Results in Journal The Biochemist: 2,110
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Published: 1 August 2009
Demodex mites, class Arachnida and subclass Acarina, are elongated mites with clear cephalothorax and abdomens, the former with four pairs of legs. There are more than 100 species of Demodex mite, many of which are obligatory commensals of the pilosebaceous unit of mammals including cats, dogs, sheep, cattle, pigs, goats, deer, bats, hamsters, rats and mice. Among them, Demodex canis, which is found ubiquitously in dogs, is the most documented and investigated. In excessive numbers D. canis causes the inflammatory disease termed demodicosis (demodectic mange, follicular mange or red mange), which is more common in purebred dogs and has a hereditary predisposition in breeding kennels1. Two distinct Demodex species have been confirmed as the most common ectoparasite in man. The larger Demodex folliculorum, about 0.3–0.4 mm long, is primarily found as a cluster in the hair follicle (Figure 1a), while the smaller Demodex brevis, about 0.2–0.3 mm long with a spindle shape and stubby legs, resides solitarily in the sebaceous gland (Figure 1b). These two species are also ubiquitously found in all human races without gender preference. The pathogenic role of Demodex mites in veterinary medicine is not as greatly disputed as in human diseases. In this article, we review the key literature and our joint research experience regarding the pathogenic potential of these two mites in causing inflammatory diseases of human skin and eye. We hope that the evidence summarized herein will invite readers to take a different look at the life of Demodex mites in several common human diseases.
Published: 1 June 2010
Semiconductor quantum dots (QDs) are tiny light-emitting particles that have emerged as a new class of fluorescent labels for biology and medicine. Compared with traditional fluorescent probes, QDs have unique optical and electronic properties such as size-tuneable light emission, narrow and symmetric emission spectra, and broad absorption spectra that enable the simultaneous excitation of multiple fluorescence colours.
The Biochemist, Volume 33, pp 18-20; https://doi.org/10.1042/bio03306018
Nearly all species employ mechanosensitive channels to detect mechanical cues, such as touch and sound waves, and convert these mechanical forces into electrochemical signals. Genetic, biochemical and electrophysiological studies of touch-insensitive mutants in model organisms such as Caenorhabditis elegans and Drosophila melanogaster provide insights into the molecular basis of mechanosensory transduction.
The Biochemist, Volume 44, pp 29-31; https://doi.org/10.1042/bio_2022_128
The Biochemist, Volume 44, pp 9-12; https://doi.org/10.1042/bio_2022_125
Infertility and development of contraceptive methods have profound societal affects; however, the genetic mechanisms underlying this are still largely unknown. Here, we describe how using the small worm Caenorhabditis elegans has helped us to discover the genes involved in these processes. Nobel Laureate Sydney Brenner established the nematode worm C. elegans as a genetic model system with a powerful ability to discover genes in many biological pathways through mutagenesis. In this tradition, many labs have been using the substantial genetic tools established by Brenner and the ‘worm’ research community to discover genes required for uniting sperm and egg. Our understanding of the molecular underpinnings of the fertilization synapse between sperm and egg rivals that of any organism. Genes have been discovered in worms that share homology and mutant phenotypes with mammals. We provide an overview of the state of our understanding of fertilization in worms as well as exciting future directions and challenges.
The Biochemist, Volume 44, pp 1-1; https://doi.org/10.1042/bio_2022_124
The Biochemist, Volume 44, pp 2-8; https://doi.org/10.1042/bio_2022_119
Mitochondria, special double-membraned intracellular compartments or ‘organelles’, are popularly known as the ‘powerhouses of the cell’, as they generate the bulk of ATP used to fuel cellular biochemical reactions. Mitochondria are also well known for generating metabolites for the synthesis of macromolecules (e.g., carbohydrates, proteins, lipids and nucleic acids). In the mid-1990s, new evidence suggesting that mitochondria, beyond their canonical roles in bioenergetics and biosynthesis, can act as signalling organelles began to emerge, bringing a dramatic shift in our view of mitochondria’s roles in controlling cell function. Over the next two and half decades, works from multiple groups have demonstrated how mitochondrial signalling can dictate diverse physiological and pathophysiological outcomes. In this article, we will briefly discuss different mechanisms by which mitochondria can communicate with cytosol and other organelles to regulate cell fate and function and exert paracrine effects. Our molecular understanding of mitochondrial communication with the rest of the cell, i.e. mitochondrial signalling, could reveal new therapeutic strategies to improve health and ameliorate diseases.
