bluuebunny/crossref_metadata_2025 huggingface dataset:
Training Day: biophysical techniques for probing biological systems: 1–2 July 2014, University of East Anglia, UK
Authors: AlOnazi Mona
Published: October 2019

Earlier this year one of the first Biochemical Society-supported Training Days took place at the University of East Anglia (UEA). The opportunity to host a practical handson event based upon ‘Biophysical Techniques for Probing Biological Systems’ was provided by the well-established Centre for Molecular and Structural Biochemistry (CMSB). This centre which straddles the Schools of Chemistry and Biological Sciences at UEA offers world-leading research across a unique range of biophysical techniques including NMR, EPR, CD, MCD, protein electrochemistry and rapid reaction kinetics. Well over 30 students from around the UK attended and received hand-on experience and dedicated instruction from world-leading experts in all these techniques. One of the organisers, Fraser MacMillan, said “the event was an overwhelming success and plans are already afoot to repeat this training event, which also receives key CPD credits, on a regular basis”.
Parliamentary Links Day 2014 – Science and Public Trust
Authors: Ball Catherine
Published: October 2019

The biggest science event in the parliamentary calendar certainly lived up to its billing this year; it was standing room only at Parliamentary Links Day. Organized by the Society of Biology on behalf of the whole science and engineering community and supported by a wide range of scientific societies and organizations including the Biochemical Society, this year's event was held on 24 June 2014 in Portcullis House, Westminster. The theme was Science and Public Trust and the day explored the ways in which the scientific community contributes to the public's trust in science. The importance of effectively engaging UK citizens with science and policy was emphasized throughout the day.
Life on Mars: Unlocking the biochemical secrets of the red planet
Authors: Sephton Mark A.
Published: October 2019

The planet Mars is a focus for numerous life search missions. As a near neighbour to Earth and with evidence of similar conditions in its early history, contemporaneous with the origin of life on Earth, there is a reasonable possibility of finding evidence for alien life on the red planet. With a whole planet to choose from and only a limited number of in situ analyses possible, the selection of samples to analyse is crucial. Fortunately, clues from analogues on Earth can provide effective guidance for sample choice. The harsh environment of Mars suggests that fine-grained sediments with features suggestive of past liquid water are the most likely to host organic records of past life. Also, with high doses of radiation experienced at the surface, digging deep will increase the probabilities of success for detecting carbon-based records. Past and current in situ missions to Mars are experiencing problems with unexpected amounts of aggressive salts on the planet surface, but the future holds the potential for returning samples of Mars to Earth where multiple sophisticated techniques can be employed to reveal the biochemical secrets of the red planet.
Helen Walden: A conversation with the winner of the 2015 Colworth Medal
Authors: Ball Cat
Published: October 2019

The Colworth Medal, one of the most distinguished awards that an independent, early career biochemical researcher can receive in the UK, will be awarded in 2015 to Dr Helen Walden, a principal investigator at the University of Dundee MRC Protein Phosphorylation and Ubiquitylation Unit.
Redox control of plant energy metabolism: The complex intertwined regulation of redox and metabolism in plant cells
Authors: Obata Toshihiro , Geigenberger Peter , Fernie Alisdair R.
Published: October 2019

Maintenance of the cellular redox status is crucial both to keep metabolic processes running and to prevent oxidation of cellular components by reactive oxygen species under fluctuating environments. The plastid is a plant-specific organelle in which considerable redox-active reactions occur and therefore the redox status in this energy organelle, as well as that of the mitochondria, must be tightly regulated. Plants employ multiple mechanisms to actively regulate energy metabolism in response to the redox status and to integrate subcellular redox signals to orchestrate redox status at the cellular level. In this article, we describe the redox regulation of the major flux bearing reactions in these two energy organelles and survey recent advances concerning interorganellar redox communication. The sum action of this complex regulatory network allows both the fine-tuning of metabolic activities for cellular redox homoeostasis and that of redox to allow optimal metabolic function.
An amazing experience: “One that no one regrets and everyone will remember”
Authors: Moffat Lewis
Published: October 2019

In 2014, the Biochemical Society helped fund students taking part in the iGEM (the International Genetically Engineered Machine) competition. This synthetic biology competition allows university students to work in teams to solve real challenges by building genetically engineered biological systems using BioBricks, from the Registry of Standard Biological Parts. Each team has to manage their own project, secure funding and advocates their research. In 2014 iGEM celebrated its tenth anniversary, which meant that all teams had the opportunity to present their accomplishments at the Giant Jamboree in Boston, MA. Lewis Moffat (iGEM team, University College London, UK) and Jessica Martyn (iGEM team, Dundee, UK) took part in the competition. They have written accounts of their experiences throughout the project and what they gained from taking part.
Careers in industry – more than just drug discovery
Authors: Christou Skevoulla
Published: October 2019

