Methods and their relevance to proteomic studies.
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The authors have covered keratitis theory and practice. Onchocersias, even though found on one continent, has its impact on population, epidemiologists, ophthalmologists, NGOs, public health planners and care providers. \nThe goal of this book is to provide information on ancient eye diseases; their investigation and management to prevent corneal blindness. 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\r\n\tChemical vapor deposition (CVD) is a coating process that uses thermally induced chemical reactions at the surface of a heated substrate, with reagents supplied in gaseous form. CVD technology has recently grown at a rapid rate, and the number and scope of its applications and their impact on the market have increased considerably. Among several challenges associated with the CVD technique, the main challenge is a limited mechanistic understanding of the CVD growth process, which makes the predictions of desirable growth conditions difficult. Numerous important aspects of the process include nucleation, the nature of reaction intermediates, and the role of long-range transport that is still under exploration. The second challenge arises from the convoluted relationship between the system-specific process variables that can be conveniently controlled and the intrinsic thermodynamic and kinetic properties that ultimately govern crystal growth. There are a number of process parameters that need to be tuned to adjust the growth environment, including the heating zone temperature, vapor pressure, the number of precursors, and the distances between the substrate and the sources.
\r\n\r\n\tThe book is an update with a considerably expanded and revised scope.
\r\n\t
Proteins, key players responsible for good muscle function, are the main structural and functional constituents of the muscle [1]. In the last three decades, a considerable amount of skeletal muscle proteins that present a vast variation in size, shape, abundance, and expression have been identified. Based on their localization, muscle proteins are grouped as muscle membrane (dystrophin, sarcoglycans, dysferlin, and caveolin-3), the extracellular matrix (a2-laminin and collagen VI) and from the sarcomere (telethonin, myotilin, titin, and nebulin), the muscle cytosol (calpain 3, myotubularin, TRIM32), the nucleus (emerin, lamin A/C, SMN) [2]. Mutation in the gene that encodes for specific muscle proteins is responsible for the changes in expression of most of them and lead to different forms of neuromuscular diseases.
\nEvaluation of the localization of a protein on tissue, its expression, cellular level, and understanding of the interactions with different other proteins can elucidate the molecular basis of muscle pathology.
\nThe differences in terms of size (from titin with a molecular mass around 1200 kDa, nebulin 700 kDa, to caveolin 3–25 kDa) and location of each of them make their investigation difficult [3].
\nHowever, the examination of the muscle protein expression by immunostaining reactions, as well as investigation of the abundance and size using SDS gel electrophoresis by methods based on antigen-antibody interaction method, has been developed and improved over time [4]. The immunoassay methods represent a powerful tool that offers comprehensive details about the molecular alteration of different muscle pathology. Different strategies have improved over time in terms of quality and sensitivity, but each of them has the specific requirement as well as limitations.
\nApplications of immunoassay techniques contribute to both diagnostic and research purposes for biomarkers identification and therapeutic drug monitoring.
\nThis chapter presents the most used techniques based on the interaction between antibodies (Ab) with a specific antigen (Ag) for muscle protein analysis, providing necessary knowledge for obtaining a good result, and provides some suggestions for the inherent problems that may be encountered in different stages.
\nImmunoassay methods, technologies based on the properties of the antigen-antibody interaction, allow both qualitative and quantitative analysis of interest protein. Most important and used
Both immunoassay methods have various applications and have been widely used in the identification of biomarkers, diagnosis of diseases, therapeutic drug monitoring, and drug discovery, as well as characterization of protein expression and function by use of antibodies (Table 1).
\nAbbreviation | \nMethod | \nRelevance to muscle proteomic studies | \n
---|---|---|
IHC | \nImmunohistochemistry | \nLocalization of a protein Accumulation of a protein in a tissue Qualitative pattern: presence, absence, or reduction Secondary reduction | \n
IF | \nImmunofluorescence | \nLocalization of a protein Accumulation of a protein in a tissue Qualitative pattern: presence, absence, or reduction Secondary reduction | \n
ICW | \nIn-cell Western | \nDetect and quantify target proteins localized in-cell Quantitative analysis of cellular signaling pathways | \n
WB | \nWestern blot | \nEvaluation of molecular mass and abundance Differential diagnosis Level of expression | \n
MWB | \nMultiplex Western blot | \nLocalization of a protein Accumulation of a protein in a tissue Qualitative pattern: presence, absence, or reduction Secondary reduction | \n
Methods and their relevance to proteomic studies.