The Biochemist; https://doi.org/10.1042/bio_2022_121
Speaking at a conference for the first time can be daunting for anyone. For as long as I can remember, I’ve wanted to be a biochemist… No, really – I was a keen kid. So hours away from giving my first talk at the European SMALP conference, organized by the Biochemical Society, it would appear that I had achieved my life’s goal. Yet, peering out of my hotel window at the busy morning skyline, a downpour of worries started to cloud the day.
The Biochemist; https://doi.org/10.1042/bio_2022_116
The Biochemical Society and Portland Press are committed to open scholarship. In 2020 we launched our Unlimited Read & Publish programme. This article summarizes the progress that has been made since then and explores the effect that our transitioning sales offerings have had on paywalls to published content. The share of content in our transitioning (hybrid) journals published open access (OA) is the highest it has ever been and continues to increase as more institutions take up transformative agreements with us each year. Open data and clear communication are key parts of the on-going transition, and progress with publishing workflows and data availability have been made. With over 40% of 2021’s published content in hybrid journals converted to OA, the Biochemical Society and Portland Press are also actively scoping future models. For this, we are seeking sustainable and collaborative pathways to completing our transition in a way that is globally equitable and inclusive.
The Biochemist; https://doi.org/10.1042/bio_2022_122
The ‘Mitochondria and Us’ project embodies our ambition to break new ground by working across traditionally siloed disciplines and by co-creating innovative approaches to impact research and societal awareness. Our vision is to provide a paradigm shift of knowledge integration at all levels adopting a pandisciplinary cooperation in a crucial and emerging area of medicine impacting several incurable human diseases. We describe our efforts on this journey through a series of ‘Crossover’ workshops and webinars supported by the Biochemical Society and the Royal Society of Edinburgh, by bringing together mitochondria experts from the University of Glasgow and the University of Toronto together with designers from the Innovation School of the Glasgow School of Art, artists, patient groups, social scientists and bioethicists. The global Mitochondria Collective initiative has the vision to unite research, community voices and stakeholders to bring mitochondria to the forefront of medicine as a means of sustained impact on improved healthcare and quality of life.
The Biochemist; https://doi.org/10.1042/bio_2022_118
The body and mind are fuelled by energy. But where does the energy come from? The sun beams energy through space as photons that are captured by plants, which store that energy in the improbable separation of carbon and oxygen. By reuniting carbon and oxygen in their mitochondria, breathing animals power their warm bodies, thoughts, feelings, minds and consciousness. Thus, the life-giving flow of energy proceeds from light, through chemistry, into life. Mapping the mechanisms of energy transformation among mind-imbued organisms is the challenge for the field of mitochondrial psychobiology. Emerging evidence positions energy as the substrate of the mind–body connection, linking the molecular processes in the organism and the subjective experiences in our mind. Building a bioenergetic psychobiology framework can stimulate the health sciences in three main ways: it provides an empirical foundation to examine the interconnectedness of people and their environment, highlights health as a dynamic process, and may eventually illuminate new approaches and strategies to optimize the energetic mind–body crosstalk that is the basis of human health.
