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Culture Collections

D. Smith, in Encyclopedia of Food Microbiology (Second Edition), 2014

Networking Collections: Improving Access to Strains and Addressing Common Challenges

Bioscience industry and academia require improved access to high-quality, value-added products and services from culture collections. BRCs are being enhanced to meet these needs. A requirement for quality, avoidance of duplication, research, training, and networking is part of their main recommendations for development. The ultimate goal is a distributed network of collections concentrating in the areas of their expertise and operating to universal high standards. Several national, regional, and global networks (Table 1) support and promulgate the activities of culture collections. The World Federation for Culture Collections has been fighting the cause for over four decades, supported in Europe by the European Culture Collection's Organization (ECCO). However, a lot of work needs to be done both by collections and governments if they indeed wish to harness the power of microbial diversity. There are 17 national collection organizations listed in Table 2, all of which can help researchers access the products and services of their member collections.

Table 1. Contacts for some regional and global culture collection organizations

AcronymNetworkLinkABRCNAsian Biological Resource Centers Networkhttp://www.abrcn.net/FELACCFederación Latinoamericana de Colecciones de Cultivosmir@qb.fcen.uba.ar, gdavel@anlis.gov.arECCOEuropean Culture Collection's Organizationhttp://www.eccosite.orgGBRCNGlobal Biological Resource Center Networkhttp://www.gbrcn.orgWFCCWorld Federation for Culture Collectionshttp://www.wfcc.info

Table 2. Some national culture collection organizations

AcronymNetworkLinkAMRINAustralian Microbial Resources Information Networkhttp://www.amrin.orgBCCM™Belgium Co-ordinated Collections of Microorganismshttp://bccm.belspo.beSBMCCBrazil – Sociedade Brasileira de Microbiologia Coleções de Culturascolecao@sbmicrobiologia.org.brCCCCMChina Committee for Culture Collections of Microorganismshttp://micronet.im.ac.cnFCCMFederation of Czechoslovak Collections of Microorganismshttp://www.natur.cuni.cz/fccm/CCRBFrench Comité Consultatif des Ressources Biologiqueshttp://www.crbfrance.frSCCCMOMBCuban Culture Collection and other Biological Materials Section;elsie@finlay.edu.cu (President);KFCCKorean Federation of Culture CollectionsShinchondong Sodaemunku, Seoul 120-749, KoreaHPACCUK Health Protection Agency Culture Collectionshttp://www.hpa.org.uk/business/collections.htmFORKOMIKROIndonesia – Communication Forum for Indonesian Culture Collection Curatorshttp://www.mabs.jp/kunibetsu/indonesia/indonesia_04.htmlJSCCJapan Society for Culture Collectionshttp://www.nbrc.nite.go.jp/jscc/aboutjsccc.htmlMICCOFinnish Microbial Resource Center OrganizationErna.Storgards@vtt.fiPNCCPhilippines National Culture CollectionsRosario G. Monsalud, rosegm@laguna.netRFCCThe Microbial (Non-Medical) Culture Collections of the Russian Federationhttp://www.vkm.ru/TNCCThailand Network on Culture Collectionhttp://www.biotec.or.th/tncc/UKNCCUK National Culture Collection – UK affiliation of national collectionshttp://www.ukncc.co.ukUSFCCUS Federation for Culture Collectionshttp://www.usfcc.us/

It is now recognized that research infrastructures provide the new dimension in life science research. To this end, BRCs are being networked through the GBRCN. The GBRCN Demonstration Project emanates from an OECD Working Party on Biotechnology initiative (1999–2007). Presently, the German Ministry of Science and Technology provides a small, central Secretariat to coordinate activities to deliver improved support to the life sciences. No one single entity can provide the necessary coverage of organisms and data; therefore, the enormous task of maintaining biodiversity must be shared. There are vast numbers of novel microbial species still to be discovered (the majority of which are not yet grown in culture), and large groups of specialized organisms are not readily available for study. The GBRCN will help to provide legitimate access to high-quality materials and information facilitating innovation in the life sciences.