Antigens, also called immunogens, are any macromolecule of natural or synthetic origin such as proteins, polypeptides, polysaccharides, nucleic acids, and infectious agents that stimulate the immune system to induce an immune response (e.g., to produce a specific antibody). An antigen (Ag) molecule consists of two components: a carrier that is the largest part of the molecule and specific antigenic determinants or epitopes that are immunologic active regions of the antigens recognized by an antibody. An epitope is usually a protein segment by 5 to 8 six amino acids in length, specific for each antigen. The fixation of the antigen at the combining site of the immunoglobulin occurs based on the complementarity between epitope and paratope by multiple noncovalent bonds, van der Waals forces, hydrogen, and hydrophobic-type interactions. The rate formation of the antigen-antibody complex depends not only on the preservation and accessibility of epitopes to the antibodies [8] as well as the concentration of the reactants but also on the mutual affinity. The alteration or destruction of epitopes by different treatment determines the reduced or abolished antigen-antibody interaction.
\nBecause proteins are the most powerful antigens, the immunohistochemistry reaction is primarily concerned on their identification and localization as well as glycoprotein and lipoprotein compounds. The successful rate of immunohistochemistry reaction‑detection of the antigen-antibody complex‑depends on several factors of which the most important are: (i) the reactivity and quality of the reagents; (ii) antigen concentration in the analyzed tissue; (iii) antigen retrieval methods; and (iv) labeling conditions and methods used [9].
\nAntibodies also called immunoglobulins (Ig) are large Y-shaped animal glycoproteins made up of four polypeptide chains: two identical heavy chains (H) and two identical light chains (L) linked together by disulfide bonds.
\nWhile there are two main types of light chains
Ig is also a bifunctional molecule presenting two antigen-binding sites called Fab fragment and one complement-binding site called Fc fragment. For both heavy and light chains, the C terminal parts contain constant regions of the antibody, while the N-terminal contains variable domain through the antibody that binds to the antigen named
The use of antibodies for the identification of protein antigen in human tissue was a revolutionary step for methods like western blotting, immunofluorescence, and immunohistochemical studies. The two most used types of antibodies in these studies are monoclonal and polyclonal antibodies.
\nFor a successful immunohistochemistry experiment, a few things related to antibodies must be known such as whether the antibody will react with the antigen under conditions of fixation and processing system used, the immunoglobulin class to which the antibody belongs, the species in which the antibody was generated, which epitope to be targeted, type of antibody used (monoclonal or polyclonal), and analysis methods.
\nBesides the crucial and active role, which it plays in producing the mammal’s normal immune response following the action of pathogens, antibodies are powerful tools for research and diagnostic purposes. Due to high exquisite specificity and selectivity, antibodies are an excellent tool utilized in a wide variety of therapeutic applications including detection and quantification of molecules of interest [13].
\nAntibodies used for research and diagnostic applications are produced by repeatedly injecting a laboratory animal (e.g., mice, rats, rabbits, and goats) with a specific antigen until it confirms the occurrence of antigen-specific antibodies in the blood serum. Generally, based on production and purification methods, antibodies can be classified into two groups: polyclonal or monoclonal.
\nFor the identification of the same antigen, both monoclonal and polyclonal antibodies are available. Choosing a primary monoclonal or polyclonal antibody for a specific target in immunoassay methods depends on the purpose of the experiment.
\nIn the immunostaining methods based on antigen-antibody interaction, higher specificity and lower affinity of the mAbs as well as lower specificity but higher affinity of pAbs must be taken into account. To assess changes in molecular conformation, protein-protein interactions, as well as to identify the members of protein families, mAbs are more useful because of their monospecificity [14]. Polyclonal antibodies prove their usefulness in the studies they are aiming to detect variants of a particular protein of interest [15] by being able to amplify the signal of interest protein with low expression level (Table 2).
\n\n | Monoclonal antibodies | \nPolyclonal antibodies | \n
---|---|---|
Advantages | \nHigher specificity to a single epitope Higher reproducibility Moderate sensitivity Reduced cross-reactivity Provide better results | \nRapid generation and less expense costs Higher affinity–recognize and bind to many different epitopes of a single antigen Less technical skill required for production Easy to store Quicker binding to the target antigen Stable to pH and buffer conditions | \n
Disadvantages | \nMore time − 4-6 months to produce and develop Expensive costs for production Less tolerance to pH and buffer condition changes | \nCross-reactivity due to a recognition of multiple epitopes High variability between different lots produced in different animals at different times | \n
Characteristics of monoclonal and polyclonal antibodies.
“Sensitivity” refers to the limit of detection of an assay for a specific target in a sample.
“Specificity” refers to the ability of a method to measure a specific target in a sample.
Antigen-antibody complex (immune complex) is a bimolecular association that occurs when an antigen combines with an antibody based on the affinity of the antibody for the antigen. The reaction of the antibody-antigen is highly specific. The antibodies recognize the epitope region of the antigens and interaction between them is maintained due to exclusively noncovalent bonds such as hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals forces [16]. The bonds are irreversible, but the antigen-antibody interaction can be affected during washing steps leading to dissociation of the complex. A lot of factors can influence the Ag-Ac complex such us temperature of incubation, pH buffer, the concentration of antigen/antibody, and incubation time as well as the number of antigen sites per cell (zygosity) [16, 17].