The Biochemist; https://doi.org/10.1042/bio_2022_120
Mitochondria are complex factories that provide our cells with most of the energy we need to survive and perform daily tasks. They comprise their own small genome, mitochondrial DNA (mtDNA), which contains genes for parts of the energy-producing machinery. Mutations in mtDNA can lead to mitochondrial diseases, which are a devastating group of heterogenous inheritable diseases that can develop at any stage of life. Despite rapid developments in genome engineering for nuclear DNA, the incompatibility of certain techniques in mitochondria has meant that the field of mitochondrial genome modification has been impeded for many years. However, recent advances in mtDNA engineering techniques, such as programmable nucleases and base editors, will allow for a deeper understanding of the processes taking place in mitochondria and improve the prospects of developing treatments for mitochondrial diseases.
The Biochemist, Volume 44, pp 1-1; https://doi.org/10.1042/bio_2022_117
The Biochemist, Volume 44, pp 6-8; https://doi.org/10.1042/bio_2022_112
Enzymes are the catalytically active proteins, responsible for carrying out biochemistry in nature. Today, they are also finding use as catalysts in organic chemistry, both in the laboratory as well as in large-scale manufacturing of chemicals in industry. Their special properties enable sustainable syntheses, supported by tools such as protein engineering so they can be tuned to operate efficiently, thereby meeting industrial requirements.
The Biochemist, Volume 44, pp 19-22; https://doi.org/10.1042/bio_2022_109
The use of enzymes (protein catalysts from biological origin) has been key to the development of our society and daily life since the dawn of humanity. Nowadays, the better understanding of how enzymes work and their manipulation has enabled enzymes to become a crucial technology in the current biotechnological revolution. In this sense, while enzymes in their naturally occurring form are excellent biocatalysts, they are not yet broadly implemented in industry due to their instability and poor reusability. As a solution, enzyme immobilization is a strategy that enables the preparation of more resistant, reusable and more cost-efficient biocatalysts that, combined with continuous flow technologies, have the potential to make their promise true: transition towards more cost-efficient, sustainable, and environmental friendly chemical manufacturing.
The Biochemist, Volume 44, pp 9-12; https://doi.org/10.1042/bio_2022_114
Farmed animal agriculture is facing big challenges in today’s world. Genome editing technology now offers some solutions, and these need to be melded into the other approaches and strategies that can be deployed to produce a sustainable food system. If we embrace these technologies, and do so within a basic justice framing, we can achieve food security for all, while providing enhanced welfare and reduced environmental footprint contributing to a fair and sustainable carbon-zero future.
The Biochemist, Volume 44, pp 30-34; https://doi.org/10.1042/bio_2022_115
The work and contribution of 12 bioscientists and early career researchers has been honoured in the Biochemical Society’s Awards 2023. Each recipient has been recognized for excellence in their field, ranging from RNA-binding proteins and centrosome assembly to molecular medicine and anti-cancer drugs, as well as the profound impact their research has had on the scientific community and wider society.
The Biochemist, Volume 44, pp 13-18; https://doi.org/10.1042/bio_2022_113
As we continue searching for the technologies that will halt global warming, let us take a moment to think about plants. A key contributor to our climate crisis is the accumulation of carbon dioxide in the atmosphere. Plants have been capturing carbon dioxide for billions of years, making them the most tried and tested carbon capture machinery on the planet. Plants fix carbon dioxide as part of photosynthesis. After years of research, we now know the key regulators of this process and have the knowledge to start engineering plants with increased photosynthetic capacity. In addition to improving the efficiency of carbon fixation, we must also find a way to stably store the carbon captured by plants. To achieve this, we can look to the below-ground part of the plant body – the root system. Plant roots are packed full of carbon and also exude carbon-rich molecules into the soil. Engineering future plants with deeper, more extensive root systems, with enhanced chemical composition that increases carbon content and reduces the rate of biodegradation, offers a way to store atmospheric carbon fixed by plants below ground for years to come. With optimized root systems, these plants would also be better equipped to explore their surrounding soils for water and nutrients, which would ultimately improve plant performance. This approach also offers a way to replenish our carbon-depleted soils, which would increase soil quality by improving water and nutrient retention. Harnessing the plants' natural ability to capture carbon, thus provides a way to not only restore balance to the carbon cycle, but also improve soil quality and future crop performance.