In Europe, the European Strategy Forum for Research Infrastructures (ESFRI) was established in 2002 to support a coherent and strategy-led approach to policy-making on research infrastructures in Europe, and to facilitate multilateral initiatives leading to the better use and development of research infrastructures at the EU and international level. ESFRI are establishing pan-European structures to drive innovation to provide the resources, technologies, and services as the basic tools necessary to underpin research. The ESFRI strategy aims at overcoming the limits due to fragmentation of individual policies and provides Europe with the most up-to-date research infrastructures (RI), responding to the rapidly evolving science frontiers and also advancing the knowledge-based technologies and their extended use. The European microbiology collection community led by the GBRCN Secretariat, EMbaRC consortium and ECCO, has succeeded in placing the Microbial Resources Research Infrastructure (MIRRI) on the ESFRI roadmap. The resultant high-quality global platform will be designed to accommodate the future needs of biotechnology and biomedicine. MIRRI will provide coherence in the application of quality standards, homogeneity in data storage and management, and workload sharing to help release the hidden potential of microorganisms.

MIRRI brings together European microbial resource collections with stakeholders (their users, policy makers, potential funders, and the plethora of microbial research efforts) aiming at improving access to enhanced quality microbial resources in an appropriate legal framework, thus underpinning and driving life sciences research. Similar initiatives worldwide will establish the microorganism platform within the future GBRCN. A global network of BRCs will be able to enhance the efficiency in collections of laboratory held, living biological material by harmonization of procedures. Implementation of adequate collection management of well-preserved and authenticated organisms is essential to guarantee quality and safety in the various areas of application, to allow controlled access to potentially hazardous organisms, and to ease and improve the advantageous utilization of the materials for food, health, and environment. Creating a critical mass of high-quality data will allow its combination with data from other fields to produce information landscapes, and through modern, interactive tools, allow new interpretations and innovation. It will enable economies of scale, the efficiency of sharing skills and technologies, and the capacity to bridge gaps and focus activities without duplication of effort. User needs can be addressed more efficiently, and as a result scientific endeavor is more likely to deliver the desired outcome.

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Volume 3

G. Dorado, ... P. Hernández, in Encyclopedia of Biomedical Engineering, 2019

Pacific Biosciences Single-Molecule Real-Time Sequencing

The Pacific Biosciences Single-Molecule Real-Time (SMRT) sequencing uses special loop adapters to generate ssDNA from dsDNA fragments by Strand Displacement Amplification (SDA) or Multiple Displacement Amplification (MDA), which is based on the Rolling Circle Amplification (RCA) (see PCR chapter) (Eid et al., 2009). Then dNTP with fluorescent phosphate groups (instead of fluorescent nitrogenous bases) are added by the DNA polymerase, with cleavage of the phosphate chain and light emission, effectively removing the fluorescent dye from the growing nucleic acid chain. The single-molecule real-time sequencing reactions are carried out in parallel on thousands of nanophotonic visualization chambers, generating the sequencing reads. Bioinformatics tools are then used to assemble them to generate the contigs, chromosomes and eventually the genome sequence (Figure 8).



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Figure 8. Pacific Biosciences SMRT sequencing. The fragments of dsDNA are made circular using loop adapters, being subsequently amplified as ssDNA by strand-displacement. Special dNTP with fluorescent phosphate groups are incorporated by the DNA polymerase on nanophotonic chambers. The readings are finally assembled with bioinformatics tools.

As described above, the Pacific Biosciences SMRT approach is capable of sequencing single molecules (thus being classified as a third-generation sequencing technology), albeit previously amplified by strand-displacement as long ssDNA molecules. In such respect, it differentiates from Helicos BioSciences tSMS.