\nThe Ag-Ab complexes are not visible with standard microscopy and must be labeled. A wide range of fluorochromes is commercially available. An important property of a fluorochrome is the absorption spectrum. Fluorochromes absorb light at one wavelength [18] and emit light at a different wavelength.
\nThe most commonly used markers for labeling are:
Fluorochromes: mostly used are fluorescein (absorbs blue light and emits yellow-green) and rhodamine (absorbs yellow-green light and emits deep red)
Enzymes for histochemical techniques (e.g., peroxidase, alkaline phosphatase, and glucose oxidase)
Metals for use in electron microscopy (ferritin and colloidal gold)
Most often, the sensitivity of an immunolabeling reaction depends on the selection of the detection system, which makes the choice of detection to be done carefully. The permanent attempt to obtain better results and significant advances in the biology field has led to the development of numerous methods for visualizing the antibody-antigen complex. Detection systems are classified as direct or indirect methods depending upon whether the fluorochrome is attached to the primary, secondary, or tertiary antibody. Regardless of the method chosen for labeling, both direct and indirect assay make possible distribution and precise localization of a specific protein or specific cellular components within a tissue or cell as well as the study of protein expression and function (Table 3).
\n\n | Direct | \nIndirect | \n
---|---|---|
Advantages | \nSingle labeling step Short time procedure No cross-species reactivity | \nGreat sensitivity‑high amplification of the signal Production of the secondary antibodies is inexpensive | \n
Disadvantages | \nLess sensitivity Lower signal Higher costs Restricted availability of direct conjugate antibodies | \nDouble labeling steps Long procedure Extra incubation and wash steps are required High background due to endogenous activity | \n
Advantage and disadvantage of immunofluorescence methods.
The direct labeling method is used for the detection of the point of interest in a specimen using a single primary Ab directly coupled with a reporter molecule (Figure 1). The method is usually shorter, involves one incubation step reaction, and is widely used for detecting highly expressed antigens in a tissue. The advantage of the direct labeling method is the avoidance of antibody cross-reactivity or nonspecificity.
\nSchematic representation of immunolabeling mechanisms. (1) Direct labeling; (2) Indirect labeling with secondary antibody conjugate with fluorophore; (3) indirect labeling with biotinylated secondary antibody.
Nevertheless, direct labeling is not routinely employed in clinical and research applications due to insufficient sensitivity of the method in detecting of antigens in a tissue, the weak intensity of obtained signal, as well as optimal given preparation process of attaching fluorochrome to the antibody, which can affect antibody affinity. To date, for muscle protein analysis is used indirect labeling due to the higher sensitivity of the method.
\nThe need to improve the sensitivity of detection methods of antigens with low expression led to the development of labeling methods in several stages, which intensifies the signal.
Thus, the indirect method is no longer used in its original form but continues to develop both the identification and production of a large number of fluorescent molecules, as well as the improvement of specific methodologies for coupling fluorochromes with antibodies.
\nTherefore, even the immunostaining methods may seem simple in concept, there are many critical steps in performing it. To ensure success and to obtain good results, several parameters should be considered as follows:
The use of antibodies in immunohistochemical microscopy-based experiments is a helpful tool for identification, localization, and expression patterns of muscle proteins. This technique is still routinely used in research to study the role of interest protein both in healthy and in pathological muscle as well as for diagnostic purposes or optimized treatment regimes and therapeutic drug monitoring. However, the use of one method only for the complete characterization of a muscle protein is not enough. The advances in the proteomic field led to the improvement of the analytical method for identification and quantification of proteins avoiding thus inconsistent and confusing immunocytochemical results.
\nThe most used method for confirmation of immunohistochemical results as well as for the size of the protein is western blot. There are many different types and methods for Western blotting.
\nThe Western blot (WB) method also known as protein immunoblotting is an important analytical and quantitative technique used to identify, to separate a specific protein from a given complex biological mixture of proteins from a tissue/cellular homogenate, and to determine the amount of antigens (proteins) in reaction with a specific antibody. Initially, the proteins are electrophoretically separated into a polyacrylamide (PAA) gel electrophoresis. The most widely used technique for large scale protein from a mixture of proteins is sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) due to the possibility of separation of proteins based on their molecular weight under the action of electric current after linearization of the proteins. Special gradient gels are used to separate proteins with a wide variety of molecular mass. After the separation, the proteins are electrophoretically transferred on a solid substrate such as nitrocellulose, PVDF, or cationic nylon membrane. To suppress nonspecific adsorption of the antibodies, the unreacted nonreactive binding sites on the membrane are blocked, which causes immobilized proteins to react specifically with monoclonal or polyclonal antibodies. Primary antibodies can be applied single when we target the expression of a single protein or in a cocktail when a simultaneous analysis of several proteins is necessary. Commonly used conjugates for secondary antibody are color, radioactivity, enzyme, as well as biotin. Antigen-antibody complexes are radiographically, chromogenically, or chemiluminescently visualized.