The Biochemist, Volume 44, pp 23-29; https://doi.org/10.1042/bio_2022_100
Microbial communities are immensely important and occur nearly everywhere, but their inner workings are still being discovered. The early years of microbiome research have been dominated by cataloguing the sheer diversity of microbes in these communities. Now, more and more studies try to understand connections between the microbes, between the way communities are built and how they function, and between their activity and the effects on their surroundings, including host organisms like humans. Omics measurements, or meta-omics as they are called when multiple organisms are measured at the same time, are a cornerstone in this endeavour. Here, we will discuss why their integration is important, how it can be achieved, what pitfalls may be avoided and which approaches are taken by integrative studies.
The Biochemist, Volume 44, pp 2-5; https://doi.org/10.1042/bio_2022_110
Do you want to make your research more efficient and reliable? Have you wondered whether science could be environmentally sustainable and what you can do to help bring this about?
The Biochemist, Volume 44, pp 35-39; https://doi.org/10.1042/bio_2022_103
Many aspects of doing a PhD feel like being thrown into the ocean without any help or support. This is especially the case when it comes to doing data analysis and coding. Unsurprisingly, as a PhD student you end up being inefficient with time and effort when it comes to doing your work. Sadly research culture currently doesn’t appreciate, fund or support these aspects of science as much as would be required to solve these problems. One of the first steps to changing this culture is through training and education of PhD students and early career researchers. Taking a course on being reproducible and open can lead you to being more productive and less stressed and, over time, teaching courses like these can help spread the awareness of these issues and slowly improve research culture.
The Biochemist, Volume 44, pp 1-1; https://doi.org/10.1042/bio_2022_111
The Biochemist, Volume 44, pp 22-27; https://doi.org/10.1042/bio_2022_105
The Biochemist, Volume 44, pp 18-21; https://doi.org/10.1042/bio_2022_108
The last two years have been a crash course in educating the world about viruses, virology and infectious diseases. Unsurprisingly, viruses have emerged as the harbingers of doom. However, with their newly acquired knowledge, the new armchair virologists fail to grasp the importance of viruses in the living world. They may cause us harm, but without their relentless activity, we’d all be dead anyway. In addition to owing them our lives, they also have the potential to improve our lives with novel biotechnological applications.
The Biochemist, Volume 44, pp 2-7; https://doi.org/10.1042/bio_2022_106
The Darwin Tree of Life (DToL) project has been established to collect all eukaryote species in Britain and Ireland for genomic sequencing. New tech developments have enabled high-quality genomic data to be a feasible outcome for some of Earth’s smallest inhabitants. This project will create a new resource of data open to all, which will contain the blueprint of thousands of organisms, holding the key to the evolutionary histories of understudied single-cell protists alongside more well-understood animals like the grey seal. This ambitious project is a collaboration of experts from different geographic and intellectual areas. It will provide the templates for new ways of working and uncover new scientific ground. In a world struggling under the threat of ecological collapse, this project will provide new bio-tech and engineering information to aid our understanding and management of natural ecosystems and the creatures which create them. The Marine Biological Association UK, based in Plymouth, is currently in the process of collecting marine organisms for the project. The marine environment has not been as well studied as terrestrial environments, and this offers a huge opportunity to expand our understanding of this underexplored realm and the creatures that live there, as well as providing context and detail to marine science which will provide new insights to marine research.
The Biochemist, Volume 44, pp 8-12; https://doi.org/10.1042/bio_2022_107
A cancer patient treated with a molecule found in algae-eating sea hares native to the Indian Ocean. Jet fuel produced by algae in open urban ponds. A tonne-scale synthesis of pharmaceuticals using enzymes from a green biofilm growing in your backyard. The first example is a reality, but the others are not necessarily confined to a utopian future. All these scenarios can be linked to blue-green algae (cyanobacteria). These talented microbial biochemists generate a vast set of unique secondary (specialized) metabolites. Initially infamous for being potent toxins that have resulted in human deaths, some cyanobacterial secondary metabolites have proven useful and are currently used in the clinic. The enzymes that biosynthesize some of these compounds are likewise remarkable and could find future industrial use. Here, I discuss some aspects of past and current secondary metabolite discovery in cyanobacteria, the potential impact of these small molecules for human activities and how the study of their biosynthesis has unearthed exciting new enzymatic reactions.
