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New machines for the life sciences

Hardware and software applications have become an integral part of the everyday life of life sciences researchers, developers and service providers. It is impossible to imagine life science applications without effective hardware and software applications – from computer-assisted drug screening to the automatic production of biosensors for rapid, mobile, purse-size bacterial test devices. Trends such as automation and miniaturisation lead to ever smaller and more independent devices. Will machines soon replace humans?

These days, people often share their workplaces with huge, computer-controlled equipment. © GATC Biotech AG

Over the last few years, microsystems technology for example has been used for applications in the fields of biotechnology, pharmacy, medical technology and biosensor technology, i.e. fields in which small amounts of samples need to be handled. Microsystems technology is also used to produce hardware, ranging from microstructured reactors in the field of medical technology, to innovative biochips and specific measurement techniques for individual cells.

New biophotonics and optoelectronics devices and software are increasingly entering the field of life sciences. Novel two-photon microscopes enable researchers to look at processes in the brains of mice in order to investigate the causes of Alzheimer's. In 2009, the Berlin-based company LTB Lasertechnik developed a non-invasive method that enables the early optical identification of melanomas in which a skin scanner rapidly scans conspicuous pigment areas. This high-tech device was the first to measure the fluorescence of melanin and use these data diagnostically. It is the stated goal of the hardware and software industry to make processes and technologies quicker and more effective at the same time as contributing to a reduction in the costs of producing and selling the products. It therefore does not come as a surprise that there is a trend towards automation (e.g., in drug discovery involving high-throughput screening) and miniaturisation.

Innovative 3D technologies are emerging

In the software area, 3D technologies have become highly effective modelling tools, e.g., for modelling molecule structures, for use in medicine (medical technology) and for presenting the effects of drugs in the human body. Prevention is better than treatment. However, if a patient has been diagnosed with cancer, innovative 3D technologies can be used to improve the patient’s chances of recovery. Novel handheld laser scanners enable the production of made-to-measure prostheses in only 30 minutes, for example for melanoma patients who need parts of organs such as the nose removed. Without the use of prostheses, the tissue around the nose might loosen or permanently deform, thereby precluding plastic surgery. The increasing application of IT enables numerous biological datasets to be interpreted and complex issues to be analysed.

Effective algorithms to count colonies at the click of the mouse

Unthinkable many years ago, but now standard in many laboratories: highly modern hardware carries out biochemical analyses and resistance testing automatically. © Labor Dr. Brunner

Analyses that previously had to be done manually by biologists, physicians and microbiologists, are now done rapidly and effectively by sophisticated software. The company Kapelan Bio-Imaging launched an application in 2009 that analyses all kinds of colony plates within a few seconds by electronically counting colonies of bacteria or other microorganisms, as well as measuring the area, perimeter, diameter and circularity of the colonies. It only takes a few clicks of the mouse to extract the number of colonies or spot analyses from a digital image.

The Centre for Bioinformatics in Tübingen recently developed a piece of software (Biochemical Algorithms Library, BALL) for drug research that uses 3D modelling and simulation to select 50 substances that are highly likely to have the desired effect out of a possible 100,000. Another new direction in the use of intelligent software solutions in the life sciences is "computational epigenetics": scientists from the Max Planck Institute and geneticists from Saarland University developed the "EpiGRAPH" programme based on statistical and mathematical methods (data mining) in order to predict the distribution of methyl groups in the genome of healthy cells. The software compares the methylation pattern of cancerous and healthy cells in order to enable the search for more targeted epigenetic drugs with fewer side effects. The system scans large-scale datasets within a short period of time.

Robots: Replacing humans and reducing costs

Based on new software and hardware developments, the transfer of dangerous and monotonous work tasks to robots is becoming increasingly important. Two examples are the analysis and processing of medical samples in order to reduce diagnosis time, and the automated cultivation of cells for testing potential drug candidates. At the end of 2009, the University of Rostock presented the first fully automated cell culture system, i.e., a complete laboratory only three square metres in size, costing 500,000 euros. Experts believe that the development of new hardware for laboratory automation is the only way that the German biotechnology sector will be able to keep up with global competitors in the development of new drugs. Opinion leaders believe that the high demand for automated solutions is down to the demographic change that will lead to thousands of laboratory workplaces being unmanned in the years or decades to come.