\nWith this technique, the size (molecular mass) and abundance of the interest protein are evaluated by comparing with the control. The need for the analyses of multiple different target proteins simultaneously led to great improvement of sample separation resolution.
\nThe multiplex detection methods have improved over the past few decades and have led from the analysis of a single specific protein to the detection of simultaneously multiple target proteins with a different molecular weight in a complex of cellular homogenates [25, 26]. For the simultaneous analysis of muscle proteins, a biphasic polyacrylamide gel system with different concentrations is used. With this system, the separation of muscle proteins is done based on their molecular weight (proteins with molecular weight more than 200 kDa are separate in the top part of the gel, e.g., dystrophin, while the smaller proteins under 150 kDa, e.g., calpain 3 in the bottom). Highlighting of proteins is achieved with a cocktail of specific primary antibodies.
\nSimultaneous analysis of multiple proteins involved in different muscle pathologies revolutionized the medical diagnosis, reduced cost and time for analysis, and improved differential diagnosis in muscle pathology.
\nICW also known as in-cell ELISA (ICE) is quite a novel quantitative immunofluorescence-based technique suitable for the detection of protein levels and signaling events performed in cell culture grown on microplate format [27]. It is an extremely sensitive method and accurately quantifies, which can detect two targets normally labeled with specific primary antibody followed by incubation with secondary antibody fluorescent conjugated with spectrally distinct dyes and quantification of the signals from fluorophores conjugated at different wavelengths on two detection channels. The technique allowed the quantification of proteins directly in cell culture [28]. The accuracy of quantification is increased by normalization due to adjustments of the cell number in wells. This technique is also useful in the study of the drug effect on multiple points.
\nFor the evaluation of antigen expression by
In bright-field microscopic IHC, antigen expression in muscle is visualized by a combination of a secondary antibody with an enzyme and utilizing a colorimetric substrate that produces a colored reaction product detected by light microscopy. The most widely used enzymes in chromogenic detection are the horseradish peroxidase (HRP) and alkaline phosphatase (AP), which convert 3,3′ diaminobenzidine (DAB) and 3-amino-9-ethylcarbazole (AEC) into brown and red end color, respectively. The reaction product is stable for a long time and visualization can be done any time. Multiple labeling is also possible since different substrates are now available for the same enzyme, but low contrast and resolution for samples is a limitation of bright-field microscopy.
\nAlthough a lot of muscle proteins can be detected by IHC with peroxidase and visualized in light microscope field, the labeling of antigen with an antibody coupled with a fluorochrome permitted a superior viewing of many muscle proteins and offered significant advantages in accurately identifying certain protein localizations and distinguishing subtle difference in protein expression patterns. The major advantage of fluorescence microscopy is given with the possibility of uses of different dyes that span the entire visible spectrum to track different target proteins. Also, the identification of the interaction between proteins as well as their specific localization is better observed by colocalization when the color of two or more different fluorescent dyes used appears changed as a result of the overlap. One limitation of fluorescence microscopy remains the loss of the fluorescent capacity
In combination with laser confocal scanning microscope, fluorescence is preferable to evaluate the degree of colocalization and relative quantitation of proteins by specialized software [30].
\nConfocal microscopy is a powerful laser scanning method used for the imaging analysis of fluorescently labeled specimens.
\nThe technique provides high-resolution detailed information about the 3D structure of the tissue sections and cells allowing detailed analyses and measurements of double, triple, and even quadruple stained sections [31, 32]. This is possible due to labeling of secondary antibodies with different fluorophores, which emitted on a different wavelength.
\nThe z-stack mode permitted three-dimensional reconstructions of optical sectioning useful for the study of the relationship between stained structures.
