new treatments in a laboratory setting.
The team – led by Dr Knut Woltjen and based at the Centre for iPS cell Research and Application at Kyoto University, Japan – use the method to insert an SNP modification along with a fluorescent report gene as a marker for the modified cells.
As adding the reporter gene is another modification to the genome, the researchers created a duplicated DNA sequence that flanks the gene in order to remove it.
These strands hang over the sequence of the reporter gene so that once the latter is removed, the two resulting strands can join together – a method known as microhomology-mediated end joining.
In the Alzheimer’s affected brain, abnormal levels of the beta-amyloid protein clump together to form plaques (seen in brown) that collect between neurons and disrupt cell function. Image:NIH Image Gallery
Unique target sites were also added to remove the gene using the enzyme CRISPR, which cuts DNA. As a result, only the modified SNP is left in the genome of the cell.
One of the isogenic twins receives the mutant SNP and the other receives the normal SNP, allowing for a comparison to be made.
Dr Woltjen calls the new technique Microhology-Assisted eXcision, or MhAX. ‘To make MhAX work, we duplicate DNA sequences which are already present in the genome. We then let the cell resolve this duplication. At the same time, the cells decide which SNPs will remain after repair,’ said Woltjen. ‘One experiment results in the full spectrum of possible SNP genotypes.’
The team have already collaborated with other Japanese universities on the application of their novel method, using the HPRT gene – a mutation that can lead to gout – as the first example of its potential use in therapy.
Their work shows that cells with the HPRT mutant SNP had similar issues with metabolism associated with gout patients, while the isogenic control cells had no problems.
Following on from this success, Woltjen and his team are now applying the technique to different diseases associated with SNPs, including diabetes.
Some could argue the greatest threat to life as we know it is the slow, invisible war being fought against antibiotic resistant bacteria. The accidental discovery of penicillin by Fleming in the late 1920s revolutionised modern medicine, beginning with their use in the Second World War.
Over-prescription of these wonder drugs has allowed bacteria, which multiply exponentially, the ability to pick up on deadly cues in their environment at a phenomenal rate. They’re adapting their defence mechanisms so they’re less susceptible to attack. In theory, with an endless supply of different drugs, this would be no big deal.
Alexander Fleming, who discovered penicillin. Image: Wikimedia Commons
Unfortunately, the drug pipeline seems to have run dry, whilst the incidence of resistance continues to climb. For the gnarliest of infections, there’s a list of ‘drugs of last resort’, but resistance even to some of these has recently been observed. A report published by the World Health Organisation echoes these warnings – of the 51 new drugs in clinical development, almost 85% can be considered an ‘upgraded’ version of ones on the market right now. These drugs are a band aid on a snowballing problem.
Are viruses the answer?
Bacteriophages, or phages for short, are viruses that infect only bacteria, wreaking havoc by hijacking cellular machinery for their growth and development.
A bacteriophage. Image: Vimeo
Phages can find themselves in one of two different life cycles: virulent and temperate. The first involves constant viral replication, killing bacteria by turning them inside out (a process known as lysis). The second life cycle allows the phage in question to hitch a ride in the cell it infects, integrating its genetic material into the host’s and in doing so, propagating without causing immediate destruction. It’s the former that is of value in phage therapy.
Long before Fleming’s discovery, phages were employed successfully to treat bacterial infections. In areas of Eastern Europe, phages have been in continuous clinical use since the early part of the 20th century.
Why did their use not take off like that of penicillin’s in the West? ‘Bad science’ that couldn’t be validated in the early days proved to be disheartening, and phages were pushed to the wayside. Renewed interest in the field has come about due to an improvement in our understanding of molecular genetics and cell biology.
Phages are highly specific and, unlike antibiotics, they don’t tamper with the colonies of bacteria that line our airways and make up a healthy gut microbiome. As they exploit an entirely different mode of action, phages can be used as a treatment against multiple drug-resistant bacteria.
Repeated dosing may not even be necessary – following initial treatment and replication of the phage within infected cells, cell lysis releases ever more phages. Once the infection is cleared, they’re excreted from the body with other waste products.
What is holding it back?
A number of key issues must be ironed out if phage therapy is to be adopted to fight infection as antibiotics have. High phage specificity means different phage concoctions might be needed to treat the same illness in two different people. Vast libraries must be created, updated and maintained. Internationally, who will be responsible for maintenance, and will there be implications for access?
Scientists are looking at new ways to tackle antibiotic resistance. Video: TEDx Talks
Despite proving a promising avenue for (re)exploration, under-investment in the field has hindered progress. Bacteriophage products prove hard to patent, impacting the willingness of pharmaceutical companies investing capital. AmpliPhi Biosciences, a San Diego-based biotech company that focuses on the ‘development and commercialization of novel bacteriophage-based antibacterial therapeutic,’ was granted a number of patents in 2016, showing it is possible. This holds some promise – viruses might not save us yet, but they could be well on their way to.