bluuebunny/crossref_metadata_2025 huggingface dataset:
Plant Cuticle
Authors: Kerstiens Gerhard
Published: April 2010

Plant cuticles are protective lipophilic membranes that cover leaves and many stems and fruits. They consist of a polymer matrix that is covered with epicuticular waxes and incorporates intracuticular waxes. Together, these constituents provide a good but imperfect barrier against the loss of water and solutes and ingression by pests and pathogens. The thickness, structure and chemical composition of cuticular matrices and epicuticular and intracuticular waxes vary very widely, and the potential functional consequences of such differences are poorly understood. Transport across the cuticle can occur by random diffusion within the lipophilic network (relevant for lipophilic and moderately polar substances) or along clusters of water molecules that form a continuous hydrophilic phase reaching across the membrane (relevant for polar and ionic substances).

Key concepts:

All leaves and nonwoody stems are covered by a protective and resilient membrane called the cuticle.

Its permeability is low but it can accumulate lipophilic xenobiotics. Thicker or waxier cuticles are generally not less permeable than thinner or less wax‐rich ones.

The
trans
‐cuticular diffusion paths for ions and lipophilic compounds are different.
Centrosomes: Methods for Preparation
Authors: Habermann Karin , Lange Bodo MH
Published: April 2010

The centrosome of higher eukaryotic cells is the main microtubule‐organising centre. To understand the molecular mechanisms underlying this organelle's biogenesis and important functions in several cellular processes, such as microtubule nucleation, cell division and stress response, it was critical to develop methods for isolating biochemically meaningful quantities of centrosomes. Centrosomes have been isolated from a variety of organisms and based on these preparations, numerous aspects of this intriguing organelle's morphological, functional and biochemical properties have been uncovered. Better isolation procedures along with the development of new technologies, like RNAi (
ribonucleic acid
interference) and the increasing accuracy of mass spectrometry and electron microscopy techniques, have profoundly improved our knowledge of the centrosome, leading to a better understanding of its implications in various cellular processes and in diseases.

Key concepts

Cultured animal cells, animal tissue, Drosophila embryos, green algae, budding yeast, fungi and surf clams are suitable starting materials for centrosome isolation.

Centrosome isolation from animal cells requires cell lysis in low ionic strength buffers.

Enrichment of centrosomes is achieved by density centrifugation in sucrose step gradients.

Immunoaffinity purification has been employed to further enrich centrosomes from Drosophila embryos.

Isolated centrosomes are competent to nucleate microtubules.

The analysis of isolated centrosomes has provided a wealth of information on their biochemical composition and novel structural and functional features.

Many centrosome components have been identified by applying mass spectrometry and antibody approaches.

RNAi has been used to study centrosome functions in cellular signalling pathways and the cell cycle and to identify novel components.

Electron tomography will be an informative tool to study the supramolecular structures of isolated centrosomes.
Proline Residues in Proteins
Authors: Deber Charles M , Brodsky Barbara , Rath Arianna
Published: April 2010

As the only commonly occurring imino acid in proteins, proline has been found to play unique structural and dynamic roles in guiding protein folding, fibre formation and protein–protein interactions. The cyclic pyrrolidine side‐chain fixes the backbone dihedral ϕ angle and renders proline unable to act as a hydrogen bond donor. These properties are reflected in its preference for protein secondary structure elements such as turns and polyproline II helices, and its generally destabilizing effect on α helix and β‐strand conformation. The ability of proline to undergocis‐transisomerization is important in protein folding and forms the basis of molecular switches that help to control cellular growth and regulation. Proline and its posttranslationally modified analogue, hydroxyproline, are additionally the major components of collagens, proteins that are the major fibrous proteins in animals and account for approximately 30% of total human body protein.

Key Concepts:

The structural and dynamic properties imparted to proteins by the amino acid proline arise from the unique cyclic structure of its side‐chain.

Interconversion of proline fromcistotransconformation, which can be facilitated by peptidylprolyl isomerases, is a rate‐limiting step in protein folding and can act as a molecular switch in the regulation of cellular growth and signalling.

Proline residues facilitate the formation of protein secondary structure elements such as turns and the polyproline II helix, but typically disfavour α helix and β‐strand conformations.

Proline and its posttranslationally modified analogue hydroxyproline are key components of the structural protein collagen.