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Case Studies—Green Chemistry in Practice

Paul T. Anastas, David G. Hammond, in Inherent Safety At Chemical Sites, 2016

4.15.1.1.1 Novel Pest Control Agent Acts by Fortifying Plants' Own Defense Mechanisms

EDEN Bioscience Corporation has developed a new class of nontoxic, naturally occurring, biodegradable proteins as an alternative to pesticides. The newly discovered proteins, called harpins, function by activating a plant's existing defense and growth mechanisms without altering the plant's DNA, thereby increasing crop yield and quality, and minimizing crop losses. When applied to crops, harpins increase plant biomass, photosynthesis, nutrient uptake, and root development.

Sold under the name Messenger®, the harpin-containing product is commercially available and is manufactured using a water-based fermentation system that uses no harsh solvents or reagents, requires only modest energy inputs, and generates no hazardous chemical wastes. Fermentation byproducts are fully biodegradable and safely disposable, and 70% of the dried finished product consists of an innocuous food grade substance that is used as a carrier for the harpin protein.

The Food and Agriculture Organization of the United Nations estimates that annual losses to growers from pests reach $300 billion worldwide. Growers in modern agricultural systems have relied heavily on either chemical pesticides or crops that are genetically engineered for pest resistance as ways to limit their economic losses and increase yields. Each of these approaches has come under criticism from environmental groups, government regulators, consumers, and labor advocacy groups due to lasting impacts on the environment.

Messenger® has been demonstrated on more than 40 crops to effectively stimulate plants to defend themselves against a broad spectrum of viral, fungal, and bacterial diseases, including some for which there currently is no effective treatment. In addition, it has been shown through a safety evaluation to have virtually no adverse effect on any of the non-target organisms tested, including mammals, birds, honey bees, plants, fish, aquatic invertebrates, and algae. Only 0.004–0.14 pounds of harpin protein per acre per season is reportedly necessary to protect crops and enhance yields. As with most proteins, harpin is a fragile molecule that is degraded rapidly by UV and natural microorganisms, and has no potential to bioaccumulate or contaminate surface or groundwater resources.

Deployment of harpin technology conserves resources and protects the environment by partially replacing many higher-risk products and enhancing the plant's own defense mechanisms, rather than introducing toxic biocides to the agricultural ecosystem. Decreasing the need to manufacture large volumes of pesticides also decreases the opportunity for terrorists to cause harm and panic by targeting pesticide production facilities.

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Three-dimensional culture systems in central nervous system research

Itse Onuwaje, James B. Phillips, in Handbook of Innovations in Central Nervous System Regenerative Medicine, 2020

16.4.1.1.2 Matrigel

Matrigel (BD Bioscience) constitutes a mixture of naturally derived ECM proteins such as laminin, type IV collagen, and entactin, in combination with a cocktail of growth factors and proteoglycans [85]. The gel complex is isolated from Engelbreth-Horn-Swarm mouse sarcoma, and has notably positive effects on cell behaviors due to the host of natural biomolecules and signals present that encourage CNS growth and development. Matrigel is able to support cell interactions through receptors that bind to peptide sequences and mediate cellular processes of adhesion, growth, and differentiation [85]. It follows that it is widely used as a scaffold in 3D CNS culture for a variety of modeling purposes; for example, Ishihara et al. used Matrigel-based systems to create 3D in vitro models of CNS injury for evaluating nerve regenerative potential, while Cullen et al. employed Matrigel scaffolds in a 3D in vitro model of CNS cell response to mechanical loading, which is relevant for studies of neural trauma [86,87].

While Matrigel is commonly used as a cell culture substrate, its use in the construction of CNS models is associated with some major limitations. The undefined and heterogeneous nature of its composition can compromise the level of uniformity and reproducibility required in experimental procedures, which is particularly concerning if Matrigel-containing models are to be applied in the context of routine drug predictive screens. In addition to this, its tumorigenic origin may render Matrigel incapable of providing a microenvironment truly reflective of the healthy CNS. The presence of bioactive levels of growth factors in such matrices have been shown to alter cell behavior, confounding experiments where the concentration of growth factors could influence results [88].

