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4968 results in Wits University Press

Page 218 of 249

  • Two Newspapers, Two Nations? The Media and the Xenophobic Violence

  • Edited by Shireen Hassim, University of the Witwatersrand, Johannesburg, Tawana Kupe, University of Pretoria, Eric Worby, University of the Witwatersrand, Johannesburg
  • Photographs by Alon Skuy
  • Foreword by Paul Verryn
  • Book:
    Go Home or Die Here
    Published by:
    Wits University Press
    Published online:
    04 June 2019
    Print publication:
    01 November 2008, pp 161-174

  • Summary

    What is it we want from our media at a time of ugly anti-social violence? Brutal honesty, which would show that many of our compatriots are proud xenophobes? Caution and sensitivity, which would favour careful language and a choice of pictures to capture the hate which gripped our streets without offending or falling into tastelessness? Determined optimism, which would prioritise coverage of the few who show compassion above the many who show hatred? Or cold analysis, which would have us move quickly to probe the causes and effects?

    These are questions I asked while taking a close look at the coverage of the first few days of the violence in May in two leading Johannesburg newspapers: the Daily Sun and The Star.

    The Daily Sun is a mass market tabloid which has grown in the last few years to become the country's biggest daily by far, selling over 500 000 copies nationally, mostly to a working class readership. In its flamboyant way, the most noticeable aspect of this paper's coverage of the initial week of violence in May 2008 was its frequent and consistent use of the word ‘aliens’ to describe non-South Africans. The violence was flagged repeatedly in headlines as a ‘war on aliens’ (‘It's war on aliens – 20 bust for attacks’, 13 May; ‘War against aliens: Thousands forced to flee Alex’, 14 May).

    In the tabloid tradition, ‘aliens’ usually refers to little green visitors from outer space, but the Daily Sun was referring to black visitors from much closer to home. The word has the same effect: emphasising foreigners as outsiders, different and strange, not part of us, even threatening. To describe the violence as ‘war’ implies a formal exercise in defending the country against this invasion, and invokes such dramatic phrases as ‘war on terror’.

    It is striking that the Daily Sun, in contrast with most other media, downplayed the violence. On the first Monday after the violence broke out in Alexandra, the Daily Sun had no coverage, though this was probably due to early Sunday deadlines. On day two, it had only a short inside story. The first time the story appeared on its front page was on Wednesday, three days after the violence broke out and when it had dominated national headlines for 48 hours.

  • Crossing Borders

  • Edited by Shireen Hassim, University of the Witwatersrand, Johannesburg, Tawana Kupe, University of Pretoria, Eric Worby, University of the Witwatersrand, Johannesburg
  • Photographs by Alon Skuy
  • Foreword by Paul Verryn
  • Book:
    Go Home or Die Here
    Published by:
    Wits University Press
    Published online:
    04 June 2019
    Print publication:
    01 November 2008, pp 119-132

  • Summary

    Interviewed in the Sunday Independent (Johannesburg) of 25 May 2008 about the recent attacks on foreign nationals, an unknown ‘student’ who had participated in the attacks on African immigrants is

    … adamant that all the problems started at South Africa's borders. They are too porous, are not properly policed and border posts are manned by corrupt officials who let anybody in … The government must work hard to secure our borders. Home Affairs must be sorted out. We're helping the government, now, to send them back.

    While some may wish to argue that we are somehow ‘all Africans together’, the political facts on the ground are that South Africa, like any other sovereign national state, has the right to decide which foreign citizens should or should not be admitted at its borders, and under what conditions. The South African government also has the right to pick and choose among applicants for entry or residence on the basis of its own interests, priorities and policies. All countries do this, and some observers, like migration expert Dr Wilmot James, say that South Africa has a responsibility to control its borders as an obligation to the Constitution and the rule of law. Certainly South Africa is not required to accept any number of people either from Africa or anywhere else simply because they are destitute or see better opportunities for themselves here than elsewhere.