It is likely that if you were asked to name an industry where a biology background is vital, drug discovery would come to mind, but perhaps little else. Yet there are many different industries available to a biochemist in a variety of environments.
New approaches for new antibiotics
Authors: Cortes-Sanchez Emilio , Hoskisson Paul A.
Published: October 2019

Seventy years ago, Sir Alexander Fleming was awarded the Nobel Prize in Physiology or Medicine along with Howard Florey and Ernst Chain for “the discovery of penicillin and its curative effect in various infectious diseases”. Fleming was born and grew up in the small village of Darvel in Ayrshire, Scotland. His work, as a famous son of Scotland, is commemorated on a bank note. Ironically, this also demonstrates how much we have come to undervalue and take antibiotics for granted, as it is the lowest denomination note in the currency - the £5 note.
Human lymphoblastoid cell lines: a valuable tool for personalized medicine research
Authors: Gurwitz David
Published: October 2019

Over the last two decades, and in particular since the completion of the Human Genome Project, medicine has been slowly but persistently moving towards personalized medicine – medical treatments tailored for the individual patient based on genetic and genomic information derived from patients' biological samples (blood samples and biopsied tissues). A major aim of this approach is to prescribe the right drug at the right dosage and right time for each patient. Another key aim of precision medicine is allowing earlier disease diagnosis, so that patients are treated with preventive therapeutics before the disease has caused irreparable damage. However, personalized medicine research is often hampered by high costs and lack of high-quality biological samples. Human lymphoblastoid cell lines (LCLs) are an affordable research tool that can be of high value for disease and drug response biomarker discovery in the context of personalized medicine exploration and can be obtained from many human biobanks.
Molecular biomarkers of risk in rare and other cancers – identification and impact
Authors: Selfe Joanna , Shipley Janet
Published: October 2019

Cancer medicine is evolving rapidly. Advances in gene sequencing and profiling technology now means that we can obtain vast amounts of information about the genetic makeup of individual tumours and harness this to both predict which patients are at most risk of failing to be cured by current treatments and to tell us which of the myriad of new drugs targeted at individual proteins and pathways may be the most effective treatment in a highly patient-specific approach.
Using stratified medicine in diabetes
Authors: Owen Katharine R.
Published: October 2019

Diabetes mellitus is a common long-term condition characterized by raised blood glucose levels secondary to an absolute or relative deficiency of insulin production from the pancreatic islet -cells. Diabetes is highly heterogeneous in terms of aetiology1, making it a good candidate for stratified medicine approaches. Clinical studies have shown that the standard first-line treatments for Type 1 diabetes (insulin) and Type 2 diabetes (metformin) are not applicable to the rarer monogenic forms of diabetes, so in these cases making a molecular diagnosis can help to direct and optimize treatment.
The ups and downs of making a protein
Authors: Vogel Christine
Published: October 2019

Correctly adjusting the concentrations of the over 25,000 different proteins that reside in our cells is a complex task – and finely regulated via many processes. Recent technological advances allow us now to measure these concentrations and the rates of production and degradation for the different genes and provide first insights into how much protein is made per mRNA, and how the production and degradation rates change when the cell responds to a stimulus.
microRNA: emerging biomarkers in human disease and profiling challenges
Authors: Zhang J. Eunice
Published: October 2019

Over the last decade, a rapid growth in the field of micro(mi)RNA research has been evident. Profiles of miRNAs have been shown to reflect pathological conditions and have been implicated as potential biomarkers in the diagnosis and evaluation of human diseases. In this article, an overview of miRNA discovery and biogenesis is provided. Recent advances in using circulating miRNA as biomarkers in human diseases are discussed, along with the challenges researchers are facing in miRNA profiling and future diagnostic prospects.
Rose Scott-Moncrieff and the dawn of (Bio) Chemical Genetics
Authors: Martin Cathie
Published: October 2019

Between 1930 and 1940, Rose Scott-Moncrieff and her colleagues and collaborators published a series of ground-breaking papers in the Biochemical Journal1–3 and elsewhere4,5 which established the biochemical pathways of pigment biosynthesis in flowering plants and the genetic basis for these biochemical activities. This work was fundamental in establishing the field of biochemical genetics. This article reviews the work of Scott-Moncrieff, analyses her collaborative research style and reevaluates her place in the foundation of biochemical genetics.
Are plants engineered with CRISPR technology genetically modified organisms?
Authors: Jones Huw D.
Published: October 2019

We are only two or three breeding cycles from 9 billion people and an altered climate. This future population will rightly expect to access a nutritious, balanced and affordable diet, and to expect that the animals and plants it comes from are produced sustainably. However, during the same period there will be changes to the global climate resulting in local weather patterns with more frequent extreme events. To ensure medium-term food security will be challenging; to ensure it over the longer-term without permanently degrading the natural resources of our planet will need step-changes in agricultural systems. Breeding new varieties of plants will be a necessity to meet these future needs, but achieving this through conventional methods is likely to prove problematic. The novel technique of genome editing, with its ability to turn off or improve existing genes, may well be the answer to this problem.
Organ engineering: promise, progress and perspective
Authors: Scarritt Michelle E. , Badylak Stephen F.
Published: October 2019