The Biochemist, Volume 44, pp 30-34; https://doi.org/10.1042/bio_2021_196
The Biochemist, Volume 44, pp 13-17; https://doi.org/10.1042/bio_2022_102
Over the past 50 years, more than 15 pharmaceuticals derived from marine organisms have come to the market. Most of these come from filter-feeding invertebrates that contain a high proportion of microbial symbionts. Microbiology and molecular genetic studies have shown that many of these drug-like compounds are produced by the microbial symbiont. The enzymes that produce these compounds are promiscuous meaning they can process a diverse range of related substrates, making them extremely attractive to the biotechnology industry. Determining the structure of these enzymes makes them amenable to engineering, allowing them to process non-natural substrates. Using this approach, synthetic substrates can be treated with a cocktail of enzymes to prepare focused libraries of compounds to hit drug targets such as protein–protein interactions. These targets are involved in a range of diseases from cancer to immune disorders and are hard to modulate using small molecule drugs. Complex modified cyclic peptides produced using a chemoenzymatic process may be a promising approach to address these disease conditions.
The Biochemist, Volume 44, pp 28-29; https://doi.org/10.1042/bio_2022_101
Throughout my time as a student I have been fortunate enough to be involved in learned societies. A learned society is an organization (typically not for profit) which aims to promote the scholarly work of a particular discipline. This can take the form of running conferences, publishing literature and offering training and educational resources to society members. Whilst membership to a learned society is often a small fee (often discounted for students) the benefits that can be obtained from membership are extremely rewarding.
The Biochemist, Volume 44, pp 25-26; https://doi.org/10.1042/bio_2021_202
The Biochemist spoke to Deborah O’Neil, the CEO and founder of NovaBiotics, to find out about her journey to commercialization of her research. A biotechnology entrepreneur and immunologist by training, Deborah has over two decades of experience in drug discovery and development and was named as one of the 20 women leaders in European biotech in 2019. In 2020, Deborah was made OBE in the Queen’s Birthday Honours list for services to biotechnology, industry and charity. Deborah studied at University College London and then worked in postdoctoral positions in internationally acclaimed laboratories in San Diego and Ghent before moving to Aberdeen (to the Rowett Research Institute, now part of the University of Aberdeen) where she founded NovaBiotics in 2004.
The Biochemist, Volume 44, pp 6-10; https://doi.org/10.1042/bio_2021_205
Traditionally, bioenterprise has been dominated by drug development and medical technology. Today, we are experiencing an unprecedented surge in opportunities for life scientists of all backgrounds, and many are joining the sector from other areas. Hear from stakeholders across the bioenterprise community about how you can make the most of it.
The Biochemist, Volume 44, pp 11-19; https://doi.org/10.1042/bio_2021_179
Innovative products and processes are key to bioenterprise and the creation of successful bio-based businesses and economies. To create new and improved market-ready products, genuinely novel technologies and business advances are usually very necessary. These are exciting and rewarding – but also complex, exacting, expensive and risky, requiring new, often radically new, ways of scientific and business thinking and working by both individuals and companies with collective ambition, imagination, determination and conducive working environments. In this article, ways that could help emerging bioenterprises succeed are discussed, including how to work more innovatively and combine economic success with contributing ‘people’ and ‘planet’ benefits. How NamZ, now called WhatIF Foods, an emerging bio-business, began, started work and developed its first products is described, giving insights into its strategies, the multiple different challenges faced, the various advances necessary to overcome them and the range of skills required. WhatIF’s approach is to identify unmet needs, unsolved problems and under-researched opportunities – and then to devise, invent and develop a stream of new products to meet and solve these, together with processes to make them, in ways that benefit people (such as farming communities) and that are not just sustainable but can actually reverse environmental and related problems. Then WhatIF develops markets for them – right through to new product launches by partner or subsidiary companies each specializing in manufacturing, marketing, distributing, and selling specific products.