    An exception to this would be genuine refugees fleeing the immediate threat of violence or imprisonment at home, but the South African government has not shown much enthusiasm for differentiating between economic and political refugees, or for granting legal residence to either category of ‘forced migrant’. This confusion has had additional ill effects due to government denials that there are any crises in other African countries or that there is a real category of ‘genuine’ African political refugees.

    The government of South Africa shows little enthusiasm in practice for investing in the effective physical monitoring and control of its land borders. What the student said in the Sunday Independent is, by most reports, close to the mark: South African identity is for sale.

  • Behind Xenophobia in South Africa – Poverty or Inequality?

  • Edited by Shireen Hassim, University of the Witwatersrand, Johannesburg, Tawana Kupe, University of Pretoria, Eric Worby, University of the Witwatersrand, Johannesburg
  • Photographs by Alon Skuy
  • Foreword by Paul Verryn
  • Book:
    Go Home or Die Here
    Published by:
    Wits University Press
    Published online:
    04 June 2019
    Print publication:
    01 November 2008, pp 79-92

  • Summary

    Many commentators have identified one important set of factors underlying the violence in townships and squatter areas during May to be mounting difficulties faced by poor people. When asked by journalists why the violence had occurred, residents in these areas referred to issues including crime, lack of work, and lack of housing and basic services. Government – in the form of minister Essop Pahad – argued that the violence must be the work of a ‘third force’ since South Africa has done more than any other developing country for the poor. I would argue that to the extent the violence is linked to the economic circumstances of poor people, it is not the result of poverty per se, but rather of inequality. It is surely not simply that people are poor which leads them to attack other poor people, but instead the sense of unfairness engendered by inequality, of being discriminated against, which creates the resentments and hostility towards those perceived, rightly or wrongly, to be better off or to have received preferential treatment.

    INEQUALITY IS DISTINCT FROM POVERTY

    The main point of this chapter is that poverty and inequality are distinct issues: they are not the same thing and cannot be addressed by policy as if they are. There is no doubt of course that both poverty and inequality are intractable and deeply-rooted issues in South Africa. In 2005, 47 per cent of the population was in poverty using the widely-agreed poverty line of R322 per capita per month in 2000 prices. This proportion was below the 2000 level of 53 per cent, but was nonetheless inordinately high.

    Inequality is perhaps even starker. In 2006, the Gini coefficient was officially calculated at 0.73, certainly amongst the two or three highest globally. More revealing perhaps was that the richest 10 per cent of the population received 51 per cent of total household income, while the poorest 10 per cent received a mere 0.2 per cent, the ratio of average income between the two groups thus amounting to a massive 255:1. The richest 20 per cent of the population received 68.8 per cent of the total income, compared with the poorest 20 per cent obtaining only 1.4 per cent, a ratio of 49:1.

  • Foreword

    • By Wieland Gevers, Emeritus Professor of Medical Biochemistry, University of Cape Town and former President, South African Society for Biochemistry and Molecular Biology.
  • Edited by Barry Mendelow, University of the Witwatersrand, Johannesburg, Michèle Ramsay, University of the Witwatersrand, Johannesburg, Nanthakumarn Chetty, University of the Witwatersrand, Johannesburg, Wendy Stevens, University of the Witwatersrand, Johannesburg
  • Book:
    Molecular Medicine for Clinicians
    Published by:
    Wits University Press
    Published online:
    04 June 2019
    Print publication:
    01 October 2008, pp x-x

  • Summary

    Many people find it difficult to understand the idea of molecules (invisible to the eye, and usually detectable only by the use of complicated machines) being responsible for problems such as heart failure and mental disorders. We have evolved to trust what we can actively see, touch, smell, hear and taste; in the same way we like to understand what is going on, in our own bodies and in those of others, on the basis of direct sensory experience, developing an integrated picture facilitated by memorised information and the application of logical thinking against a background of varying amounts of emotional overdrive. That for millennia has been the basis of medicine as an art.

    Molecules in contrast present all sorts of obstacles to our ‘normal’ ways of addressing health issues. Compare physical anatomy with molecular structure – in the first, we can dissect cadavers with scalpels and tweezers, and see the structures and their relationships with the naked eye; in the second, the ‘dissection’ requires a combination of specialised variants of optical and electron microscopy, stains and probes, and ultimately (in the present ‘omic’ era) genomics, transcriptomics and proteomics, and the analysis of an endless complexity of dynamic interactions between the constituent molecules of the tissues in question.