Regions of water‐soluble proteins rich in proline residues are often sites of protein–protein interaction.
Polymerase Chain Reaction (PCR): Specialised Reactions
Authors: Tsirka Stella E , Frohman Michael A
Published: April 2010

The polymerase chain reaction (PCR) is a technique that rapidly amplifies selected subsets of DNA (deoxyribonucleic acid) or complementary DNA (cDNA) from initially complex biological mixtures. The efficiency of amplification or sequence of the amplified material can then be examined for any of many purposes, including genotyping or the characterisation of new genes, gene expression patterns, mutations or polymorphisms. Quantitative‐PCR (QT‐PCR) has become practical and popular over the past decade with the generation of libraries of individual primer sets and arrayed sets of primers by commercial entities. QT‐PCR machines can assay up to 384 samples at once, permitting the complete analysis of expression of families of genes, such as signalling kinases or cytokines, in a single experiment. RACE (rapid amplification of cDNA ends)‐PCR has also become popular to identify microRNAs (ribonucleic acid). PCR is highly useful in structural biology to rapidly modify the boundaries of protein domains intended for crystallisation.

Key Concepts:

PCR can be conducted on vanishingly small amounts of material.

PCR can be used for rapid genotyping or sequencing.

PCR is useful for quantitative analysis of gene expression of entire gene families or signalling networks in arrayed assays.

PCR is frequently the method of choice for genetic engineering involving mutations, truncations or extensions of existing genes.
Physcomitrella patens
: A Model Bryophyte
Authors: Knight Celia D , Perroud Pierre‐François
Published: April 2010

Physcomitrella patens

is a species of moss that has been studied experimentally for over half a century. The techniques that have been developed for the study of this model organism allow us to answer biological questions relating to plant growth and development, adaptation to environments and plant evolution. The recent completion of the

P. patens

genome sequence as the first non‐angiosperm land plant allows comparative genomic analyses and identification of conserved genes as well as genes with novel functions.

P. patens

has a special feature among plants, that of an efficient gene‐targeting mechanism, enabling gene functions to be identified by targeted mutations. Such comparative and experimental approaches allowed the determination of similarities and differences between mosses and angiosperms in their response to light and hormones. Finally, we may be able to learn how plants deal with environmental stresses by studying these processes in

P. patens

.

Key concepts:

P. patens
is a model organism because it can be studied simply within a controlled environment to address biological questions.

P. patens
is easy to culture
in vitro
because the cells are totipotent.

P. patens
undergoes highly efficient gene targeting that allows
in vivo
analysis of a gene's function by mutating the endogenous gene after introduction of a cloned homologue.

It is easy to identify mutant phenotypes in
P. patens
because the gametophytic cells are haploid.

P. patens
is the first nonangiosperm land plant to have its genome sequence published.

Genomic comparisons and other studies suggest that there are many similarities in the ways in which mosses and angiosperms use environmental cues to develop, indicating conserved evolution; however, mosses also possess some unique sequences which might present novel gene functions.
Insurance and Genetic Information
Authors: Bombard Yvonne , Lemmens Trudo
Published: April 2010

With the accelerating pace of genetic technology comes increased opportunity for individuals to obtain additional risk estimates about their susceptibilities to disease. Insurers argue that they need to have access to any information that predicts disease risk because the amount that policyholders pay for insurance coverage is determined by assessing their level of risk. Without access to genetic information, insurers are concerned that individuals may purchase more insurance at unadjusted premiums, which may lead to the collapse of the market. However, people are reluctant to share genetic test results with insurers due to the potential risk of insurance discrimination. As genetic testing becomes more prevalent, there are concerns that sections of the population will be denied insurance because of their genetic profiles. The question of what governments should do about this is one that has been debated in many countries.

Key concept:

Despite the public's fear of insurance discrimination, insurers argue that genetic health information should be shared with them to enable underwriters to make an accurate assessment of the risk.
Glycosyltransferases of Small Molecules: Their Roles in Plant Biology
Authors: Bowles Dianna , Lim Eng‐Kiat
Published: April 2010

Glycosyltransferases
are enzymes that transfer sugars from nucleotide sugars to a wide range of small molecule acceptors, from hormones and secondary metabolites to biotic and abiotic chemicals. This alters the hydrophilicity of the acceptors, their stability and chemical properties, their subcellular localization and often their bioactivity.
Glycosyltransferases
form a large multigene family in the plant kingdom and can be identified by a signature motif in their primary sequence. Considerable progress has been made in understanding the biochemistry of
glycosyltransferases
and the role of these enzymes in the plant. This article outlines our current knowledge of these enzymes, drawing on information gained from recent

in vitro

and

in planta

studies.

Key concepts:

There is a class of glycosyltransferases (GTs) that transfers sugars to small molecule acceptors.

In plants, these acceptors can be natural products such as hormones and secondary metabolites, as well as nonnatural products, such as herbicides and pesticides.

Glycosylation changes the properties of the acceptors, increasing water solubility and leading to transport of glycosides from the cytosol.