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Volume 1

Ponnambalam Ravi Selvaganapathy, in Comprehensive Microsystems, 2008

1.04.3.5 Polyimide

Polyimide has also been used as a structural material for the construction of microfluidic devices (Goll et al. 1996, Metz et al. 2001). Commercially available polyimide resin has aromatic heterocyclic chains similar to the structure shown in Figure 17. They consist of alternating carbonyl (C=O) groups that act as electron acceptors and nitrogen (N) groups that act as electron donors. This charge transfer complex stabilizes the chain and is responsible for its chemical inertness. This kind of stabilization also happens between the chains and causes structural rigidity and high strength. Polyimide synthesis is a two-step process (Figure 17) involving a reaction between a dianhydride and a diamine under ambient conditions in a dipolar aprotic solvent such as N,N-dimethylacetamide (DMAc) or N-methylpyrrolidione (NMP) to yield the corresponding polyamic acid. The acid undergoes cyclization to form the final polyimide.



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Figure 17. Chemical structure of polyimide.

Photosensitivity can be introduced into the synthesis in two ways, with both depending on prevention of cyclization and hence formation of the polyimide backbone. The first method is to attach a photosensitive group to the carboxylic acid groups and prevent cyclization. The photosensitive group detaches from the polyamic acid upon light excitation. The other method is to use an acid–ion linkage between a photosensitive group and the polyamic acid, which can be broken using light (Hiramoto 1990).

1.04.3.5.1 Microfabrication

For applications in biosciences, polyimides offer advantages over other polymers due to their excellent chemical and thermal stability, low water uptake, and good biocompatibility (Richardson et al. 1993). In microfluidics, the initial application of polyimide is as membrane materials for microvalves (Goll et al. 1996) and pumps (Goll et al. 1997). These studies used commercially available thin polyimide membranes to separate the actuation chamber from the working chamber. Later, photosensitive polyimide (PI-2723, a negative tone organic polymer) was used as a structural material for microchannel construction (Glasgow et al. 1999). A thin polyimide layer is spun, prebaked, and patterned on a substrate using optical lithography with the desired geometry and vent channels, but not cured. Next, a thin layer of solvent with dissolved precursor is used to coat a soft-baked layer polyimide on a second substrate. The two halves are placed in contact and cured. Channels with a width of 50–1000 μm and a depth of 3–30 μm have been fabricated for chemical analysis and heat transfer devices (Glasgow et al. 1999). Significant stress develops in the structure due to solvent evaporation during the final curing.

An adapted lamination technique is used to produce microchannels with embedded electrodes without the problem of solvent evaporation (Metz et al. 2001). The process uses a photosensitive polyimide PI-2732, which is microstructured using optical lithography, and a nonphotosensitive polyimide PI-2611, which is microstructured using dry etching with oxygen plasma with silicon dioxide mask. The process flow begins with the spinning of a 5- to 20-μm layer of polyimide and its curing at 350 °C for 1 h. This layer forms the base of the microchannel. A layer of Ti/Pt (50/200 nm) is sputtered and patterned using a positive photoresist. This forms the electrodes inside the microchannels. A second layer of polyimide (5–20 μm), which forms the sidewalls, is spun and partially cured at 100–150 °C for 1 h. This layer not only insulates the electrodes but also provides the structure for microchannels. Lamination is done with a nonphotosensitive polyimide layer whose surface is treated with n-methyl-2-pyrrolidone (NMP) (swelling agent). The swelling agent causes the partially cured second layer to swell, enabling higher interdiffusion with the lamination layer. A thin Mylar foil (polyimide) is spin-coated with photosensitive polyimide, partially cured, flipped over, and bonded to the substrate by lamination. This layer forms the top of the microchannel. The Mylar layer is peeled off and then the microstructure is laminated again (Metz et al. 2001). No interface was observed between the open channel prestructures and the laminated top layer, which indicates good channel sealing as shown in Figure 18. The imidization (curing) results in the shrinkage of the polyimide (30–40%), which decreases the height of the film and degrades the sharpness of the sidewalls. The channels thus fabricated withstand pressures as high as 19 bar (Metz et al. 2001).