    But the shift to molecular thinking can be made quite easily, if one learns to let one's imagination habitually enter the world below one's sensory thresholds. Everything that goes wrong (and right) macroscopically is ultimately determined by what goes on submicroscopically, and everything that happens sub-microscopically is determined by what is happening at the molecular level. The explanatory potential is accordingly usually amplified by orders of magnitude as you go down to this degree of molecular magnification. How would it be possible to discover that a host of cardiac disorders of uncertain cause are in fact caused by specific mutations in genes for proteins involved in muscular contraction and its regulation, if all we knew was what we could see, touch and feel? How would it be possible to trace the events in HIV-infected persons that are the prime causes of the phenomena observed clinically? How would it be possible to understand the workings of the immune system or the brain?

  • Chapter 10 - Chromosome Disorders

  • from SECTION 2 - MOLECULAR PATHOLOGY
    • By Sarah Walters, BSc (Hons), MSc (Med) (Genetic Counselling), worked as a genetic counsellor in the Division of Human Genetics, University of the Witwatersrand, from 2001 to 2007. In 2007 she became Honorary Treasurer of the Southern African Inherited Disorders Association and began setting up the Birth Defects and Disabilities Foundation (BDDF). She is currently coordinator of the BDDF and programme director of the Medical Genetics Education Programme for registered nurses., Nerine E Gregersen, MB BCh, MSc (Med), FCPaed (SA), Cert (Medical Genetics), DCH (SA), is a clinical geneticist and associate lecturer in the National Health Laboratory Service and Division of Human Genetics, School of Pathology, University of the Witwatersrand.
  • Edited by Barry Mendelow, University of the Witwatersrand, Johannesburg, Michèle Ramsay, University of the Witwatersrand, Johannesburg, Nanthakumarn Chetty, University of the Witwatersrand, Johannesburg, Wendy Stevens, University of the Witwatersrand, Johannesburg
  • Book:
    Molecular Medicine for Clinicians
    Published by:
    Wits University Press
    Published online:
    04 June 2019
    Print publication:
    01 October 2008, pp 133-142

  • Chapter 35 - Chronic Myeloid Leukaemia

  • from SECTION 3 - MOLECULAR THERAPEUTICS
    • By Nerina Savage, PhD, is an Honorary Professorial Research Fellow, Division of Molecular Medicine and Haematology, School of Pathology, University of the Witwatersrand.
  • Edited by Barry Mendelow, University of the Witwatersrand, Johannesburg, Michèle Ramsay, University of the Witwatersrand, Johannesburg, Nanthakumarn Chetty, University of the Witwatersrand, Johannesburg, Wendy Stevens, University of the Witwatersrand, Johannesburg
  • Book:
    Molecular Medicine for Clinicians
    Published by:
    Wits University Press
    Published online:
    04 June 2019
    Print publication:
    01 October 2008, pp 405-412

  • Summary

    INTRODUCTION

    The question may be asked: why discuss therapy of chronic myeloid leukaemia (CML), a relatively rare condition that mainly affects people beyond the fifth decade? The answer is simple; CML is the first cancer found to be associated with a genetic defect the product of which is a protein with oncogenic properties, exclusively confined to the cancer cells. The knowledge gained from this information stimulated additional investigations on other cancers. It also raised the possibility of an alternative approach to cancer treatment by specifically targeting the molecular defect.

    CML is cancer of the white blood cells of the bone marrow. It is a unique disease because it is the first cancer found to have a specific genetic defect, the Philadelphia (Ph) chromosome, which is associated with the production of an oncogene, BCR-ABL, the causative agent of the leukaemia. To appreciate therapy for CML, it is necessary to understand the cytogenetic changes that occur and the resultant molecular defect associated with the malignant phenotype of the cell.