Glycosylation can also affect activity of the acceptors, both in the plant, such as inactivation of hormones and in industrial applications, such as bioactivity and bioavailability.
Genome Analysis of the Platypus
Authors: Wong Emily SW , Lillie Mette , Belov Katherine
Published: April 2010

The sequencing of the platypus genome represents a significant milestone in the study of mammalian evolution. The platypus is an egg‐laying mammal, a member of the order Monotremata, the most divergent mammalian clade. It is the first monotreme to have its genome sequenced. Its unique evolutionary position, as an offshoot between the early divergence of birds and the later emergence of therian (eutherian and marsupials) mammals, provides an unrivalled opportunity to understand the evolution of all mammals. Much like the physical characteristics of the platypus, the platypus genome shows traces of an amalgamation of mammalian and reptilian traits. Key findings to emerge from the genome project include the complex evolution of mammalian sex chromosomes, the transition from egg‐laying to live birth in mammals, and the evolution of immune genes and venom molecules in this unique species.

Key concepts:

The platypus genome is the first monotreme genome to be sequenced. The platypus's unique evolutionary position, as an offshoot between the early divergence of birds and the later emergence of therian (eutherian and marsupials) mammals, provides an opportunity to increase our understanding of the evolution of all mammals.

The platypus genome shows features of mammalian and reptilian traits.

The platypus has 10 sex chromosomes, some of which have homology to chicken Z. The mechanism used by platypuses to determine sex is not known.

The density of interspersed repeat elements in the platypus genome is greater than that seen in any other vertebrate genome.

The platypus genome contains a high G+C content (45.4%).

The platypus possesses a unique class of over 40 000 noncoding RNA known as snoRTE.

The platypus contains the largest repertoire of V1R vomeronasal receptors seen in any vertebrate.

The platypus genome contains the major egg yolk protein, vitellogenin.

Key mammalian milk genes, caseins, are present in the platypus.

The platypus genome contains an expansion of antimicrobial peptide genes.

Platypus venom molecules evolved independently to snake venom molecules.
Aneurysms:
CNS
Authors: Rubin Mark N , Lanzino Giuseppe , Rabinstein Alejandro
Published: April 2010

Intracranial aneurysms are a source of clinical concern because their rupture can cause subarachnoid haemorrhage, which is associated with high risk of death and disability. The prevalence of intracranial aneurysms has been difficult to assess but is estimated to be roughly 2% of the general population in North America. The size of an intracranial aneurysm is the greatest predictor of rupture. Other predictors of rupture include a prior history of subarachnoid haemorrhage and the location of the aneurysm. The majority of intracranial aneurysms discovered incidentally in the general population are smaller than 10 mm in diameter and pose little risk of rupture. Aneurysms requiring treatment can be treated with surgical clipping or endovascular coil embolisation. A large randomised study has shown that the functional outcome at 1 year is better after endovascular coiling than with surgical clipping in patients suitable for either therapy.

Key concepts:

Intracranial aneurysms occur in an estimated 2% of the North American general population.

Rupture of an intracranial aneurysm leads to a devastating type of stroke called subarachnoid haemorrhage.

Size of an intracranial aneurysm is the greatest predictor of rupture.

More than 90% of unruptured aneurysms are less than 10 mm in diameter and have a low yearly risk of rupture.

Intracranial aneurysms at risk for rupture can be treated with surgical clipping or endovascular embolisation.

Ruptured aneurysms require prompt treatment to prevent a catastrophic recurrent haemorrhage.
Identifying Genes Underlying Human Inherited Disease
Authors: Stein Catherine M
Published: April 2010

The field of genetic epidemiology seeks to identify the genetic risk factors underlying human disease. First, one must assess whether the trait has an underlying genetic influence; this is done by estimating familial relative risk and conducting segregation analysis. In order to discover genes influencing human disease, both family‐ and population‐based studies are designed, and linkage and association methods are used to analyse the relationship between the trait(s) of interest and genetic markers. A variety of approaches to both linkage and association analysis exist, each having strengths and weaknesses for differing situations. In general, linkage analysis is more powerful for detecting rare genes, whereas association analysis is more powerful for detecting common allelic effects that might be weaker. In addition, when studying complex traits, other issues must be considered, including interactions with other genes and the environment, parent‐of‐origin effects, as well as the effect of structural variants.

Key Concepts:

Genetic epidemiologists design both family‐ and population‐based studies to find genes influencing disease risk.

Before conducting a gene mapping study, one must first ascertain whether the trait is influenced by genetic effects.

Linkage and association analysis are two complementary methods used to analyse the relationship between trait(s) and genetic markers.

The approach used (linkage versus association) depends on the study design, and these approaches depend on the genetic parameters (rare versus common, large versus small effects).

Other factors – gene–gene interaction, gene–environment interaction, existence of structural variants and parent‐of‐origin effects – further complicate the search for disease genes.
Studying Genomic Aberrations by Microarray Profiling
Authors: Walker Logan C , Waddell Nic
Published: April 2010

Inherited genetic variation between individuals is the main reason why we are different from one another. Genomic aberrations also play an important in the development of human diseases. An important tool for the study of these genetic changes is the microarray. Array technology has evolved over the years from traditional comparative genomic hybridization arrays to high‐resolution single nucleotide polymorphism (SNP) arrays, which can be used for SNP genotyping and the determination of copy number and loss of heterozygosity. These platforms will continue to play an important role in unravelling the complexity of diseases.