The Biochemist, Volume 44, pp 2-5; https://doi.org/10.1042/bio_2021_201
Following the outbreak of COVID-19 and facing the challenges and opportunities of a post-Brexit world, the UK government must deliver on the vision of its innovation strategy with increased funding for scientific research. The success of the life sciences sector will be key to the delivery of the government’s scientific superpower ambitions. Boosting public funding will depend on continued political, and therefore public, support. With reference to his career in politics and industry, Ian Taylor shows how effective communication with the public, providing reassurance and dispelling myths, is central to the sector sustaining success in the long term.
The Biochemist; https://doi.org/10.1042/bio_2021_206
The Biochemist, Volume 44, pp 20-24; https://doi.org/10.1042/bio_2021_181
Lipidomics refers to the large-scale analysis of the complete set of lipids – the ‘lipidome’ – in any biological system. Methodologically, it heavily relies on mass spectrometry, an analytic technique enabling the identification and quantification of molecules in a complex sample based on slight differences in their mass and charge. Recent advances in this field have fuelled the development of novel approaches including tracer lipidomics and spatial lipidomics, allowing an unprecedented insight into this complex class of biomolecules. As lipids play numerous physiological roles and are affected in a wide range of pathologies, the study of lipids and their metabolic pathways offers great potential for biomarker discovery and for the development of novel therapeutic interventions.
The Biochemist, Volume 43, pp 4-7; https://doi.org/10.1042/bio_2021_151
In these last years, we are witnessing the emergence of a new class of biopharmaceuticals based on messenger RNA (mRNA). One of the most promising applications of mRNA is its use as vaccines. Many reports, including ours, have demonstrated the preclinical efficacy of mRNA vaccines. mRNA vaccines have several advantages over traditional vaccines or even DNA vaccines. Unlike attenuated or inactivated vaccines, mRNA encodes for a specific antigen that will be expressed in situ and stimulates both the innate immune system and an adaptive immunity to promote both humoral and cellular immune responses.
The Biochemist, Volume 44, pp 27-27; https://doi.org/10.1042/bio_2021_203
The Biochemist, Volume 43, pp 78-81; https://doi.org/10.1042/bio_2021_204
The 4th of october 2021 signified 70 years since the untimely death of Henrietta Lacks, a daughter, wife and mother. On the same day, the University of Bristol unveiled a statue of Henrietta that sits in the heart of its campus in Royal Fort Gardens, by local artist Helen Wilson-Roe. The unveiling came amidst a year of celebratory events for the legacy of a woman whose contribution to science is, in many ways, unrivalled. To many cell biologists, Henrietta Lacks is a household name; however, to the general public her name remains largely unknown. So, who is Henrietta Lacks? And why are the Lacks family and their family-led HELA100 initiative working in collaboration with the University of Bristol to honour her legacy?