\nMuscle pathology usually involves changes in level and protein expression. For muscle protein diagnosis, a good knowledge is required of the expected cellular location: at sarcolemmal
Disease | \nGene | \nPrimary protein defect | \nSecondary changes | \nLocalization level | \nClue to diagnosis | \nReferences | \n
---|---|---|---|---|---|---|
IF/WB | \n||||||
DMD | \nDMD | \nDystrophin | \nUtrophin upregulated Sarcoglycans reduced/absent Dystroglycan reduced/absent nNOS absent | \nSubsarcolemmal | \nAbsent, reduced/absent | \n[2, 43] | \n
BMD | \nDMD | \nDystrophin | \nUtrophin upregulated Sarcoglycans reduced/absent Dystroglycan reduced/absent nNOS reduced/absent | \nSubsarcolemmal | \nReduced/Reduced in size/amount Absence of at least one antibody | \n[2, 43] | \n
DMD/ BMD carriers | \nDMD | \nDystrophin | \nUtrophin upregulated Sarcoglycans reduced/absent Dystroglycan reduced/absent nNOS may be absent | \nSubsarcolemmal | \nMosaic pattern/ Reduced in size | \n[2, 43] | \n
LGMD2C-F | \nSGCG SGCA SGCB SGCD | \nSarcoglycans | \nReduction of other sarcoglycan Β-Dystroglycan reported Possible reduction Dystrophin Loss of nNOS reported | \nSarcolemmal | \nVariably reduction/absent | \n[44] | \n
LGMD2B | \nDYSF | \nDysferlin | \nCaveolin-3 reduced | \nSarcolemmal | \nAbsent/reduced | \n[45] | \n
LGMD1C | \nCAV3 | \nCaveolin-3 | \nDysferlin reduced | \nSarcolemmal | \nAbsent/reduced | \n[45] | \n
CMD | \nLAMA2 | \nLaminin α2 | \nDeficiencies of laminin β2, α-dystroglycan and integrin α7 | \nExtracellular matrix | \nCompletely or partially absent | \n[46] | \n
Bethlem or Ullrich myopathy | \n\n | Collagen VI | \nDeficiency of laminin β1 chain | \nExtracellular matrix | \nReduced/absent | \n[47] | \n
LGMD2G | \nTCAP | \nTelethonin | \n— | \nSarcomere | \nReduced/absent | \n[44, 48] | \n
LGMD2J | \nTTN | \nTitin | \nCalpain 3 reduction | \nSarcomere | \nAbsence of calpain 3/loss of C-terminal fragments of titin results in the reduction of higher molecular weight | \n[48, 49] | \n
LGMD1A | \nMYOT | \nMyotilin | \nSecondary laminin γ reduction | \nSarcomere | \nProtein aggregates | \n[45, 48] | \n
LGMD 1E | \nDES | \nDesmin | \nMyotilin, αB-crystallin, VCP cytoplasmic aggregates | \nExosarcomeric | \nDesmin cytoplasmic aggregates | \n[50] | \n
LGMD2A | \nCAPN3 | \nCalpain 3 | \nDysferlin reduced | \nCytosol | \nLabeling may be absent or reduced on sections/ Calpain 3 bands may be variably reduced | \n[44, 50] | \n
LGMD 2H | \nTRIM32 | \nTrim 32 | \n— | \nCytosol | \nReduced expression/reduced level | \n[51] | \n
Emery-Dreifuss MD | \nEMD | \nEmerin | \n— | \nNucleus | \nAbsent /reduced level | \n[52] | \n
LGMD1B | \nLMNA | \nLamin A/C | \nLaminin β1 reduction | \nNucleus | \nLamin A/C normally expressed | \n[44] | \n
The skeletal muscle-specific proteins.
Immunohistochemical staining is useful for the identification of the interest markers and provides valuable information about their distribution, localization, and expression in a tissue or cell. The obtained results should be interpreted by comparing a given protein pattern in normal and affected tissue in the presence of the controls of the reaction mentioned above. The evaluation of muscle protein expression is generally made in a qualitative manner based on their presence, absence, or variable reduction. Depending on the manifestation of the protein identified by immunohistochemical analysis, the progression of different neuromuscular disorders can be evaluated.
\nThe usefulness of the method lies in the identification of the primary protein abnormalities in recessive diseases [33] and secondary reduction of interconnected proteins. For example, in the primary reduction of dystrophin, protein involved in Duchenne/Becker muscular dystrophy and secondary reduction of sarcoglycans [22] and of cytosolic calpain 3 [25] was reported. The reduction of dysferlin also is accompanied by the reduction of calpain 3.
\nBecause of the currently limited access to next-generation sequencing that permitted analysis of simultaneous gene involved in a different type of muscular dystrophies, analysis of muscle biopsy by the immunoassay method is still a helpful method in many laboratories. Different computational methods developed in the last decade for quantitative immunohistochemical (IHC) image analysis of proteins have begun to be increasingly used.
\nHow much protein is needed for proper muscle function has always been a problem that researchers have been trying to solve. Immunohistochemistry quantification of dystrophin proteins involved in the most severe type of muscular dystrophy has come to the attention of researchers with the improvement of image analysis software. Thus, L. E. Taylor [34] and Antony K [35] developed a method of image analysis that allows immunofluorescent quantification of dystrophin expression in sections that proved to be robust and reliable method of biomarker detection. These methodologies contribute to and improve the final diagnosis and especially are used in the analysis of a protein after a drug and specific treatment.
\nHowever, increasing the contradictory results obtained by this method and reported in the literature, a final and accurate diagnosis requires the confirmation of the results by another quantitative method, such as Western blot.
\nWestern blot methods have become very popular in diagnostic laboratories due to the ability to analyze several proteins simultaneously avoiding thus the preservation of large portions from an affected muscle [36, 37].
\nThe rapid evolution of the quantitative methods has improved over time from the analysis of one protein to simultaneous analysis by SDS gel electrophoresis of several proteins with different molecular mass. Multiplex Western blot technique developed by Andreson [25] represented a significant improvement in muscle protein analysis regarding efficiency and cost. By this method, can be evaluated the molecular mass (normal or reduced size) and abundance of the proteins by comparison with controls and the use of quantitative software analysis.