    CYTOGENETICS

    The Ph chromosome, an acquired genetic abnormality, uniquely characterises leukaemic cells in CML. The Ph chromosome, a remnant of chromosome 22 and a portion of chromo - some 9, results from an unequal translocation between the long arms of chromosome 9 and chromosome 22, as depicted in Chapter 22.

    In 1984/85 two genes involved in the trans location were identified, the Abelson proto-oncogene (ABL) located on chromo - some 9 and the breakpoint cluster region (BCR) on chromosome 22. The translocation results in the two genes being placed adjacent to each other on the Ph chromosome to produce a fusion or chimeric (chimera – derived from two parts of different origin) gene BCR-ABL. Two different fusion genes may arise. On the derivative 22q– is BCR-ABL, the fusion gene responsible for development of CML, and ABL-BCR is on 9q+ The latter fusion gene is not believed to have clinical significance.

  • Chapter 2 - Digital Concepts in Molecular Medicine

  • from Section 1 - Principles Of Cellular And Molecular Biology
    • By Barry V Mendelow, MB BCh, PhD, FCPath (Haematology), MASSAf, FRSSAf, Emeritus Professor, University of the Witwatersrand and National Health Laboratory Service, was formerly the founding Professor and Head of the Division of Molecular Medicine and Haematology at the School of Pathology and Executive Director (Research) for the University of the Witwatersrand.
  • Edited by Barry Mendelow, University of the Witwatersrand, Johannesburg, Michèle Ramsay, University of the Witwatersrand, Johannesburg, Nanthakumarn Chetty, University of the Witwatersrand, Johannesburg, Wendy Stevens, University of the Witwatersrand, Johannesburg
  • Book:
    Molecular Medicine for Clinicians
    Published by:
    Wits University Press
    Published online:
    04 June 2019
    Print publication:
    01 October 2008, pp 15-18

  • Summary

    INTRODUCTION

    Arguably the most important conceptual foundation of modern biology is that genetic information is essentially digital in nature. As it happens, the information technology organisational paradigm, built as it is on the special semiconductor properties of silicon, is a convenient framework for a modern understanding of cell and molecular biology and biotechnology, based as they are on the special properties of carbon, and vice versa. Just as a strategic understanding of the basis of information and communication techno - logy (ICT) is becoming an essential life skill in modern society, so a strategic understanding of the conceptual basis of molecular medicine is becoming an essential life skill for virtually all medical practitioners. The analogy of computer viruses, which traces its origins to the 1970s, introduced a useful model for the understanding of both information technology in the language of biology and molecular biology in the language of information technology. The ICT analogy is also a useful conceptual framework for the understanding of disease in a wider setting, because many noninfectious diseases are also ultimately caused or driven by inherited or acquired abnormalities in sequences of digital information. Increasingly, practical use is being made of this concept in the diagnostic process, by applying a small set of tools to identify such disease-causing digital sequences across a wide variety of diseases, whether infectious or otherwise.

    Multicellular organisms are each clones of a single cell, of which the genome, normal or abnormal, is effectively the digitally encoded design blueprint for the whole organism. The genome of any organism, be it a micro-organism, plant or animal, is the sequence of the fundamental digital units of information that constitute the specification for the construction and function, or in the case of inherited disease, dysfunction, of that organism. Disease caused by infectious microorganisms can be diagnosed by demonstrating digital sequences that define the presence of those organisms in a highly specific way that not only demonstrates the unambiguous presence of particular organisms, such as HIV, but also often contains the additional information that specifies drug resistance, virulence, etc.

  • Chapter 13 - Population Genetics

  • from SECTION 2 - MOLECULAR PATHOLOGY
    • By Anthony B Lane, PhD, heads the Serogenetics Laboratory in the Division of Human Genetics, National Health Laboratory Service and School of Pathology, University of the Witwatersrand., Himla Soodyall, PhD (Human Genetics) is a medical scientist at the National Health Laboratory Service and has a joint appointment as Associate Professor in the Division of Human Genetics at the University of the Witwatersrand.
  • Edited by Barry Mendelow, University of the Witwatersrand, Johannesburg, Michèle Ramsay, University of the Witwatersrand, Johannesburg, Nanthakumarn Chetty, University of the Witwatersrand, Johannesburg, Wendy Stevens, University of the Witwatersrand, Johannesburg
  • Book:
    Molecular Medicine for Clinicians
    Published by:
    Wits University Press
    Published online:
    04 June 2019
    Print publication:
    01 October 2008, pp 167-176