The Biochemist, Volume 43, pp 74-77; https://doi.org/10.1042/bio_2021_197
The most notable moment in my career as a biochemist was the discovery of phosphotyrosine, a somewhat serendipitous finding that turned out to have some very important consequences, notably, in human cancer. My career as a biochemist which has spanned nearly 60 years, began when I was 16. At the time, I was in the sixth form at Felsted School, a boarding school in Essex England, and my biology master, David Sturdy, elected to teach me some extracurricular biochemistry, giving me one-on-one tutorials on glycolysis and the TCA cycle. These early biochemistry lessons turned out to be invaluable because I was able to regurgitate them to answer a question in the University of Cambridge scholarship exam in the autumn of 1960. As a result, I was lucky enough to be awarded an Exhibition at Gonville and Caius College, the college where my father had studied for a medical degree during World War II. When I arrived in Cambridge in October 1962 to read natural sciences (see Figure 1), it was a natural choice to take biochemistry as one of my three required first-year courses. The Part I biochemistry course was taught by a series of excellent lecturers, including Philip Randle (a prominent diabetes researcher who described the Randle Cycle), Brian Chappell (who discovered mitochondrial transporters) and Asher Korner (a pioneer of cell free systems to study protein synthesis). It quickly became clear that biochemistry was an exciting subject, and Brian Chappell, my biochemistry supervisor at Caius, made supervisions a lot of fun. I also took Part I courses in invertebrate zoology and, importantly, organic chemistry, which gave me insights into how the metabolites we were learning about in biochemistry worked as chemicals.
The Biochemist, Volume 43, pp 84-84; https://doi.org/10.1042/bio_2021_199
The Biochemist, Volume 43, pp 88-89; https://doi.org/10.1042/bio_2021_200
The Biochemist, Volume 43, pp 52-57; https://doi.org/10.1042/bio_2021_186
Carbohydrates are ubiquitous in nature and present across all kingdoms of life – bacteria, fungi, viruses, yeast, plants, animals and humans. They are essential to many biological processes. However, due to their complexity and heterogeneous nature they are often neglected, sometimes referred to as the ‘dark matter’ of biology. Nevertheless, due to their extensive biological impact on health and disease, glycans and the field of glycobiology have become increasingly popular in recent years, giving rise to glycan-based drug development and therapeutics. Forecasting of communicable diseases predicts that we will see an increase in pandemics of humans and livestock due to global loss of biodiversity from changes to land use, intensification of agriculture, climate change and disruption of ecosystems. As such, the development of point-of-care devices to detect pathogens is vital to prevent the transmission of infectious disease, as we have seen with the COVID-19 pandemic. So, can glycans be exploited to detect COVID-19 and other infectious diseases? And is this technology sensitive and accurate? Here, I discuss the structure and function of glycans, the current glycan-based therapeutics and how glycan binding can be exploited for detection of infectious disease, like COVID-19.
The Biochemist, Volume 43, pp 10-15; https://doi.org/10.1042/bio_2021_187
Since December 2019, the world has found itself rocked by the emergence of a highly contagious novel coronavirus disease, COVID-19, caused by the virus SARS-CoV-2. The global scientific community has rapidly come together to understand the virus and identify potential treatments and vaccine strategies to minimise the impact on public health. Key to this has been the use of cutting-edge technological advances in DNA and RNA sequencing, allowing identification of changes in the viral genome sequence as the infection spreads. This approach has allowed a widespread ‘genomic epidemiology’ approach to infection control, whereby viral transmission (e.g. in healthcare settings) can be detected not only by epidemiological assessment, but also by identifying similarities between viral sub-types among individuals. The UK has been at the forefront of this response, with researchers collaborating with public health agencies and NHS Trusts across the UK to form the COVID-19 Genomics UK (COG-UK) Consortium. Genomic surveillance at this scale has provided critical insight into the virulence and transmission of the virus, enabling near real-time monitoring of variants of concern and informing infection control measures on local, national and global scales. In the future, next-generation sequencing technologies, such as nanopore sequencing, are likely to become ubiquitous in diagnostic and healthcare settings, marking the transition to a new era of molecular medicine.
The Biochemist; https://doi.org/10.1042/bio_2021_189
The Biochemist, Volume 43, pp 46-50; https://doi.org/10.1042/bio_2021_194
The genetic signature of natural CRISPR-Cas systems were first noted in a 1989 publication and were characterized in detail from 2002 to 2007, culminating in the first report of a prokaryotic adaptive immune system. Since then, CRISPR-Cas enzymes have been adapted into molecular biology tools that have transformed genetic engineering across domains of life. In this feature article, we describe origins, uses and futures of CRISPR-Cas enzymes in genetic engineering: we highlight advances made in the past 10 years. Central to these advances is appreciation of interplay between CRISPR engineering and DNA repair. We highlight how this relationship has been manipulated to create further advances in the development of gene editing.