\nWestern blot has greater importance in muscle protein analysis especially in the differential diagnosis of muscular dystrophies (distinguish between DMD and BMD patients); for analysis of calpain 3 in it, there are no antibodies available for immunoreactions on the sections.
\nThe immunohistochemical reactions are widely used both in the investigation and in the pathological diagnosis evaluations of diseases based on the antigen-antibody reactions. The identification and localization of an antigen in a tissue or cells can provide valuable information, which otherwise could not be obtained by other methods. Because most of the antigens are usually proteins, identifications of abnormal expression patterns of proteins in diseased tissue are also helpful in differential diagnosis and detecting primary protein defect involved in the pathology. Besides the identification of a primary defect and protein expression chances, immunohistochemistry is also helpful in the pharmaceutical analysis area for drug discovery and therapeutic drug monitoring.
\nWith knowledge advance in disease pathogenesis and the development of novel therapeutic strategies, there is a need to generate new treatments for specific neurodegenerative disorders. In the last few years, the use of antisense oligonucleotides (AOs) has increased interest in the treatment of the different types of muscular dystrophy such as Duchenne muscular dystrophy.
\nAntisense oligonucleotides, a new class of the synthetic single-stranded molecules of nucleic acids as RNA or DNA, have been reported that modulate the gene expression and splicing process interacting with specific gene transcripts through a variety of mechanisms and restore the expression of functional protein [38, 39].
\nThe quantification of protein levels after treatment will be monitored by the immunoassay method after administration of a specific dose of specific AOs. Positive results obtained in clinical trials with AOs for different diseases increase the interest in the clinical application of antisense strategies. However, more clinical trials and more data are necessary to make this strategy clinically available.
\nDifficulties, limitations, and disadvantages of immunostaining methods and troubleshooting are discussed further.
Difficulties
Although it is a simple technique, many parameters must be considered and optimized before. The quality of the results depends on these critical factors that begin from handling the specimen to tissue fixation procedure, detection system, staining protocol, antibody selection, and sensitivity. Also, the ability, experience, the rigor of execution of the researcher in performing the reaction, and good knowledge and understanding of the methodology and morphological changes in a specific pathology are necessary for an accurate overview of protein expression and interpretation of the results to avoid misinterpretation [40, 41].
Limitations
One of the major limitations of the immunoassays is antibody specificity. The nonspecific binding occurs when an antibody attaches to a cell without a specific epitope for that antibody. Several reasons are responsible for nonspecific binding such as higher concentrations of the antibody and binding by
The nonspecific binding of the antibody can cause errors and confusion in the interpretation of the obtained results. To eliminate the interpretational error, antibody specificity controls must be introduced into the reaction to obtain reliable staining [43].
\nA limited number of available antibodies for muscle protein represent another limitation of this method as well as the choice of an insufficiently specific and sensitive antibody for the desired target. Often, the resolution microscope is a limitation in determining the proper intensity of the signal of the target antigen as well as subtle differences in protein expression level. This problem can be solved by confocal laser scanning microscopes, which offer a possibility to overcome this problem by providing images in the highest resolutions and can predict accurately variation in staining intensity. It must be considered that the image quality degrades over time.
Disadvantages
Both direct and indirect immunofluorescence methods have some advantages and disadvantages, which are presented in Table 3. Besides, these immunostaining methods have some disadvantages among which we mention the lack of worldwide standardized protocol that determines the introduction of a level of subjectivity both in the working procedure and in the interpretation of the obtained results. Once again, the experience of the personnel who work this technique is crucial.
\nImmunoassay methods are a powerful tool for characterization of the proteins regarding localization, understanding the quantitative and qualitative characteristics, as well as interactions of proteins at the cellular level. The progress of the development of the specific antibodies, as well as improvement in image analysis software, leads to more sensitive and specific immunoassay methods used for characterization of the proteins. However, a combination of qualitative and quantitative methodologies offers great value for the results. Further advances in immunoassay methods will lead to a better understanding of the functional role of proteins.
\nThis work was funded by Ministry of Research and Innovation in Romania, under Program 1-The Improvement of the National System of Research and Development, Subprogram 1.2-Institutional Excellence-Projects of Excellence Funding in RDI, Contract No. 7PFE/16.10.2018; National Program 31 N/2016/PN 16.22.02.05; COST Action Delivery of Antisense Oligonucleotides.
\nThe author declares that there are no competing interests.