  • Summary

    INTRODUCTION

    Mendel's investigation of heredity and the major interest in heredity in the nineteenth century arose from two related problems: how to breed improved crops and domestic animals, and how to understand the nature and origin of species. What these problems have in common is that they are concerned with populations rather than individuals. Most population concepts involve a hierarchical classification in which units are defined in terms of the extent to which individuals can be identified by common characteristics. The definition of a population for demographic purposes can be made entirely on arbitrary grounds. It can involve social, ecological or genetic criteria.

    Population genetics is the study of allele and genotype frequency distribution and change under the influence of four main evolutionary forces: mutation, genetic drift, gene flow and natural selection. These forces can result in different allele frequencies in different populations and one of the forces can dominate at one time in the evolution of a population, while others can have a major effect at another. For example, endemic exposure to pathogenic infectious organisms would select individuals with increased survival potential (determined by their phenotype, which in turn is partly determined by their genotype) and lead to an increase in the frequency of advantageous alleles during the time that the selective pressure is active. A population must be defined before an allele frequency within it can be determined.

    Human populations are made up of the old, the middle-aged and the young, those who have reproduced and those who have not. Each mature member of a population has some chance of reproducing with any other mature individual in the population. The magnitude of that chance depends on factors such as proximity, sub-culture, age, physical attributes, education and socio-economic status. The fraction of a generation that produces the next generation is called the effective population (Ne), even though non-breeding individuals certainly play important supporting roles.

    GENETIC VARIATION

    It is obvious that all individuals of the same gender in any human population are not the same; they do not look the same or react in the same way. These differences are due to their life stage, the environment in which they have developed and their genetic make-up.

  • Chapter 19 - Mammalian DNA Repair

  • from SECTION 2 - MOLECULAR PATHOLOGY
    • By Alexio Capovilla, BSc (Hons), PhD, PDM, is a lecturer in the Division of Molecular Medicine and Haematology, University of the Witwatersrand, and is also employed as a senior research scientist by Elevation Biotech, a spin-out biotech company attached to the Division.
  • Edited by Barry Mendelow, University of the Witwatersrand, Johannesburg, Michèle Ramsay, University of the Witwatersrand, Johannesburg, Nanthakumarn Chetty, University of the Witwatersrand, Johannesburg, Wendy Stevens, University of the Witwatersrand, Johannesburg
  • Book:
    Molecular Medicine for Clinicians
    Published by:
    Wits University Press
    Published online:
    04 June 2019
    Print publication:
    01 October 2008, pp 227-237

  • Summary

    INTRODUCTION

    This chapter provides a basic description of the major biochemical pathways that operate in mammalian cells to maintain the structure and integrity of genomic DNA. This is no trivial task for multicellular organisms, since, as we shall see, they are continually exposed to a plethora of agents that cause DNA damage. Failure to repair damaged DNA efficiently and consistently is incompatible with cellular life as we know it, and a large number of severe clinical disorders can now be attributed to defects in the cellular DNA repair machinery. We will look at examples of these in a little more detail below.

    The importance of this vital function is further illustrated by the fact that DNA repair mechanisms are, for the large part, functionally conserved from primitive prokaryotes through to higher-order eukaryotes such as humans. Furthermore, at the time of writing (2006), over 150 gene products had been identified in humans that appear to have evolved primarily as either structural or catalytic components of DNA repair pathways, or gatekeepers of various stages of the cell cycle that are deliberately manipulated when DNA repair pathways are invoked. Readers are encouraged to consult an interesting web resource that has been constructed to describe the growing list of DNA repair genes at www.cgal.icnet.uk/ DNA_Repair_Genes.html

    THE SPECTRUM OF DNA DAMAGE

    For many years molecular biologists described DNA as a highly stable component of the cellular machinery that changes very little in structure or chemistry over time. The well established fact that DNA is the repository of coding information for all cellular life, and is responsible for the inheritance of this information from generation to generation, suggested that inherent physicochemical properties of DNA rendered it essentially chemically immutable. Recent evidence, however, has revealed a vastly different scenario, one in which all organisms are constantly exposed to a plethora of agents that cause significant structural and chemical changes in their DNA. Moreover, these changes are now known to occur through ongoing inter actions between DNA and by-products of normal cellular metabolism.