The only curative treatment option for patients with end-stage organ failure is transplantation. Organ engineering offers an alternative to traditional transplantation that may address the critical shortage of donor organs and eliminate the need for recipient immunosuppression. Organ engineering may be accomplished through the use of scaffold – support structures that contain the architecture of an organ. As organs are exceedingly complex, creating an organ scaffold is a difficult task; however, organ scaffolds can be derived through a process known as decellularization, which is the mechanical, chemical and/or enzymatic removal of cells from a tissue or organ. Through decellularization of xenogenic (animal) organs, biocompatible extracellular matrix (ECM) scaffolds can be produced that retain the complex macroscopic and microscopic structure and composition of the native organ ECM. These 3D ECM scaffolds are ideal for engineering human organs.
How to make a magneticallycontrolled mouse
Authors: MacDonald Donald Iain
Published: October 2019

The Science Communication Competition is now in its sixth year. As in previous years, it aims to find young talented science writers and give them the opportunity to have their work published in The Biochemist. In 2015, a new branch of the competition was launched to include video entries. Overall this year's competition attracted 62 entries and these were reviewed by our external panel of expert judges. The first prize in the written category was awarded to Donald Iain MacDonald from University College London, whose article is presented here; the winner of the video category was Joe Tickle from the University of Birmingham. Joe Tickle's winning video can be viewed on the Society's website: [http://bit.ly/2a6Wq2l]
Linking cardiovascular disease, erectile dysfunction and preeclampsia: NO problem
Authors: Burke Suzanne D.
Published: October 2019

Nitric oxide (NO) is a colourless free radical gas, which has diverse and potentially opposing biological effects, depending on the local environment. The identification of NO and discovery of the mechanism of signalling are interesting tales on their own, leading to the Nobel Prize in Physiology or Medicine (1998) awarded to Murad, Furchgott and Ignarro. This article focuses on two very different – and important – consequences of the effects of NO on blood vessels: erectile dysfunction and pre-eclampsia.
Painting cells with light
Authors: Costantino Santiago , Kleinman Claudia L.
Published: October 2019

Humans perceive, interpret and remember the world based mainly on sight. Images are at the basis of our understanding and our behaviour, and we mould the world using vision as our most important sense. Indeed, two of the technological advances that have revolutionized the way we understand the universe are the telescope and the microscope, which act by extending the power of human vision. They magnify and improve image resolution of immense distant bodies and of miniscule objects at the tip of our fingers.
Oropouche virus: poised for headlines?
Authors: TilstonLunel Natasha Louise
Published: October 2019

Oropouche virus (OROV) is a midge-borne human pathogen that causes periodic outbreaks of a flulike illness predominately in the Northern parts of Brazil. However, despite its significant public health importance in Central and South America the virus remains rather obscure to the rest of the world.
Computational chemistry in the search for improved therapeutics for inflammatory and autoimmune diseases
Authors: Afantitis Antreas , Kollias George
Published: October 2019

Rheumatoid arthritis (RA), Crohn's disease and multiple sclerosis are common diseases, which are directly related to interactions developed between a protein called the Tumour Necrosis Factor (TNF) and its receptors. Current drugs that effectively disrupt TNF–receptor associations also cause serious side effects. In this feature, we present a computational scheme that resulted in the discovery of two non-toxic compounds, which directly inhibit TNF function. Moreover, the polypharmacology of these compounds was demonstrated as they were also found to inhibit the function of RANKL, a member of the TNF protein family. Optimization of the compounds may lead to the development of new medications for inflammatory and autoimmune treatments.
Reactive oxygen species: rapid fire in inflammation
Authors: Ingram Sonia , Diotallevi Marina
Published: October 2019

Everyone has encountered it at some point: inflammation. That horrible feeling when you've hurt yourself and the skin and tissue around the injury swells, goes red, feels hot and painful. It is even worse if it gets infected, then you really know about it! You can feel sick, weak and feverish as your body tries to fight off the infection and heal itself. Inflammation is really important for keeping us healthy. Sometimes, however, the body's inflammatory response can be a bit overzealous, not shutting down when it's supposed to, which can lead to various problems and even a state of disease. To fully understand and be able to effectively treat these diseases, we need a better understanding of how and why this chronic inflammation occurs. Could a crucial element in our lives, oxygen, be key to furthering our understanding?
Epigenetics can free us from the tyranny of selfish DNA
Authors: Turner Bryan
Published: October 2019

Richard Dawkins' The Selfish Gene was published in 1976. It promulgates a philosophy that places DNA firmly in charge; you are what your DNA (acting in its own evolutionary interests) tells you to be. We know of course that things are not so simple, but the enthusiasm that greets scientific advances in gene editing may reflect a subliminal wish to escape the implacable determinism of DNA. Biochemistry shows us how the environment influences genome function by acting on nucleosomes and their component histones. But, to build on this, we need to know to what extent environmentally induced changes can persist through mitosis and the germ line. The nucleosome and the modifications to which it is subject, offer a conceptual framework within which a heritable, environmentally sensitive epigenetic code might exist. If this can be proved, then we may finally escape the hegemony of DNA and realize the true potential of epigenetics.
Biomimetic spider silk fibres: from vision to reality
Authors: Salehi Sahar , Scheibel Thomas
Published: October 2019