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Figure 18. SEM image of microchannels constructed of polyimide. Reproduced with permission from Metz S, Holzer R, Renaud P 2001 Polyimide-based microfluidic devices. Lab Chip 1, 29–34, © 2001 Royal Society of Chemistry.

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Sensor Materials, Technologies and Applications

M. Aliofkhazraei, N. Ali, in Comprehensive Materials Processing, 2014

13.10.7.16 Application of Nanosensors in Biosciences

Its applications in bioscience studies, specifically at the cellular level, have led particular stimulation roles of nanotechnology in medical areas, including surgery, treatment, detection, imaging, implant technology, bioscience processes, liver active surfaces, tissue engineering, textiles, stimulators, and delivery systems. It is predicted that the new nanomaterials have significant effects on each of these fields. Carbon nanotubes and inorganic nanowires have extraordinary mechanical, electrical, thermal, and optic properties. Due to their low prices and simple synthesis process, quantum dots (QDs) were introduced to medical imaging. Complicated spherical dendrimer molecules have modified physical, chemical, and biological properties compared to the conventional polymers.

Some of their unique properties relate to their spherical shape. The presence of inner hollows has enabled them to serve as medical nanocarriers. Essentially, increase of surface area and roughness properties led to some changes in their absorption and catalyzer properties. Control of surface properties in nanoscale leads to increase of biological compatibility in these materials. In the near future, application of nanomaterials and nanotechnology-assisted structures will play a key role in medical technology. So far, surgical assistances have been largely benefited from nanomaterials, e.g., surgical blades coated with diamond with nanothickness and nanoroughness as well as suturing needles that are bonded with stainless steel nanoparticles. The other accomplishments of nanotechnology might assist nanosurgery to gradually dominate traditional surgery. This is based on nanoprobes and laser technologies, including optic tweezers and nanoscissors. Nanotechnological revolutions in biomedicine have enabled humans to deal with many diseases. On the potential grounds for these revolutions is that the molecules related to illnesses such as cancer and diabetes can appropriately detect (degenerative disorder of the central nervous system) Parkinson's diseases and viruses with infections induced by pathogen bacteria, fungi, and HIV viruses.

Large scale systems made of nanoscale high sensitive components such as micro (nano)-cantilevers, nanotubes, and nanowires can detect biomolecular signals in first stages of the illness. Since getting different outcomes from molecular deliveries of the live tissue requires application of sensors, which can be implanted in an in vivo manner, long-term stability of the sensors is interrupted due to creation of sediment in the blood. Through nanotechnology, it is possible to obtain some nanostructural surfaces which can prevent the absorption of these unusual proteins. Molecular imaging allows the study of diseases in animal models and application of these techniques in clinical investigation as noninvasive tools to monitor disease process and response to the illness. Furthermore, illness diagnosis in the earliest stage makes it easier to be treated. Accurate targeting using specific antibodies and high capabilities of the nanoparticles imaging is the key to enhancing capability techniques such as magnetic resonance, optic imaging, core, and ultrasonic imaging. One of the main goals predicted for this technology is its ability to detect cancer tumors in their initial stage, where they are not detectable in such an early phase. These techniques are expected to have promising applications, particularly in cancer treatment.