\n antigen antisense oligonucleotides Becker muscular dystrophy Duchenne muscular dystrophy congenital muscular dystrophy in-cell Western immunofluorescence immunoglobulins immunohistochemistry limb-girdle muscular dystrophy monoclonal antibodies muscle-eye-brain disease polyclonal antibodies Western blot
Rape, an unlawful carnal knowledge of man or woman is assuming a threatening dimension in Nigeria. While Nigeria has no reliable statistics which could show the extent and prevalence of the crime, media reportage and statement from law enforcement agency such as the police provides insight into the magnitude of the problem. Between January and May, 2020, Nigeria’s Inspector General of Police stated that the force arrested 799 suspects associated with 717 rape cases. Out of this figure, six hundred and thirty-one of these cases have been charged to court while 55 cases were still being investigated (
As a global concern, problems associated with rape have to do with how to prevent its occurrence or reduce it to its barest minimum and the challenge of low convictions of rapists [5]. These two problems of rape are exacerbated by the prevailing rape myths supporting attitudes. Kimberly and Fitzgerald [6] define rape supporting attitudes as beliefs and notions which tend to deny and justify male sexual aggression against women. Of course, this conception favours women and does not capture the interests of males who are also victims of rape from women. Even in Nigeria, the percentage of male victims captured by the media is small [4].
In relation to convictions, behaviours of the Criminal justice actors (police, lawyers and jurors) influence the outcomes of a rape case. Whitey [5] argues that if rape myths are reduced or neutralised, there is the possibility of getting more rape convictions. What this implies is that when CJS actors are influenced by rape myths, their judgement and reactions to rape reduces conviction rates and vice versa. This is true as Whitey [5] notes that such myths legitimises offending behaviour and inhibits women from relating experiences as rape. While not all rape cases get reported to the police, the few ones reported may also suffer attrition [7]. This attrition may be caused by the decision of the handling officer who is to determine how far the case can go, the possibility of securing a conviction, or insufficient evidence. Worse still, the police may decide what should be recorded into the crime record or simply treat what is reported as mere information or intelligence. While rape attrition has been a major cause of concern in the past three decades [8], Stanko and Williams [9] unpacks how context of reported rape could impact on its outcomes. They show how social believability vulnerabilities (mental ill-health, under 18 years, under the influence of drugs/alcohol at the time of rape, were former partners of assailants or mental issues) could affect the outcomes of the rape. In particular, victims with mental health issues may suffer their allegations not being framed as rape and their cases are not likely to result into conviction.
In South Africa, Rumney and van der Bijl [10] found that rape supporting culture exists and this is shared by CJS professionals. Where such rape supporting culture exists, victims of rape do not generally come out to report their victimisation. Indeed, Jewkes and Abrahams [11] describe South Africa has a climate tolerant of violence and rape. Rape is also a social problem in South Africa where significant law reforms have been made to arrest the menace. The reforms were thought as a way of protecting victims of rape. Indeed, South African Courts joins the condemnation of the legal system which fails to protect rape victims. Burt [12] did not absolve the complicity of parents, families and society in exerting pressure on males to discourage rape. Accordingly, Jewkes (2005) notes that males are permitted to do anything they can get away with while coercion is only queried if it affects victims of higher social status in the society. Wood et al. [13] also found that women are blamed for their victimisation. They are accused women straying beyond expected boundaries of female behaviour such as being intoxicated. This social attitude and beliefs also influence CJS response to rape and the eventual outcomes. Temkin and Krahé [14], p. 209 argue that social definition of rape narrows the understanding of rape by law enforcement agents. To them: “rape stereotypes affect the judgements made by individuals dealing with rape cases, for example as police officers, judges or members of a jury, and thereby shape the understanding of rape as it is represented and dealt with in the criminal justice system”. Consequent upon these attitudes, the CJS utilises stereotypical notions to ascertain if a woman has been raped or not. Certainly, these erroneous assumptions surrounding rape affect the way victims or rape are treated along the Criminal justice system corridor. Shelley et al. [15] contend that the highly gendered nature of law enforcement organisations may have influence the situation where jaundiced notions about males and females influence the norms and practices in the agency. It remains inconclusive in literature whether women officers are more likely to believe the stories of rape victims or whether they will be more hostile to them [16, 17].
Since its birthing by Cohen and Felson [18], routine activity theory (RAT) has been variously deployed to explain how time and space are important factors in criminal victimisation. Their basic idea was that the convergence in time and space of a motivated offender, suitable or attractive target in the absence of capable guardianship would result in criminal victimisation. According to Cohen and Felson [18], p. 589 “the lack of any one of these elements is sufficient to prevent the successful completion of a direct contact predatory crime”. In other words, no criminal victimisation will take place if there is a motivated offender and there is no attractive target and vice versa. We are also unlikely to have a criminal victimisation take place where there is capable guardianship and attractive target because the presence of capable guardianship will neutralise any victimisation instinct. This is rightly captured by Pratt and Turanovic [19], p. 2, when they averred that “one gets victimised if the three key elements converge, if any of the three are missing victimisation does not happen and the probability has little or nothing to do with it”. In deploying this theory to understand how selected cases of rape occurred in Nigeria, I argue that rapists are masters of the routines of their victims, sufficiently knowledgeable of when their attractive targets will be unprotected and more vulnerable for their sexual predation. It follows therefore that rapists’ understanding of the routines of their victims and when they will be more vulnerable to attack makes sexual violence of rape to be successful.