Silk is a well-known and unique material that has been used in different applications for more than 5,000 years. The shiny silk fabrics that we know are actually made of threads created by the Chinese silkworm, but various arthropods can produce silks. Spider silk, for instance, is known to be the toughest fibre on Earth, outperforming both naturally and human-made fibres. Due to the problems of farming typically cannibalistic spiders, biotechnological approaches have been developed for producing spider silk proteins, which can be subsequently spun into biomimetic fibres. Here, we discuss recent developments in recombinant spider silk production and processing.
From mammoths to materials: synthetic biology moves into the biomaterial space
Authors: Behrens Michael R. , Ruder Warren C.
Published: October 2019

Synthetic biology is a relatively new research field that employs synthetic recombinant DNA technologies to engineer capabilities for addressing a wide variety of scientific and societal problems. We highlight a few noteworthy projects and achievements spanning the field of synthetic biology. In particular, some of the ways synthetic biological tools have been used to create novel biomaterials. Biological systems, like cells or larger organisms, can be made not only to synthesize new biomaterials but also to act as biomaterial constituents themselves, imbuing the materials with useful biological properties like the ability to respond dynamically to environmental cues. Looking into the future, there are many promising research directions synthetic biologists can take to develop tomorrow's biomaterials.
Society News
Authors: Downes Pete
Published: October 2019

Professor Sir Pete Downes succeeded Professor Sir David Baulcombe as the Society's President in January 2018. Pete is Principal and Vice Chancellor of the University of Dundee and was the Society's Chair from 2001–2004.
Brexit uncertainty looms over government policies
Authors: Tooze James
Published: October 2019

Brexit is causing much uncertainty and insecurity for the scientific community. It can seem like little has moved on since the referendum over 18 months ago, with limited detail arising from negotiations so far. However, the scientific community has collectively worked hard to speak clearly in the midst of myriad voices in the Brexit debate, and there are concrete signs that our voice has been heard as a sector that drives productivity, economic growth and improves people's lives.
AlcheMeat—how the future of animal production rests with biochemistry
Authors: Gibbons Marie
Published: October 2019

Innovations in regenerative medicine, stem cell biology, tissue engineering, and biopharmaceutical production are responsible for saving countless lives and completely transforming healthcare. But what if this research could be applied to more than individual medical treatments? New applications within these fields could further address public safety concerns, global malnourishment, environmental issues, and animal abuse. In fact, these types of studies could lead to prevention of many of the diseases they initially set out to treat! Foci within these areas, such as telomerase expression, cell differentiation, induced pluripotency, three-dimensional tissue formation, recombinant protein production and CRISPR, are now being used for something entirely different — making meat.
Meat by the molecule: making meat with plants and cells
Authors: Specht Liz
Published: October 2019

Our notion of meat has undergone a redefinition in recent years. New technologies for producing meat are challenging our assumptions regarding whether meat production need involve animal farming at all. In this article we'll explore opportunities in the growing fields of plant-based meat and clean meat, both of which are predicated upon the concept of deconstructing and reconstructing meat at the cellular and molecular level.
RDA for microbes — are you getting your daily dose?
Authors: Hill Colin
Published: October 2019

For almost all of human evolution our food and water has contained large numbers of microbes. Our immune systems evolved to cope with this daily intake, and our microbiomes (the collection of microbes on and in the human body) are increasingly recognized as playing an important role in human health. However, in recent times we have gone to great lengths to eliminate microbes from our diets, using food processing, water purification and hygiene to reduce our exposure. But has this come at a cost? Could our immune systems, primed to deal with trillions of microbes with every meal, be struggling to cope with their absence? Could this be a factor in the rise of modern inflammatory diseases in which the immune system misbehaves in response to dietary antigens or to our own epithelial cells? Perhaps we need to go back to consuming large numbers of (safe) microbes every day — a microbial RDA?
Starch: the best and worst of nutrients
Authors: Warren Fred , Harris Suzanne
Published: October 2019

The link between diet and health has been long known, as well as the fact that an increase in saturated fats and simple, refined carbohydrates in the diet, combined with our modern sedentary lifestyle, is contributing to an epidemic of diseases such as obesity and diet-related metabolic conditions. Although these can be multi-factorial disorders, simple lifestyle changes such as eating more fruit and vegetables in the diet and physical activity are known to be major factors in decreasing their prevalence. This has led to a focus on how dietary habits are affecting our overall health and how this information can be utilized to provide dietary solutions to combat the obesity epidemic. Of particular interest is the relationship between the digestion of starchy foods, which comprise 55–75% of dietary energy intake, and the subsequent effects on health.
Evidence, engagement and informed policy making
Authors: Sykes Emma
Published: October 2019