Key concepts:

Microarrays are a useful tool to assay changes in copy number, single nucleotide polymorphisms and loss of heterozygosity.

There is inherited genetic diversity between individuals.

Genomic aberrations play a key role in the development of many diseases.
Multiple Testing in Genetic Epidemiology
Authors: Han Buhm , Eskin Eleazar
Published: April 2010

If multiple statistical tests are performed simultaneously, we should take into account multiple testing to properly control the false positive rate. In association studies performing statistical tests for a large number of correlated markers, the traditional Sidák correction is overly conservative and the permutation test is inefficient. This article discusses recently proposed approaches for correcting for multiple testing in association studies. We first explain basic concepts of statistics such as thep‐value, false‐positive rate, correctedp‐value and family wise error rate. Then we discuss recently proposed methods in three categories: methods using multivariate normal distribution, methods calculating the effective number of tests and methods increasing the efficiency of permutation test. We compare the relative performance of these methods. Many of the methods are shown to be highly efficient and accurate compared to the traditional approaches and can readily be applied to the genome‐wide datasets.

Key Concepts:

In a statistical testing procedure performing multiple tests, multiple testing must be taken into account to properly control the false positive rate.

In association studies, the traditional Sidák correction is overly conservative and the permutation test is inefficient.

Recently proposed multiple testing correction methods are highly efficient and accurate and can be applied to the genome‐wide datasets.
Whole Genome Resequencing and 1000 Genomes Project
Authors: Chee‐Seng KU , En Yun Loy , Yudi Pawitan , Kee‐Seng Chia
Published: April 2010

The recent advances in sequencing technologies have enabled the whole human genome to be sequenced within weeks. To date, several human diploid genomes have been sequenced and the number of genomes being sequenced is expected to increase in the years to come. In fact, a 3‐year international collaborative project, the 1000 Genomes Project, was initiated in 2008 to sequence at least 1000 individual genomes from different populations around the world. The aim is to create the most detailed and comprehensive map of genetic variations in the human genome for future disease‐association studies and biomedical research. While waiting for this ambitious project to be completed, several whole genome sequencing studies have already provided some exciting results, where hundreds of thousands of new SNPs and short indels have been identified. In addition, these studies also address many important questions and issues in the experimental design and data analysis of whole genome sequencing.

Key concepts:

The arrival of next generation sequencing (NGS) and third generation sequencing technologies has empowered the sequencing of the whole human genome to be completed within weeks.

The first human whole genome sequencing (WGS) study using a next generation sequencer was completed in 2008, which marked the beginning of a new era in personalized genome sequencing.

To date, several WGS studies have been done using NGS technologies.

The NGS technologies are Roche
®
454 Life Science Genome Sequencer FLX (GS FLX), Illumina
®
Genome Analyzer (GA) and Applied Biosystems
®
(ABI) Supported Oligonucleotide Ligation Detection System (SOLiD).

The WGS studies have clearly demonstrated the feasibility of using all the NGS and third generation sequencing technologies to decode the DNA sequence of human genome efficiently and at an affordable price per genome.

In addition, these studies have also addressed many important questions and issues surrounding the experimental design and data analysis in whole genome sequencing.

The more significant finding from the WGS studies is that they have conclusively revealed the richness of genetic variations in the human genome. The genetic variations in the human genome are more abundant than previously expected.

Several thousands of structural variations are found in all the WGS studies, and the studies also identified hundreds of thousands of indels.

Personalized genome sequencing is able to provide full DNA sequences and identify the enormous number of genetic variations in the genome. However, personalized medicine aims to predict individual susceptibility risks to various diseases and responses to drug therapies using the genetic variation information.

To achieve personalized medicine, the first steps are to detect and validate all the genetic variations in the human genome in population‐based studies, and catalogue them properly in databases, so they can be used as the genetic markers for future disease association studies.
Acrylamide, Microbial Production by Nitrile Hydratase
Authors: Zheng Ren‐Chao , Zheng Yu‐Guo , Shen Yin‐Chu
Published: April 2010

Acrylamide is one of the most important commodity chemicals widely used in coagulators, soil conditioners, adhensives, paints and petroleum recovering agents. The demand for acrylamide is readily growing yearly. Acrylamide is traditionally produced by chemical hydration of acrylonitrile employing sulfuric acid or copper salt as catalyst. Both of the processes were complicated and caused severe environmental pollution. The search for simpler and greener manufacture methods of acrylamide has never ceased. Discovery of nitrile hydratase and its application in nitrile hydration offers a novel method for the production of acrylamide. The worldwide development of biocatalytic acrylamide technology including the improvement of three generations of industrial strains as well as its current status is described. Microbial production of acrylamide affords both economic and technical advantages over the traditional chemical synthesis including high energy efficiency, high selectivity and purity. This is the first example of the introduction of an industrial bioconversion process for the manufacture of a commodity chemical and has been widely regarded as a milestone in the development history of industrial biotechnology.
Bacillus Megateriumand Other Bacilli: Industrial Applications
Authors: Bunk Boyke , Biedendieck Rebekka , Jahn Dieter , Vary Patricia S.
Published: April 2010