The Biochemist, Volume 43, pp 34-38; https://doi.org/10.1042/bio_2021_190
Algae made our world possible, and it can help us make the future more sustainable; but we need to change the way we live and adopt new more efficient production systems, and we need to do that now. When the world was new, the atmosphere was mainly carbon dioxide, and no animal life was possible. Along came algae with the process of photosynthesis, and things began to change. Ancient cyanobacteria algae turned carbon dioxide into enormous sums of lipids, proteins and carbohydrates, while they secreted oxygen into the atmosphere. Over a billion years, as oxygen filled the air and algae filled the seas, animal life became possible. Eventually all that algae biomass became petroleum and natural gas, which for eons sat undisturbed in vast underground reservoirs, holding enormous sums of untapped energy. Less than 200 years ago humans learned to tap these energy reserves to create the world we know today, but in so doing, we have released millions of years of stored CO2 back into the atmosphere. Algae can again help make the world a better place, but this will require new thinking and new ways of producing our food, feed and fuels. We need an algae revolution 2.0.
The Biochemist, Volume 43, pp 66-73; https://doi.org/10.1042/bio_2021_198
Open science is a movement to allow scientific information, data and outputs to be more widely accessible and reusable, with the active engagement of all the stakeholders. Open science can also describe openness within a research group where all participants share their data, analysis code, ideas and feedback. These ideas can be applied to all aspects of science, from large research consortia to student projects. With great accessibility comes greater reproducibility, leading to better code quality and better research. Here we describe what we have learned and gained from taking an open-science approach in undergraduate and masters student research projects, from the perspective of the student, the day-to-day supervisor, and the principal investigator (PI) or research group leader. We argue for the importance of clear expectations, communication, documentation, and of modelling collaborative behaviour. To design a good student project, we recommend planning the project outcomes so that everybody wins, and planning a pathway from novice to expert within the project.
The Biochemist; https://doi.org/10.1042/bio_2021_182
Science policy can be broadly defined as a two-way dialogue between science-related sectors and government. It involves the exchange of scientific findings and opinions with policy makers to inform the decision-making process, as well as the scrutinization of legislation around science-related topics to ensure it is based on sound evidence. Science policy covers a variety of issues, including research, education, funding, ethics, public health and equality, diversity and inclusion (EDI).
The Biochemist, Volume 43, pp 40-43; https://doi.org/10.1042/bio_2021_191
It is surprisingly common for us to think that we are the apex of evolution. Similarly, it is easy to convince ourselves that after nearly 3bn years, life on Earth has tried everything: every possible chemical reaction, every possible solution and every possible arrangement. Fortunately, both statements are wrong. We now know that the DNA (and RNA) life on Earth is one solution, of many, on how chemistry can turn towards life. As we discover new ways to code genetic information, in what is an interdisciplinary basic science endeavour, we develop many of the technologies that will establish significant biotechnological and life-saving applications. Welcome to life orthogonal.
The Biochemist, Volume 43, pp 4-8; https://doi.org/10.1042/bio_2021_192
Following the completion of the Human Genome Project in 2003, sequencing has become one of the most influential tools in biomedical research. Sequencing took off in earnest with the development of next-generation sequencing techniques in the early 2000s, making sequencing high throughput, faster, more affordable and commercially available to individual laboratories. With the improved understanding of the role of genetics in human disease, coupled with rapid advancement in sequencing technology, we are progressively unlocking the secrets of how our genes control the development of diseases. This has the potential to revolutionize medicine and healthcare, providing a significant step towards personalized medicine. How did we arrive here? What are the major achievements of sequencing technologies of the past two decades and how does it help us to piece the clues together towards personalized treatments and diagnosis?