June 2018 saw the successful launch of the UK's first Evidence Week, a collaboration between Sense About Science, The House of Commons Library, and the Parliamentary Office of Science and Technology (POST). A week-long event filled to bursting with high-profile speakers, workshops and roundtable discussions, Evidence Week highlighted the importance of evidence-based policy making in the heart of Parliament. Members of both Houses couldn't escape the stands, the banners and the Voice of Young Science Network who were enthusiastically sharing the importance of evidence against a broad backdrop of issues ranging from solving the UK housing crisis to regulating genome editing.
Biosignatures in the solar system
Authors: Slade David , Price Alex , Hamp Rachael , Ramkissoon Nisha
Published: October 2019

Humanity's interest in whether or not we are alone in the universe spans generations, from Giordano Bruno's 16th century musings on other worlds and Giovanni Schiaparelli reporting seeing ‘canali’ in 1877 on the surface of Mars (which were thought to have been created by intelligent life) to alien invasions portrayed in today's movies. However, it is still unclear if other planetary bodies are capable of supporting life.

In the search for life there are two broad areas we look into, the requirements of life and actual signs of life. The identification of the key requirements for life enables scientists to focus life detection efforts onto planets and satellites that are considered habitable and more likely to support life. However, our ability to find life or detect signs of life is based on our understanding of life on Earth.
Life without organic molecules – exploring the boundaries of life
Authors: Ellery Alex
Published: October 2019

We are familiar with the notion of carbon-based life forms, but are there alternatives? In this article, I describe an approach to build a living machine from engineering materials that lacks any biochemistry but uses engineering methods to live. In devising this self-replicating machine, we explore broader scientific notions of what life might be and how it might be realized, rather than being limited to what it is on Earth.
CAR-T: expanding the horizons
Authors: Abel Peter
Published: October 2019

Immunotherapy in cancer treatment

The human immune system provides a powerful response to invading organisms, destroying bacteria and viruses, as well as aberrant cells that turn cancerous and proliferate uncontrollably. The enquiring mind naturally wonders whether this system could be exploited to treat cancers that have somehow evaded our immune defences. Those cancers that do not respond to chemotherapy or radiotherapy, necessarily harsh and sometimes ineffective treatments, could potentially be thwarted by harnessing the power of our antibodies. Evidence to date suggests that this approach is feasible, although there is still much work to be done before we can say we have finally found a ‘cure’ via this route.
Cancer vaccine: how far are we from curing cancer?
Authors: Choudhury Ruhul , Durrant Lindy
Published: October 2019

Although cancer treatment has developed considerably in the 21st century, there are still 8–9 million people dying of this disease each year. One strategy, using a patient's own immune system to combat their cancer, has recently led to a significant improvement in survival rates. The concept of immunotherapy is not new; as far back as 1893, William Coley reported tumour regression following repeated injections of bacterial toxin from Streptococcus pyogenes in a patient with advanced sarcoma. Over 100 years later, the use of cancer vaccine has come a long way, with a better understanding of the immune system's interaction with the tumour microenvironment.
Age-associated inflammation alters the aging trajectory
Authors: Teskey Grace , Bundalovic-Torma Cedoljub , Bowdish Dawn
Published: October 2019

Jonathan Swift said, ‘Every man desires to live long, but no man wishes to be old’. Most of us have ambivalent feelings about aging. We may want a long life, but those extra years hold less appeal if we are too ill to enjoy them. At one extreme of the aging trajectory are those who become frail, immobile and dependent in their 5th or 6th decade. At the other extreme are those who live to 100 or beyond remaining cognitively intact, active and engaged in their communities. We wonder what causes underlie this diversity in the aging process? Why do some of us age well and others poorly? The immune system plays a central role in health in our later years.
Microscale thermophoresis: warming up to a new biomolecular interaction technique
Authors: Mrozowich Tyler , MeierStephenson Vanessa , Patel Trushar R.
Published: October 2019

Biomolecules, such as RNA, DNA, proteins and polysaccharides, are at the heart of fundamental cellular processes. These molecules differ greatly with each other in terms of their structures and functions. However, in the midst of the diversity of biomolecules is the unifying feature that they interact with each other to execute a viable biological system. Interactions of biomolecules are critical for cells to survive and replicate, for food metabolism to produce energy, for antibiotics and vaccines to function, for spreading of diseases and for every other biological process. An improved understanding of these interactions is crucial for studying how cells and organs function, to appreciate how diseases are caused and how infections occur, with infinite implications in medicine and therapy. Many biochemical and biophysical techniques are currently being employed to study biomolecular interactions. Microscale thermophoresis (MST) is a relatively new biophysical technique that can provide powerful insight into the interactions of biomolecules and is quickly being adopted by an increasing number of researchers worldwide. This article provides a brief description of principles underpinning the MST process, in addition to benefits and limitations.
Minding the dynamic gap: measuring ultrafast processes in biomolecular systems
Authors: Hunt Neil T.
Published: October 2019