Novel nanoparticles, through their appropriate treatment method, respond to external physical stimulators. For instance, magnetic ferrite oxide particles, gold-coated silicon nanolayers, and carbon nanotubes can convert electromagnetic energy to thermal energy, where this produces a fatal heat for cancer cells. By rise of magnetic field or radiation by an external laser source through close infrared light, these nanoparticles become limited to the engines or their insides. In addition, this is also possible through chemotherapy and sensitizing the tumors by light. Drug delivery is another main application of nanotechnology. Indirect delivery of nanoparticles from blood to the brain does not provide an effective treatment for either brain tumors or other central neural systems associated with illnesses such as Alzheimer's or Parkinson's disease. The other applications are delivery of nonviral genes for gene therapy, nanoprobes for cellular surgery and delivery of molecules to cells' nucleus, sliver crystalline nanoparticles with antimicrobial properties or blood stanching in wound care products, drug delivery systems based on microchips and their programmed release, and porous nanodrugs.

Stent deposition is among the examples of nanotechnology materials and devices applied in drug delivery. Another area for nanotechnology applications is using biomaterials in orthopedic applications, tooth implants, or as a substrate for tissue engineering. If, for example, a hip joint is implanted at the nanolevels, this implant is likely to be compatible with mechanical features of the bone. Furthermore, modification of biomaterials surface at nanolevels or their deposition enhances their compatibility when reacting with live cells.

It is a rather difficult task for a nanomaterial to remain as separate particles. One reason for this is their tendency to stick together, since their agglomeration reduces their large surface, which is an unfavorable issue in energy aspects. Application of bottom-up approaches and their application in surface engineering assists the particles in overcoming this cohesion. Nanotechnology has developed in various aspects; for instance, bionic devices such as an artificial retina organ. Will this organ be rejected or accepted? Are these drugs of any help in this process? Will the live organ be restored? These are some questions that can be answered by transcending to the nanoscale. Dealing with materials involving human biology and physiology is among new exciting boundaries for applications of nanotechnology in medicine. The concerning medical fields are surgery, treatment, diagnosis, imaging, implant technology, bioactive surfaces, tissue engineering, textiles, stimulators, stimulators, materials, as well as gene and drug delivery systems.

Semiconductor SWCNTs are sensitive to the detection of chemical compounds in the atmosphere at room temperature. Chemical gas sensors designed based on carbon nanotubes are capable of being applied in a wide range from medicine, environmental observations, and agricultural applications to chemical industries and further. Also, a sensor has been devised for capnography. A biosensor is defined as a measuring system that includes a probe with a sensitive biological detecting material or a biological receptor, a physics-chemistry detector element, and a transducer. A nanobiosensor or nanosensor is a biosensor in nanoscale dimensions. Nanosensors can be suitable devices for the research and study of important biological processes on cellular level of the live organs. There are two types of nanosensors with medical applications: linear network sensors and nanotube/nanowire sensors (10,14,17–20,41,42,55,58,59,95,107,109,110,116,129,141,145,166,203–211).

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Understanding the Diversity of Penicillium Using Next-Generation Sequencing

Monika Asthana, Avnish Kumar, in New and Future Developments in Microbial Biotechnology and Bioengineering, 2018

2.4.3.3.7 Pacific Biosciences SMRT Sequencing DNA Sequencer

Launched in 2010 by Pacific Biosciences, the SMRT Sequencing DNA sequencer is a single-molecule real-time sequencing platform. It is scalable and has high-throughput, delivering unprecedented sequencing results through long reads, uniform coverage, and high consensus accuracy. The SMRT sequencer is built on two key innovations: zero-mode waveguides (ZMWs) and phospholinked nucleotides. ZMWs allow light to illuminate only the bottom of a well in which a DNA polymerase/template complex is immobilized. Phospho-linked nucleotides allow observation of the immobilized complex as the DNA polymerase produces a completely natural DNA strand. Each incorporated nucleotide is marked with a fluorescent dye read by a detector. The SMRT sequencer has been used mainly in genome sequencing, resequencing, and methylation. A rare Penicillium species—Penicillium capsulatum strain ATCC 48735—has been sequenced and reported as a human-invasive opportunist. Previously it was used in paper industries (Yang et al., 2015). Genome sequence of Penicillium solitum RS1, which causes postharvest apple decay, was reported for the first time by Yu et al. (2016). The SMRT sequencer provides novel strategies to prevent and reduce economic losses during storage of the fruit.