  • Keynote Essay 6: Molecular Research Case Study: Developing Novel RNA Interference-based Therapy

  • from SECTION 3 - MOLECULAR THERAPEUTICS
    • By Patrick Arbuthnot, MB BCh, BSc (Hons), PhD, is a reader in the Division of Molecular Medicine and Haematology at the Medical School of the University of the Witwatersrand, Johannesburg. He has a research interest in using nucleic acid transfer to develop new approaches to treating viral infections of South African importance., Marc S Weinberg, PhD, is a senior lecturer in the Division of Molecular Medicine and Haematology, University of the Witwatersrand, and a member of the Antiviral Gene Therapy Research Unit.
  • Edited by Barry Mendelow, University of the Witwatersrand, Johannesburg, Michèle Ramsay, University of the Witwatersrand, Johannesburg, Nanthakumarn Chetty, University of the Witwatersrand, Johannesburg, Wendy Stevens, University of the Witwatersrand, Johannesburg
  • Book:
    Molecular Medicine for Clinicians
    Published by:
    Wits University Press
    Published online:
    04 June 2019
    Print publication:
    01 October 2008, pp 441-448

  • Summary

    THE VALUE OF ACADEMIC RESEARCH

    Research can be defined as the process of discovery and creation of new knowledge. A vital role for universities is to carry out research, and success in this activity is a good gauge of the well-being of these academic institutions. All leading universities of the world (such as Harvard, Cambridge and Oxford universities) have a strong commitment to supporting research, and this is the foundation of their good reputations. Research is vital to any society and positive outcomes go way beyond the direct practical application of new discoveries. By nurturing creativity, critical thinking, open-mindedness and enquiry, research has the broad benefits of building a strong democratic ethic in society. Today we refer to the importance of the ‘knowledge based economy’ where societies become more reliant on creation and exploitation of new knowledge to understand and overcome economic and political challenges. An active research community allows countries to benefit directly from new developments of the twenty first century and to participate in developing a knowledge-based economy. The benefits of an active research environment can have both direct and indirect effects on society. Some of these benefits are listed below.

  • • Improved training of students. An often under-appreciated role of research is that it is beneficial to teaching in universities. By and large, research activities are supportive of university educational programmes, and teachers who are immersed in active research generally make better instructors. Research leads to more meaningful insight into a subject, and educators pass this benefit on to students through better teaching. High-level training of students that is not based on a foundation of academic research risks becoming stale and outmoded.

  • • Promoting innovation for patient care. Insights gained from research on medical challenges contribute significantly to understanding and overcoming patient problems, which collectively makes for better patient management and care.

  • • Broadening the knowledge base for the good of humanity. Some of the most significant breakthroughs in technology have come from unlikely research contributions. Research does not always produce immediately obvious practical benefits, and it is often only after several years that the utility of research becomes apparent.

  • Chapter 41 - Bioinformatics and Molecular Medicine

  • from SECTION 4 - RESEARCH AND THE CONTINUING EVOLUTION OF MOLECULAR MEDICINE
    • By Andries J Oelofse, BSc, BSc (Hons), MSc (Bioinformatics), held the position of Bioinformatics Consultant at Wits Bioinformatics, a node of the National Bioinformatics Network, at the time of writing. He has a keen interest in the contribution of bioinformatics to molecular medicine., Michèle Ramsay, PhD (Human Genetics), is currently Professor and Head of the Molecular Genetics Laboratory, Division of Human Genetics, National Health Laboratory Service and University of the Witwatersrand.
  • Edited by Barry Mendelow, University of the Witwatersrand, Johannesburg, Michèle Ramsay, University of the Witwatersrand, Johannesburg, Nanthakumarn Chetty, University of the Witwatersrand, Johannesburg, Wendy Stevens, University of the Witwatersrand, Johannesburg
  • Book:
    Molecular Medicine for Clinicians
    Published by:
    Wits University Press
    Published online:
    04 June 2019
    Print publication:
    01 October 2008, pp 456-466