Nevertheless, despite the progress made in the field of automatisation, human beings will remain indispensable. Dr. Oliver Nolte, head of molecular biology at the Konstanz-based “Labor Dr. Brunner”, a company that has recently installed a unique, fully automated sample processing device as part of its high-tech strategy, confirms: “Highly modern optical technologies are not sufficient when it comes to analysing samples that contain mixtures of different pathogens because the texture, the appearance under the microscope as well as the smell of the bacterial colonies all play a major role.”

Glossary

  • A base is a component of nucleic acids. There are four different bases: adenine, guanine (purines), cytosine and thymine or uracil (pyrimidines). In RNA, thymine is replaced by uracil.

Glossary

  • A base is a component of nucleic acids. There are four different bases: adenine, guanine (purines), cytosine and thymine or uracil (pyrimidines). In RNA, thymine is replaced by uracil.
  • A gene is a hereditary unit which has effects on the traits and thus on the phenotype of an organism. Part on the DNA which contains genetic information for the synthesis of a protein or functional RNA (e.g. tRNA).
  • Being lytic is the feature of a bacteriophage leading to the destruction (lysis) of the host cell upon infection.
  • There are two definitions for the term organism: a) Any biological unit which is capable of reproduction and which is autonomous, i.e. that is able to exist without foreign help (microorganisms, fungi, plants, animals including humans). b) Definition from the Gentechnikgesetz (German Genetic Engineering Law): “Any biological unit which is capable of reproducing or transferring genetic material.“ This definition also includes viruses and viroids. In consequence, any genetic engineering work involving these kinds of particles is regulated by the Genetic Engineering Law.
  • Pathogenity is the ability to cause a disease. One differentiates between human, animal, and plant pathogens which specifically cause a disease in either humans, animals or plants.
  • Screening is a systematic test procedure that is used to identify certain characteristics within an array of samples or persons. In molecular biology screening is used to filter a designated clone out of a gen bank, for example.
  • Bioinformatics is the science of managing and analyzing biological data using advanced computing techniques. Currently it is used mainly for the forecasting of the meaning of DNA sequences, the protein structure, the molecular working mechanism and the properties of active substances. (2. sentence: mwg-biotech)
  • Plasticity is the attribute of organisms to change their characteristic values under the influence of environmental factors. Therefore, neuroplasticity is the characteristic of neurons to change their response behaviour dependent from their activity. In most cases, the strength of the synaptic transmission is influenced (synaptic plasticity). The neuroplasticity or synaptic plasticity, respectively, is considered to be the basic mechanism in learning processes and in the formation of memories.
  • Alzheimer's disease (also called Morbus Alzheimer) is a slowly progressing dementia that manifests itself in an increasing reduction of brain functions. This disease mainly affects older people. It is primarily caused by intracellular deposits of a fragment of amyloid precursor protein (APP). This leads to a proceeding loss of neurons and therfore to a loss of brain mass. At the beginning of this disease, the concerned people only show a marginal obliviousness. In later stages, speech, the ability to reason and memory are mainly affected. In the end, the concerned people lose their entire sanity and personality.
  • Fluorescence is the spontanous emission of light in a certain wavelength after excitation of a molecule with light of another wavelength.
  • Methyl groups are groups of atoms composed of the chemical structure -CH3.
  • Methylation is the implementation of methyl groups in organic structures.
  • Biomolecules which can bind active agents are called targets. They can be receptors, enzymes or ion channels. If agent and target interact with each other the term agent-target-specific effect is used. The identification of targets is very important in biomedical and pharmaceutical research because a specific interaction can help to understand basic biomolecular processes. This is essential to identify new points of application.
  • Biophotonic describes all optical sciences and technologies dealing with the interaction of photons and organic material.
  • Optoelectronic describes all studies and applications which are related to electrical-to-optical or optical-to-electrical transducers.
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