Strains of the genusBacillusare Gram‐positive microorganisms. Many of them, such asBacillus subtilis, Bacillus licheniformis, Bacillus megaterium, Bacillus amyloliquefaciens, Brevibacillus brevis, andBacillus clausiioffer several advantages in industrial applications. They all have a very efficient protein secretion system, grow on several different and cheap carbon sources, lack endotoxins, and are nonpathogenic. Proteins produced from and with the bacilli are of great industrial importance. Next toB. subtilis,B. megateriumhas attracted the most attention in recent years. A toolbox for recombinant protein production, secretion, and purification has been developed that is based on various vectors with different origins of replication, selection markers, promoters, affinity tag sequences, and sequences for a signal peptide. The number of proteins recombinantly produced byB. megateriumhas increased rapidly. The genomes of twoB. megateriumstrains namely QM B1551, which naturally contains seven different plasmids but also has a plasmidless derivative, and DSM319, a naturally plasmidless strain, have now been completely sequenced. Systems biotechnology investigations using transcriptome, proteome, and metabolome analyses in combination with bioinformatics‐based modeling approaches have already started.
Baculovirus Expression Systems
Authors: Possee Robert D. , Hitchman Richard B. , King Linda A.
Published: April 2010

Baculoviruses are insect‐specific pathogens, producing occlusion bodies containing enveloped virus particles which spread infection between insects. These occlusions or polyhedra are composed mainly of a 30 KDa virus‐encoded protein produced in the very late phase of virus replication. Polyhedrin protein is not required for virus replication in cell culture and so the gene coding region can be replaced with a foreign sequence of choice to generate a baculovirus expression vector. The inserted coding region is placed under the transcriptional control of the polyhedrin gene promoter by transfection of insect cells with circular or linear baculovirus DNA or via transposition in bacteria. The coding region can be modified to allow the addition of different secretion signal peptides or peptide tags or multiple gene promoters can be used for the expression of more than one protein. The baculovirus expression vector may also be modified by the removal of nonessential genes encoding products deleterious to recombinant protein production. High yields of protein are possible by scaling up insect cell cultures in serum‐free medium. Despite their specificity for insect cells, baculoviruses can also be use to transduce human cells, where recombinant genes can be expressed if placed under the control of mammalian‐specific gene promoters.
Bioenergetics of Microbial Growth
Authors: Heijnen Joseph J. , Kleerebezem Robbert
Published: April 2010

In this article we describe a methodology based on bioenergetic analysis of chemotrophic microbial growth systems that allows for a generalized system description. The main parameters can be estimated based on the identification of (i) the Gibbs energy supplying redox reaction and (ii) the carbon and nitrogen source for microbial growth. The calculated parameter values can be considered as a first approximation and allow for comparison with measured parameter values. Stoichiometric and kinetic parameter values that deviate strongly from the estimated values suggest that a highly specific microbial system is encountered. Herewith, the generalized method may serve as a reference framework for interpretation of stoichiometric and kinetic parameter values describing microbial growth processes.
Biominiaturization of Bioreactors
Authors: Hanson Michael A. , Rao Govind
Published: April 2010

Bioprocess development largely parallels the drug discovery process. Screening a large number of experimental conditions in the early stages, is required. As scales increase through the pilot to the manufacturing stage, process conditions get more stringent in terms of variation. Ideally, one would like the same quality of process information, independent of scale. Traditionally, early stage experiments to optimize growth media and cultivation parameters have been carried out in flasks and liter‐scale bioreactors. This has often resulted in slow development timelines due to a lack of information in the former and the low‐throughput nature of the latter. To circumvent these drawbacks in traditional technologies, much effort has been directed toward developing small‐scale culturing platforms with monitoring and control capabilities that would mimic production conditions. Such systems would enable more experiments to be carried out simultaneously without compromising the quality of information obtained. In this review, traditional as well as novel systems with monitoring and control capabilities are discussed. We have focused on their application in culture and, in many cases, comparison to larger scale systems. Many small‐scale systems have performances comparable to lab‐scale bioreactors. These advances should allow for much more efficient process development as well as impact other areas such as bioprospecting, where hitherto “uncultivable” species may now be grown by screening samples for growth under matrices of conditions that were previously impractical. Another area of impact will be to allow industry to more readily incorporate process analytical technologies.
Bioreactors: Airlift Reactors
Authors: Merchuk J.C. , Garcia Camacho F.
Published: April 2010