The Roche/454 FLX, the Illumina/Solexa Genome Analyzer, and the Applied Biosystems (ABI) SOLiD Analyzer are currently the most widely used technologies. Other recently developed methods of NGS technologies include: the Helicos sequencer released in 2009, Life Technologies Ion Torrent sequencer released in 2011, and Oxford Technologies Nanopore single molecule-sequencer with ultralong single-molecule reads that became available in 2012–13. Although the Polonator G 007 and the Helicos HeliScope have recently been introduced, they have not yet become popular within the research community (Zhang et al., 2011).

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Computational Biology Approach in Management of Big Data of Healthcare Sector

Satya Narayan Sahu, ... Subrat Kumar Pattanayak, in Big Data Analytics for Intelligent Healthcare Management, 2019

10.1 Introduction

Big data is very popular in bioscience and other fields and it plays an important role in data analysis technology. In recent times, the use of big data is growing rapidly in the healthcare sector [1]. The term "big data" is defined as the collection of huge amount of data. Most of the data is in a structured, semistructured, or unstructured format. Das and coworker [2] discussed big data, including structured or unstructured data, which demands higher storage infrastructure. There is need for the development of architecture that can accommodate the larger volume of data. The distribution of data also promotes parallel processing. One of the drawbacks of centralized storage is the slower speed as well increased cost when compared to distributed storage. The progress of cyber foraging and invention of cloudlets plays important role in providing high processing resources for users [2]. It involves adding structure to databases for domain-specific usages. It works in a circular pattern: from the web to genomic and proteomic data. In the healthcare sector, this is why the electronic health datasets are so large and complex. These large datasets are not only difficult to manage with traditional software and/or hardware; but also with conventional data management devices. Big data consists of excess datasets, which are analyzed by utilizing the computationally sources to detect the trends, different associations, and queries [3]. Pattnaik et al. [4] studied big data analytics, computing, and networking with its prospective performance in the multidisciplinary domain of engineering, which is based on wide range of theory and methodologies. Network intrusion detection systems are used to secure the overall network from different sources of attack, which help to create the straightforward way to identify the corrected field and make suitable decisions for identification from larger databases. Sahani et al. [5] discussed the details of classification of intrusion detection using data mining techniques. In the US healthcare system, biomedical data is expected to reach the zettabyte scale [1] from a variety of fields such as scientific instruments, electronic health records, and clinical decision support systems [6, 7]. Dey and coworker [8] discussed the advancements and innovations in the area of medical image and data processing that have led to creation of a secure mechanism to move images and signals over the internet. They also discussed image processing that used intelligent techniques for medical data security.