Biological processes in vivo involve interactions between large, complex molecules under conditions that are best-approximated by a viscous, multicomponent solution at temperatures often somewhat above room temperature. This means that the molecules involved are dynamic --- their structure changes --- on many timescales in ways that range from very small, localized fluctuations to fundamental changes in their overall appearance. What roles do these dynamics play in the structure–function relationship? Do very fast, local motions have any impact on well-characterized, slower structure changes? How do we go about measuring the very fastest biomolecular fluctuations to find out? Here we discuss ultrafast multidimensional (2D-IR) spectroscopy and look at the complementary information that it provides as part of a raft of biophysical experiments.
A beginner's guide to cryogenic electron microscopy
Authors: Savva Christos
Published: October 2019

The 'Beginner's Guides' are a new ongoing series of feature articles in the magazine, each one covering a key technique and offering the scientifically literate, but not necessarily expert audience, a background briefing on the underlying science of a technique that is (or will be) widely used in molecular bioscience. The series will cover a mixture of techniques, including some that are well established amongst a subset of our readership but not necessarily familiar to those in different specialisms. Our first 'Beginner's Guides' covers cryogenic electron microscopy.
Biochemical Society support in action: the Eric Reid Fund for Methodology
Authors: Marufu Michelle
Published: October 2019

Endowed by Emeritus Member Dr Eric Reid, this fund awards grants with an emphasis on methodology and a preference for cellular or bioanalytical work. Awarded to Dr Stephen Wallace, Michelle Marufu, a student in his lab, reports on the supported work.

I have always been fascinated by how microbes can be genetically programmed to produce chemicals of industrial value. During my undergraduate degree, this inevitably drew me to subjects such as molecular biology and industrial biotechnology.
A beginner's guide to nuclear magnetic resonance: from atomic spies to complex 3D structures at the heart of structural biology
Authors: Woodman Timothy J.
Published: October 2019

The 'Beginner's Guides' are an ongoing series of feature articles, each one covering a key technique and offering the scientifically literate, but not necessarily expert audience, a background briefing on the underlying science of a technique that is (or will be) widely used in molecular bioscience. The series will cover a mixture of techniques, including some that are well established amongst a subset of our readership but not necessarily familiar to those in different specialisms. This 'Beginner's Guide' covers nuclear magnetic resonance. Nuclear magnetic resonance (NMR) provides a way to explore the 3D structures of macromolecules in much more biologically relevant conditions and does this by taking advantage of the quantum mechanical property of some nuclei---nuclear spin. Here, we discuss how nuclear spin can be harnessed to provide information on the 3D structure of macromolecules in solution and how new thinking is leading to a revolution in drug discovery.
The where and when of intracellular Ca2+ signaling
Authors: Smith Holly
Published: October 2019

Ca2+ is essential for cellular functions. The ability of this ion to act as an intracellular signal, common to almost all eukaryotic cells, allows it to orchestrate an enormous repertoire of cellular activities, from initiating egg development after fertilization to synaptic transmission between neurons.
The role of DUBs in the post-translational control of cell migration
Authors: Lambies Guillem , García de Herreros Antonio , Díaz Víctor M.
Published: October 2019

Cell migration is a multifactorial/multistep process that requires the concerted action of growth and transcriptional factors, motor proteins, extracellular matrix remodeling and proteases. In this review, we focus on the role of transcription factors modulating Epithelial-to-Mesenchymal Transition (EMT-TFs), a fundamental process supporting both physiological and pathological cell migration. These EMT-TFs (Snail1/2, Twist1/2 and Zeb1/2) are labile proteins which should be stabilized to initiate EMT and provide full migratory and invasive properties. We present here a family of enzymes, the deubiquitinases (DUBs) which have a crucial role in counteracting polyubiquitination and proteasomal degradation of EMT-TFs after their induction by TGFβ, inflammatory cytokines and hypoxia. We also describe the DUBs promoting the stabilization of Smads, TGFβ receptors and other key proteins involved in transduction pathways controlling EMT.
Establishment, maintenance, and biological roles of non-CG methylation in plants
Authors: Kenchanmane Raju Sunil K. , Ritter Eleanore Jeanne , Niederhuth Chad E.
Published: October 2019

Cytosine DNA methylation is prevalent throughout eukaryotes and prokaryotes. While most commonly thought of as being localized to dinucleotide CpG sites, non-CG sites can also be modified. Such non-CG methylation is widespread in plants, occurring at trinucleotide CHG and CHH (H = A, T, or C) sequence contexts. The prevalence of non-CG methylation in plants is due to the plant-specific CHROMOMETHYLASE (CMT) and RNA-directed DNA Methylation (RdDM) pathways. These pathways have evolved through multiple rounds of gene duplication and gene loss, generating epigenomic variation both within and between species. They regulate both transposable elements and genes, ensure genome integrity, and ultimately influence development and environmental responses. In these capacities, non-CG methylation influence and shape plant genomes.
Probability analysis of axillary lymph node metastasis in breast cancer patients using particle space‐time distribution model
Authors: Chen Fang , Liu Jia , Zhang Xinran , Liao Hongen
Published: October 2019