ALRs are popular in modern bioprocess research and development and, in many cases, they have found industrial uses. The distinctive characteristics of ALRs are conferred by the fluid dynamics of the liquid‐gas or liquid gas‐solid mixtures: holdup, liquid velocity, and mixing in the riser, gas separator, and downcomer. Only a correct understanding of the interconnection of these regions can make possible the scale‐up of a laboratory device, to pilot or industrial size. Several correlations are available in the literature for the prediction of the fluid dynamic characteristics of the reactor and of the mass and heat transfer coefficients, and a selection is presented in this review. Significant progress has been made in the application of modern computational tools to the simulation and design of ALRs. In parallel, innovative and sophisticated methods have been applied to obtain a deeper insight into the mechanisms of fluid motion and the flow patterns in the reactor. However, no single research group has managed to cover all the variables over a wide range. The engineer confronting scale‐up orde novodesign of an ALR must analyze the validity of the correlations and computation methods used for the calculations.
Nanomaterials Incorporated Bioelectronics
Authors: Alwarappan Subbiah , Li Chen‐Zhong
Published: April 2010

Bioelectronics can be defined as the functional integration of biological molecules together with electronic components. Bioelectronic systems combine the specific recognition properties of proteins or DNA with the mechanical and electrical properties of metallic or semiconducting solid‐state materials. A major aspect of a bioelectronic device is the generation or modulation of electrical current in an electronic circuit by means of molecular binding of the analyte of interest. In this article, we essentially give a brief introduction to bioelectronics followed by details about biosensors and their classification based on the molecular recognition component, methods of transduction, and materials employed. Following this, we have then briefly discussed the usefulness of a nanomaterials‐based system as transducer elements. In the next section, we summarize the efforts made by different researchers to develop a framework to support the biological machinery and its working principles for self‐assembly of molecular electronics. Next, we account for the usefulness of employing various carbon materials such as carbon nanotubes, carbon fibers, carbon onion, and the recently invented graphene as a substrate to design nanoscale biosensors for various applications. Finally, we have also provided information on artificial neural networks, their development and possible applications in medicine.
Quality by Design (QbD), Biopharmaceutical Manufacture
Authors: Shah Rakhi B. , Park Jun T. , Read Erik K. , Khan Mansoor A. , Brorson Kurt
Published: April 2010

The main concepts of the quality by design (QbD) initiative and applicability to biomanufacturing are described. QbD can lead to a future where product quality will be assured by flexible, science‐based approaches. QbD is an umbrella of related concepts and approaches that include quality target product profiles, risk assessments, design spaces, control strategies using process analytical technology, continuous process improvement and others. We will also discuss the regulatory structure supporting the QbD initiative, including the International Conference on Harmonization Quality documents ICH Q8(R1) (Pharmaceutical Development), ICH Q9 (Risk Assessments), ICH Q10 (Quality Systems) and FDA's Process Analytical Technology (PAT) Guidance. A case study is presented for applying QbD to a biopharmaceutical process, viral clearance by anion exchange chromatography. It is believed that QbD will lead to more flexible processes which are justified based on risk and science rather than on a solely empirical approach.
Industrial Biotransformation
Authors: Ghisalba Oreste , Meyer Hans‐Peter , Wohlgemuth Roland
Published: April 2010

The idea of using biological systems to create more efficient, selective, and environmentally friendlier processes for the conversion of raw materials into industrial products and the concept of a more sustainable use of the limited resources has been put into action long before the now worldwide accepted vision of sustainable development. This article discusses the principles of biotransformations with the advantages, application range, and technical aspects of biocatalysis. On the basis of the driving forces for R&D in industrial biocatalysis, the main screening strategies for biocatalysts are discussed. A short description of the history and companies, the chemical market, the manufacturing facilities, reactors and biocatalytic reactions is followed by selected examples of biocatalysis products manufactured at a large scale. The application spectrum of biocatalysis for industrial processes is much broader than generally perspected and the hope seems justified that the contribution of biotechnology in medium to large‐scale production processes can, in future, be significantly increased. The production of bulk chemicals using biotransformations is entering into a new era of global sustainability and is bound to make a significant contribution. With a truly sustainable global commitment and effort of real innovation in science, industry, and society in order to make it happen, the outlook is very optimistic. The resulting creation of value should not be viewed only from the short‐term cost perspective, but more in terms of long‐term knowledge building for a future bioeconomy.
Cell Detachment
Authors: Merten Otto‐Wilhelm
Published: April 2010