  • Summary

    INTRODUCTION

    To study life at the molecular level, various types of data must be in a ‘human readable format’. There are many tools and techniques with which we can determine the sequences of the nucleic acids and proteins that allow us to draw parallels between what we physically observe and what is happening at the molecular level. The amount of data these tools generate is vast. The data can amount to several gigabytes per experiment, and all must be correctly stored and interpreted in order to be useful. There are also several related types of information that assist in the better understanding of the function of genes and proteins in the organism.

    Bioinformatics is the discipline that deals with the problem of massive data sets with diverse data in molecular research. It concerns the storage, visualisation, manipulation, analysis and integration of biological information using computers. Initially, the biological information that was required to be managed by bioinformaticists was the nucleotide and amino acid data derived from DNA and protein sequencing, but today with new technologies and approaches there are many more diverse data types that must be managed.

    A paradigm shift is starting to occur in molecular research. The emphasis on hypo - thesis-driven research is declining, and is shifting towards exploratory observations. These observations are typically done in a very high-throughput way, meaning that in some cases literally billions of data points are considered per experiment over a relatively short period of time. This would be impossible if all the observations had to be made by human observers, and computers are extremely important for data capturing, management and analysis in experiments of this type.

    A very good example of technology that requires computers for data capture, management and analysis is microarray technology. This technology enables the determination of miRNA expression levels for all genes in a sample at a given time point. It is utilised by com paring the gene expression levels between a test and a reference sample, and then identifying the genes that are up-regulated in terms of their expression as well as those that are down-regulated. These genes are very interesting to examine, since (usually in combination) they determine how the phenotype of a test sample would differ from the reference sample.

  • Keynote Essay 4: Microbes, Molecules, Maladies and Man

  • from SECTION 2 - MOLECULAR PATHOLOGY
    • By Adriano G Duse, MB BCh (University of the Witwatersrand), DTMH, MMed (Microbiology), FCPathSA (Microbiology), is currently Professor and Head of the Division of Clinical Microbiology and Infectious Diseases of the School of Pathology, National Health Laboratory Service and the University of the Witwatersrand, Johannesburg.
  • Edited by Barry Mendelow, University of the Witwatersrand, Johannesburg, Michèle Ramsay, University of the Witwatersrand, Johannesburg, Nanthakumarn Chetty, University of the Witwatersrand, Johannesburg, Wendy Stevens, University of the Witwatersrand, Johannesburg
  • Book:
    Molecular Medicine for Clinicians
    Published by:
    Wits University Press
    Published online:
    04 June 2019
    Print publication:
    01 October 2008, pp 277-283

  • Summary

    INTRODUCTION

    The planet Earth was formed, in a molten state, some 4.5 billion years ago. It cooled off sufficiently 4 billion years ago to allow the formation of the oceans. Cyanobacteria, found in rock fossil records that are approximately 3.6 billion years old, provide the earliest evidence of life in the form of complex unicellular organisms. Molecular phylogeny is the tool that enables us to understand life in all its complexity and recognise relations hips between organisms. In essence, using molecular techniques we are able to deter mine the evolutionary relationships of living creatures. By comparing the difference in sequences of homologous genes encoding ribosomal RNA (16S rRNA genes from prokaryotic cells and 18S rRNA from eukaryotic cells) we can measure the evolutionary distance between species of organisms. Computer analysis of rRNA gene sequences suggests that cellular life has evolved along three major lineages. Two of these, Bacteria and Archaea, are exclusively microbial and consist of prokaryotic cells. The third lineage, Eukarya, not only contains unicellular organisms but also myriads of multicellular organisms. Two important points have emerged from the study of molecular phylogeny: 1) unicellular organisms are the major and most diverse form of life, and 2) eukaryotes are not of recent origin, as previously thought, but as ancient as the Bacteria and Archaea lineages, all of which have emerged from a universal ancestor. Although the human race may live in harmony, and is subject to colonisation with many different prokaryotic (e.g. bacteria) and eukaryotic (e.g. fungi and parasites) organisms, this harmony is shattered from time to time when a relatively restricted number of microbial species enter our body and cause pathology – infection.