The possibility of axillary lymph node metastasis differs in different breast cancer patients and is the strongest prognostic indicator in breast cancer. The existing studies mainly explored the relationship of axillary ultrasound imaging and axillary lymph node metastasis, without exploring whether ultrasound imaging of breast tumour can affect and perform axillary lymph node prediction. Therefore, this Letter proposes a novel particle space‐time distribution model to find the correlation between contrast‐enhanced ultrasonography of breast tumour and axillary lymphatic metastasis. Starting from the imaging principle of dynamic contrast‐enhanced ultrasonography, the particle space‐time distribution model not only comprises space‐time features of contrast‐enhanced ultrasonography with an encoder–decoder network, but also the flow field information of microbubble particles is integrated into the space‐time features that better serves the metastasis prediction by enhancing the particle distribution information. Extensive experiments on real patients have demonstrated that dynamic contrast‐enhanced ultrasonography of breast tumour can be used to predict the probability of lymphatic metastasis. This conclusion can be interpretable from the clinical and pathological perspectives.
Learning colon centreline from optical colonoscopy, a new way to generate a map of the internal colon surface
Authors: Armin Mohammad Ali , Barnes Nick , Grimpen Florian , Salvado Olivier
Published: October 2019

Optical colonoscopy is known as a gold standard screening method in detecting and removing cancerous polyps. During this procedure, some polyps may be undetected due to their positions, not being covered by the camera or missed by the surgeon. In this Letter, the authors introduce a novel convolutional neural network (ConvNet) algorithm to map the internal colon surface to a 2D map (visibility map), which can be used to increase the awareness of clinicians about areas they might miss. This was achieved by leveraging a colonoscopy simulator to generate a dataset consisting of colonoscopy video frames and their corresponding colon centreline (CCL) points in 3D camera coordinates. A pair of video frames were used as input to a ConvNet, whereas the output was a point on the CCL and its direction vector. By knowing CCL for each frame and roughly modelling the colon as a cylinder, frames could be unrolled to build a visibility map. They validated their results using both simulated and real colonoscopy frames. Their results showed that using consecutive simulated frames to learn the CCL can be generalised to real colonoscopy video frames to generate a visibility map.
Stable polyp‐scene classification via subsampling and residual learning from an imbalanced large dataset
Authors: Itoh Hayato , Roth Holger , Oda Masahiro , Misawa Masashi , Mori Yuichi , Kudo Shin‐Ei , Mori Kensaku
Published: October 2019

This Letter presents a stable polyp‐scene classification method with low false positive (FP) detection. Precise automated polyp detection during colonoscopies is essential for preventing colon‐cancer deaths. There is, therefore, a demand for a computer‐assisted diagnosis (CAD) system for colonoscopies to assist colonoscopists. A high‐performance CAD system with spatiotemporal feature extraction via a three‐dimensional convolutional neural network (3D CNN) with a limited dataset achieved about 80% detection accuracy in actual colonoscopic videos. Consequently, further improvement of a 3D CNN with larger training data is feasible. However, the ratio between polyp and non‐polyp scenes is quite imbalanced in a large colonoscopic video dataset. This imbalance leads to unstable polyp detection. To circumvent this, the authors propose an efficient and balanced learning technique for deep residual learning. The authors’ method randomly selects a subset of non‐polyp scenes whose number is the same number of still images of polyp scenes at the beginning of each epoch of learning. Furthermore, they introduce post‐processing for stable polyp‐scene classification. This post‐processing reduces the FPs that occur in the practical application of polyp‐scene classification. They evaluate several residual networks with a large polyp‐detection dataset consisting of 1027 colonoscopic videos. In the scene‐level evaluation, their proposed method achieves stable polyp‐scene classification with 0.86 sensitivity and 0.97 specificity.
Robust low‐rank abundance matrix estimation for hyperspectral unmixing
Authors: Feng Fan , Zhao Baojun , Tang Linbo , Wang Wenzheng , Jia Sen
Published: October 2019

Hyperspecral unmixing (HU) is one of the crucial steps of hyperspectral image (HSI) processing. The process of HU can be divided into end‐member extraction and abundance estimation. Lots of abundance estimation methods just take some properties of abundance into consideration, such as non‐negative, sum‐to‐one and so on but ignore the noise corruption. However, in practical applications, there are always high‐noise bands in HSI due to water absorption, atmospheric transmission, and other inevitable factors, which lead to the estimation accuracy reduction. Here, we propose a new abundance estimation model which takes the mixing pattern of endmembers and low signal‐to‐noise ratio (SNR) bands of HSI into consideration simultaneously. The constraints considering not only the low‐rank feature of abundance but also the sparsity quality of noise are imposed on the new model for more robust results. Adequate experiments both on synthetic and real hyperspectral data have confirmed the superiority of our method.
New records of the invasive red swamp crayfishProcambarus clarkii(Girard, 1852) (Decapoda: Cambaridae) from Poland
Authors: Maciaszek Rafał , Bonk Maciej , Strużyński Witold
Published: October 2019