Cell detachment of adherently growing cells is a key operation in any cell culture laboratory as well as in animal cell technology in order to amplify cells for different purposes, which are the amplification for getting the cell number/mass for experimental and testing or necessary for production purposes. This monograph describes cell attachment in brief, trypsinization as reference method including a short review on the mechanisms of trypsin and the actual developments for replacing the use of trypsin which is an animal‐derived component by other enzyme‐based or nonenzymatic means to detach or dissociate cells. Specific issues concerning cell detachment at a large‐scale and under serum‐free conditions are also discussed.
Cell Separation, Centrifugation
Authors: Axelsson Hans
Published: April 2010

A review of the different types of centrifuges used in industrial biotechnology is compiled, together with brief explanations of their function. The fluid and particle dynamics in the centrifuges is reviewed with some emphasis on the behavior of cells and other particles, and susceptibility to the shear forces acting on them. The classical mathematical models for the theoretical size, Σvalue, andKQvalue are characterized. The concept of separation efficiency, the deviation from ideal capacity, due to the simplicity of the mathematical model for the Σ value is defined. The considerations when selecting type and size of centrifuge for a given process are described, as well as the evaluation and enhancement of separability of the given process stream. The importance of small‐scale lab and pilot tests for a successful scale‐up is emphasized. Applications in harvesting of bacteria, yeasts, and mammalian cells are reviewed, as well as cell debris and inclusion body separations. Extraction—solvent and two‐phase aqueous—application examples are given. Finally, some plant and operation considerations such as plant design, CIP, SIP, containment, asepsis, and sterilization are briefly reviewed.
Chiral Alcohols by Enzymatic Preparation
Authors: Borup Birthe , Daussmann Thomas , Collier Steve
Published: April 2010

Biocatalytic processes are of increasing importance in the production of chiral alcohols which are important building blocks in the synthesis of chemical catalysts, liquid crystals, agrochemicals and pharmaceuticals. Methods for the synthesis of chiral alcohols can be subdivided into three general classes: traditional (such as classic racemic resolution, chromatography, chiral pool synthesis), asymmetric chemical, and biological (enzymes, whole microbial cells) methods. The last can also be applied to the more traditional methods. Enzymatic techniques are attracting a growing interest as green catalysts because of the different advantages they offer, as compared to other methods: high selectivity, high product purity, mild reaction conditions, competitive production costs, and excellent catalyst availability.

In this contribution we give an overview of the biocatalytic approaches for the manufacture of chiral alcohols. To our knowledge there are currently about five major enzyme groups applied for the synthesis of chiral alcohols. The first one reduces carbonyl functional groups (ketones) to enantiopure secondary alcohols (dehydrogenases or reductases). The second group forms alcohols by introduction of molecular oxygen with concomitant one or two electron reduction (mono‐ and dioxygenases). The third group forms alcohols by addition of water to unsaturated carbon carbon double bonds (hydratases) whereas the fourth one forms alcohols by nucleophilic addition of small molecules such as HCN at carbonyl groups which usually also results in a new C–C bond formation (hydroxynitrile lyases and aldolases). The last major group of enzymes discussed herein belongs to the traditional methods mentioned above and resolves racemic chiral alcohols by reacting with only one enantiomer in a racemic mixture (hydrolases).

In a selection of case studies we demonstrate the high level of importance that biocatalytic processes have already gained in the industrial manufacture of chiral alcohols. There are numerous processes available that have been or still are operated in multi‐tonne scale. By solving the drawback of cofactor requirements and regeneration for a range of enzymes, especially in the area of asymmetric reduction, the dehydrogenases and oxygenases are now commonly used for commercial processes and are in several cases superior to whole‐cell microbial processes.

The highly competitive nature of enzymatic processes compared to whole‐cell (fermentation) and chemical approaches is demonstrated with the example of the manufacture of optically active ethyl (R)‐3‐hydroxybutyrate.
Chromatography, Hydrophobic Interaction
Authors: Kårsnäs Per
Published: April 2010

Hydrophobic interaction chromatography (HIC) is based on complex interactions between the separation media and biomolecules. This compexity is due to that the salt‐mediated mechanism for attraction in unusually dependent also on the individual sterical structures of the counterparts. A hydrophobic ligand thus may express different separation selectivitiy patterns when coupled to different media with different tecniques. Prediction of results therefore cannot be made based on experiments performed on another separation medium with the same ligand. HIC uses moderately hydrophobic ligands where the molecules to be separated are forced to attach to the columns by increasing the ionic strength of the eluent. It is mainly used for large biomolecules forming multipoint attraction with the medium. Elution is performed with gradients of decreasing ionic strength and short and wide columns are used to optimize the separation. Tertiary structures tend to be preserved but attached molecules should be eluted as soon as possible due to the risc of confomational changes and enhanced binding making elution difficult. An HIC medium may be characterized by the profile of elution data of a set of marker proteins using PCA making possible the comparision and classification of media and prediction of results. Optimization is facilitated by running the sample through columns eqilibrated with stepwise higher ionic strength.
Clean‐in‐Place (CIP)
Authors: Bremer Phil J. , Seale Richard Brent
Published: April 2010