    Antimicrobials, developed on a mass scale from the 1940s onwards, brought renewed hope that, to quote the UN Surgeon General in his address to Congress in 1969, ‘We can close the book on infectious diseases’. Unfortunately, nothing could have been further from the truth. With the continuous emergence of microbes that display a vast array of antimicrobial resistance mechanisms, the ‘golden era’ of antimicrobials is under serious threat.

  • Chapter 40 - Approaches to Research in Molecular Medicine

  • from SECTION 4 - RESEARCH AND THE CONTINUING EVOLUTION OF MOLECULAR MEDICINE
    • By Michèle Ramsay, PhD (Human Genetics), is currently Professor and Head of the Molecular Genetics Laboratory, Division of Human Genetics, National Health Laboratory Service and University of the Witwatersrand.
  • Edited by Barry Mendelow, University of the Witwatersrand, Johannesburg, Michèle Ramsay, University of the Witwatersrand, Johannesburg, Nanthakumarn Chetty, University of the Witwatersrand, Johannesburg, Wendy Stevens, University of the Witwatersrand, Johannesburg
  • Book:
    Molecular Medicine for Clinicians
    Published by:
    Wits University Press
    Published online:
    04 June 2019
    Print publication:
    01 October 2008, pp 451-455

  • Summary

    The knowledge presented in this book is the result of meticulous, extensive, well thought out and often very costly research. Much of this research is based on the seminal works of early pioneers in the fields of biochemistry, genetics and statistics. The modern era of molecular medicine perhaps began with the deciphering of the code of life, the structure and function of the DNA molecule, and an understanding of how it codes for the proteins that make up cells and ultimately living organisms. What were considered beautifully simple mechanisms are now, however, being understood to be increasingly more complex. Biological systems are by nature extremely intricate and subject to fluctuating information inputs and functional outputs. Consider, for example, the expression of a specific gene. This gene may be switched on only during a specific developmental stage, and depending on the position of the cell in the developing organism and its exposure to a concentration gradient of a critical factor, its expression will be attenuated to ensure appropriate synthesis in that position in the body. To understand the detailed workings of living cells requires research.

    Research is a process aimed at systematically gathering information that can be interpreted to gain knowledge related to a specific question or to support or refute a hypo thesis. A stepwise process, following ethical rules and regulations, has to be followed to obtain valid results and their interpretation has to be subjected to peer scrutiny (Table 1). There are variations on the theme depending on the nature of the research, which may range from basic research to clinically orientated research. The latter particularly needs to consider the rights and protection of the subjects involved with the research.

    THE PROCESS OF RESEARCH

    All research, irrespective of the size or complexity of the research project, needs to be preceded by an extensive literature review and a thorough understanding of the subject matter. It is not possible to formulate a relevant research question without in-depth know ledge of what is already known on the topic and an understanding of where key information is still lacking on a particular aspect of the molecular basis of disease.

Molecular Medicine for Clinicians
  • Edited by Barry Mendelow, Michèle Ramsay, Nanthakumarn Chetty, Wendy Stevens
  • Published by:
    Wits University Press
    Published online:
    04 June 2019
    Print publication:
    01 October 2008
  • The insights following the wake of the Human Genome project are radically influencing our understanding of the molecular basis of life, health and disease. The improved accuracy and precision of clinical diagnostics is also beginning to have an impact on therapeutics in a fundamental way. This book is suitable for undergraduate medical students, as part of their basic sciences training, but is also relevant to interested under and postgraduate science and engineering students. It serves as an introductory text for medical registrars in virtually all specialties, and is also of value to the General Practitioner wishing to keep up to date, especially in view of the growing, internet assisted public knowledge of the field. There is a special focus on the application of molecular medicine in Africa and in developing countries elsewhere.

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