This contribution presents new observations of the red swamp crayfish,Procambarus clarkiiin Poland. The species was detected in Żerań Canal and Krasiński Garden in Warsaw (central Poland) where 5 and 2 individuals were collected respectively as well as in Dąbie Pond in Krakow (southern Poland) with total of 4 crayfish observed. These new sites are located approximately 500 km eastward (Warsaw) and 240–260 km northward (Krakow) from the nearest European sites where this species has been previously recognised (near Berlin, Germany, Egerszalók and Budapest, Hungary), thus are the furthest north-east records of the species in European open waters. It is likely that the examined stock originates from single introductions, however, presence of the juveniles caught in Warsaw suggests that the population found there may be breeding. The findings are discussed with available literature describing possible waysP. clarkiimay use to colonize new habitats as well as the impact it has on the invaded ecosystems in general and native crayfish in particular.
The relationship between the deformation and the indentation size effect (ISE)
Authors: Petrík Jozef , Blaško Peter , Mihaliková Mária , Vasilňáková Andrea , Mikloš Vojtech
Published: October 2019

The aim of the submitted work is to study the relationship between the local deformation and the indentation size effect (ISE). A local value of reduction of the area (Z) was used as the measure of the deformation. Applied loads in the micro-hardness test ranged between 0.09807 to 0.9807 N. The micro-hardness was measured on the cross section in the longitudinal axis of the fractured sample after the uniaxial tension test. The material of the sample was 99.5% aluminium. The influence of both load and deformation on the ISE was evaluated by the analysis of variance (ANOVA). The influence of the load was also evaluated by Meyer’s index n, PSR method, and Hays–Kendall approach. The influence of both factors on the measured value of micro-hardness and therefore on the ISE is statistically significant. The ISE is normal in the areas with high deformation, on the contrary, in areas with low deformation, it has a “reverse” character. The difference between load independent “true hardness” and measured micro-hardness HV0.05 increases with increasing deformation.
Effect of composition and morphology of non-metallic inclusions on fracture toughness in as-cast AHSS
Authors: Wu Zhanfang , Liu Zhenyu , Qiu Shengtao , Li Xiangyang
Published: October 2019

A set of water-cooling copper-chill mold equipment is designed to study the precipitation behavior of different inclusion types in test steel under different cooling conditions, as well as its effects on the steel mechanical properties. As the results reveal, slow cooling treatment near the solidus temperature of test steel is conducive to forming more MnS + Al2O3 composite inclusions. The impact energy (−16 °C) of slow-cooled cast ingots at the core position is 28% higher than that of the air-cooled ingots. Scanning electron microscopy analysis of the specimens shows that small cracks are formed around single Al2O3 inclusions, but no cracks were found around composite inclusions. A calculation model of the tessellated stress of composite inclusions in steel is introduced to verify this phenomenon. The calculation demonstrates that, with a cover of ductile MnS, stress concentration around the composite inclusion is significantly decreased as compared with the single Al2O3 inclusion in the test steel.
Tumorscreening bei Nierentransplantation
Authors: Thorban Stefan , Matevossian Edouard
Published: October 2019

Aufgrund der zunehmenden Zahl von Langzeittransplantierten seit der ersten Nierentransplantation mit begleitender Immunsuppression im Jahr 1962 hat auch das Tumorrisiko für Transplantatempfänger zugenommen. Neben dem Tumor-Screening vor Aufnahme auf die Warteliste sollte bei Langzeittransplantierten auch nach einer Nierentransplantation entsprechend der vorliegenden Risikoprofile eine individualisierte Nachsorge erfolgen. Da bisher wenige Behandlungsleitlinien vorliegen, sollte das Screening in Anlehnung an onkologische Leitlinien sowie Risikofaktoren und das Alter der Patienten durchgeführt werden. In der vorliegenden Arbeit werden Tumorgenese und Tumorinzidenz unter dem Aspekt der Immunsuppression und gängiger tumorfördernder Faktoren analysiert und entsprechende Therapieempfehlungen ausgesprochen. Individuell sollte mit dem Patienten besprochen werden, inwieweit eine verminderte Lebensqualität bei Transplantatverlust gegenüber einer möglichen höheren Lebenserwartung unter Therapie akzeptiert wird.
Schmerztherapie bei schmerzenden Beinen
Authors: Lindig Martin
Published: October 2019

Hintergrund Beinschmerzen sind ein häufiges Symptom in der phlebologischen Praxis.

Methode in der vorliegenden Arbeit wird ein strategisch sinnvolles Management von Schmerzen/Beinschmerzen dargestellt.