Besides other sources, there is currently an open source data processing platform called Hadoop. It is capable of processing a large amount of data, which allocates portions of the datasets to servers, each of which resolve the various parts of bigger problems [9]. It allows the users to exploit computation through mapreduce implementation. Depending on the progress of better performance, Hadoop breaks up a file into different blocks and keeps them in various nodes within a cluster. Reddy et al. [10] provided details regarding a data aware scheme for scheduling big data application with SAVANNA Hadoop. In addition, CouchDB and MongoDB are also used as data analytics platforms to aggregate data in unique ways [11]. Mapreduce is a minimization technique that generates file indexing with sorting and mapping [12]. To regulate and handle analysis of a large amount of data in a distributing computing manner, different data analysis tools exist, including the extract transform load (ETL) process, querying, data mining [13], and online analytical processing (OLAP). Mishra et al. [14] studied the foundation, applications, and challenges of cloud computing. It presents the up-to-date computing paradigms. It plays an important role in the area of virtualization, security, and allocation of resources to monitoring of complex optimization problems. Although data analysis has rapidly increased insight into many aspects, there are still some ambiguities present. Cloud computing is a computing system that is dynamically scalable, which depends on parallel computers. It is a new solution compared to the old version, as well as traditional data analysis problem. Sarkhel and coworker [15] proposed different task scheduling algorithms such as minimum-level priority queue (MLPQ), Min-Median, and Mean-MIN-MAX to reduce the makespan with maximum utilization of the cloud. Distributed data mining (DDM), based on typical software-as-a-service, also works for fulfillment of demanding data processing. It can scrutinize the excess data based on parallel computing and storage capacity. This DDM revamps the user's demand in the workflow process, which can be set aside as parallel task sequences in terms of cloud computing platforms [16]. Behera and coworker [17] discussed particle swarm optimization that is based on the metaheuristic evolutionary optimization technique. It is quite attractive in the swarm intelligence community because of its understandable algorithm structure.

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Scientific Fundamentals of Biotechnology

H. Perreault, E. Lattová, in Comprehensive Biotechnology (Second Edition), 2011

1.50.6 Concluding Remarks

This article on MS and its applications to biosciences did not attempt to cover all aspects of this extremely useful technique, as it touched mainly on methods involving electrospray and MALDI, and relevant sample preparation or separation techniques.

Although gas chromatography–mass spectrometry (GC/MS) has not been discussed here, it is a technique which deserves much attention, and which is still relied on regularly in the detection and identification of smaller volatile molecules. An extensive review of GC/MS recent instrumentation and applications has been published [59] and readers may find there the appropriate information pertaining to this technique.

It is the same case for inductively coupled plasma–mass spectrometry (ICP/MS) for the detection of metals in their ionic or elemental forms in proteins or other samples of biological origin. The description of ICP/MS and its applications could have occupied a whole chapter on their own and it is possible to read in detail about this tandem technique in specialized reviews [60].

Also, lab-on-a-chip technology has become an important branch of the bioanalytical sciences involving MS. Interesting applications have focused on miniature systems for chromatography and electrophoresis, with emphasis on affinity methods for particular analytes. Again because these on-chip techniques do tend to reproduce in smaller systems that exist on a larger scale, the reader is referred to a review [61] for more comprehensive details.

This article will serve as a guide to researchers and scientists working in biologically related areas and who have to weigh choices between different techniques of sample analysis by MS when comes the time to establish new methods in a laboratory or purchase new instrumentation. Readers will have noticed that no company names are given along with the mention of instrument types, but rather more fundamental articles were referred to as for describing the development of each technique. Readers will thus find more extensive commercial details when searching through the proposed bibliography.

Finally, there are, at the moment of typing these lines, many applications and methods being developed in several labs around the world. As MS and attached methodologies are in constant evolution, this article gives a transient view of biological MS as it exists in 2010.

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Organometallic Complexes for Biosensing

Toshihiro Ihara, in Advances in Bioorganometallic Chemistry, 2019

14.6 Cobalt

Several metallocenes other than Fc have been studied in the biosciences. Metzler-Nolte et al., synthesized a cobaltocenium-PNA conjugate. Ferrocene and cobaltocenium groups are almost isostructural but differ in charge as well as redox properties.115 They examined the electrochemical properties and thermal stabilities in interaction between the cobaltocenium-PNA and complementary DNA. The same research group reported a cobaltocenium-peptide conjugate that showed enhanced cellular uptake and directed nuclear delivery. The cobaltocenium group is exceedingly stable under physiological conditions. The cobaltocenium-NLS (nuclear localization signal) conjugate significantly accumulates in the nucleus of HepG2 cells.116 Interestingly, the organometallic moiety in the conjugate is essential for active endocytosis and release of the conjugate into the cytoplasm.

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