Clean‐in‐place (CIP) is the cleaning of the assembled plant (vats, fermenters, tanks, processing equipment, probes) and pipeline circuits (values, flowmeters, gaskets) by the jetting or spraying of surfaces or the circulation of cleaning solutions under conditions of high temperature, turbulence and flow velocity. CIP involves little or no manual involvement from an operator. Cleaning efficiency is associated with mechanical, thermal, and chemical activity. Important factors influencing the effectiveness of the CIP include the nature of the material to be removed, the design of the plant and CIP system, the type of surface requiring cleaning, the concentration and nature of the cleaning solution, and the temperature and duration of the cleaning stages [1]. Compared to manual cleaning regimes, a well‐designed, validated, operated, and monitored CIP system will dramatically increase cleaning effectiveness and reproducibility, reduce costs, and enhance operator safety.
Cyclotides
Authors: Dörnenburg Heike , Craik David J.
Published: April 2010

The cyclotides are a recently discovered family of miniproteins that contain a head‐to‐tail cyclized backbone and a knotted arrangement of disulfide bonds. They are approximately 30 amino acids in size and are present in high abundance in plants from the Rubiaceae, Violaceae, and Cucurbitaceae families, with individual plants containing a suite of up to 100 cyclotides. They have a diverse range of bioactivities, including uterotonic, anti‐HIV, antitumor, and antimicrobial activities, although their natural function is believed to be in host defence against pests and pathogens. In addition to their natural activities, cyclotides have been proposed as a stable peptide template for applications in protein engineering and drug design. Their exceptional stability and resistance to thermal, chemical or enzymatic treatments can be attributed to the cyclic cystine knot structural motif that forms their compact molecular core. The backbone loops protruding from this core vary in their amino acid compositions and because of this tolerance to substitutions, cyclotides can be regarded as a natural combinatorial template. To date, most bioactivity studies on cyclotides have involved peptides extracted from plants. Cyclotides are amenable to chemical synthesis but this is expensive and so the development of bioprocesses for the production of cyclotides is an important objective for enabling their future industrial applications. This article gives a brief overview of the structures and properties of cyclotides and discusses new approaches to their production using bioprocesses on an industrial scale.
Scale‐Up of Chemical and Biotechnological Processes
Authors: Zlokarnik Marko
Published: April 2010

The article deals, first of all, with dimensional analysis; a method by which a complete set of parameters that fully describe a process under consideration is transformed to a set of dimensionless numbers (pi numbers). On the one hand, the application of this method leads to an essential compression of the scope which describes the process. On the other hand, the produced dimensionless products are scale invariant with respect to each dimension, therefore also to the dimension of length, which is the basis for a reliable scale‐up.

The scale‐up requires a threefold similarity: a geometrical, a material, and a process‐related one. The material similarity may cause problems if non‐Newtonian fluids (pseudoplastic and/or viscoelastic) are involved. This problem is comprehensively discussed in the second part of the article.

The third part is concerned with some important procedures relating to mechanical and thermal process engineering, which are often applied in biotechnology. Examples are given of how scale‐up may be used in such cases.
Electron Transport
Authors: White David
Published: April 2010

In this article, the electron transport process that occurs in mitochondria and bacteria is described. Topics include the protonmotive force and how it is generated, a detailed description of electron carriers, organization of electron carriers, a description of coupling sites, Q loops, Q cycles, and proton pumps, and patterns of electron flow in various types of bacteria.
Enzyme‐Catalyzed Reactions in Ionic Liquids
Authors: Gorke Johnathan , Srienc Friedrich , Kazlauskas Romas
Published: April 2010

Ionic liquids, also called molten salts, are mixtures of cations and anions that melt below 100°C. Typical ionic liquids are dialkylimidazolium cations with weakly coordinating anions such as [BF
4
] or [PF
6
]. Deep eutectic solvents are also included in this review because their properties are similar. Deep eutectic solvents are mixtures of salts such as choline chloride and uncharged hydrogen bond donors such as urea, oxalic acid, or glycerol. The advantage of using ionic liquids is enhanced solubility of substrates or products without inactivation of the enzymes. Ionic liquids as cosolvents with water help to dissolve nonpolar substrates, but do not inactivate enzymes like water‐miscible organic solvents do. The enhanced solubility of substrates usually increases the rate of reaction and often increases the regio‐ or enantio‐selectivity. Ionic liquids can also serve as solvents for nonaqueous reactions. In these cases, they are especially suitable for dissolving polar substrates. Polar organic solvent alternatives inactivate enzymes but ionic liquids do not, even when they have similar polarities. Hydrolases and oxidoreductases are particularly well‐studied in ionic liquids. Besides their solubility properties, ionic liquids and deep eutectic solvents may be greener than organic solvents because ionic liquids are nonvolatile and can be made from nontoxic components.