This paper adopts exploratory design and utilised secondary sources of data collection. Purposively, rape cases reported by the media during the COVID-19 lockdown in Nigeria formed the cases adopted for this study. During this lockdown, schools, offices and markets were shut down. While street crimes reduced, domestic violence and rape surged. Five cases of rape were selected for their uniqueness and the concern they generated both online and offline. They occurred between April 27 and June 6, 2020. They unveil different dimensions of victimisation and offenders’ use of space or mastery of routines of the victims and/or their guardians. We relied on the reported account of Nigerian national newspapers which covered the rape stories. In particular, The Punch, The Nation and the Vanguard newspapers provided account of relatives, parents and guardian of the victims on how the rape occurred. In analysing the data, I utilise the basic elements of routine activity theory: Motivated offender, attractive target and absence of capable guardianship.
Under this section, attempt is made to analyse the data concerning each of the five cases and situated within the analytical framework of the routine activities theory. While studies have been looking for the personality of the rapists, looking for how rape occurs is capable of unveiling how to keep attractive female/male targets safe from motivated sexual predators. Felson and Cohen had maintained that crime could still occur even without the traditional notion of criminogenic factor like economic deprivation. Indeed as noted by Felson and Boba [20], crime and victimisation feature in everyday life of leaving home and going to work. Just like properties can be victim of motivated offender attacks, rape victims also become objects of sexual predators. It means that the dispersal of capable guardian from suitable target could provide a loophole for the motivated offender lurking around to strike. This is why Cohen and Felson [18], p. 591 posits that “daily work activities separate many people from those they trust and the property they value”.
Everyday activity that takes one away from the protective custody of guardians to the waiting or monitoring hands of motivated offenders could include being alone at home, visiting ‘evil’ peers and selling on the streets around motivated offenders. Case 1 is the case of Jennifer which happened on April 27 when she was joined a male friend who had called him to meet him at a place where she would later be gang raped by those whom her sister said ‘she trusted’. She would later drink alcohol, lost self-guardianship to resist sexual assault and was gang raped. It follows therefore that the ‘gang’ had planned to remove their victims from the location where she could be saved from being raped to a location where all three elements of rape victimisation was sure. While we could analyse how ‘trust’ could make one vulnerable to being raped, not leaving and staying back when the other girls were leaving was itself a risky choice. Pratt and Turanovic [19] posits that people tend to self-select into the risky behavioural routines such as behaving in such a way that makes them vulnerable to attacks. This includes falling for the trick to drink alcohol, a tool to make her lose consciousness and self-guardianship. It shows how being at home or outside can both expose one to victimisation in the absence of capable guardianship. What this implies is that anyplace can be site for victimisation provided the elements of attractive targets, motivated offender and the absence of capable guardian converge to make rape victimisation a success.
A case of gang rape was reported in Kaduna state. The sister of the victim narrated what happened to the Punch reporter. “On April 27, 2020, one of the victim’s male friends called her to come and meet him somewhere. When she got there, she met two other girls and six boys. One of the boys had previously asked her for an intimate relationship and when it was time for the other two girls to leave, the victim also stood up to go, but one of the boys asked her not to leave yet that they wanted to talk to her on behalf of the young man asking her out. She trusted them and stayed back; they offered her alcohol, which she declined, but they coerced her into taking it after which she lost consciousness. Five of the boys raped her, while the sixth kept threatening his friends to stop or he would report them, but he never did. After they had raped her, the boys dropped her around 7 pm by the bridge close to the house and called her friends to come and get her, alleging that she had been sleeping since morning. As soon as she got home, she was taken to hospital, because she was unconscious and all necessary tests were conducted and the matter was reported at the Barnawa Police Station that same night. The case was transferred to the State Criminal Investigation and Intelligence Department and since then, the police have not arrested the three other boys or invite their parents to the station. The police are making no effort at all to arrest the suspects or question their parents. The police have been frustrating the case to the extent that the mother of the victim is already contemplating dropping the case. The parents of the two boys in custody are offering N15,000 each as damages for what their sons have done to the victim and the police have decided to release them on bail
Period of uncertainty or crisis could also provide opportunity for rape victimisation. Just like the case of Jennifer, Uwaila (see Case 2 narration) innocently moved away from home where she could have benefitted from the protective custody of relations who were at home during COVID-19 lockdown. However, her routine of going to the church to read had been mastered by her rapists. This is also made possible because the church did not have night guard to guide the church facility and to the victim, the church was a sanctuary where criminals ought not venture into but she was wrong. The rapists were sufficiently motivated by a woman who paid them money to get the blood of a lady for alleged ritual. From the narrations of the offenders after they were arrested, they positioned themselves to ensure that their operation was successful. They entered the church, initiated a conversation with their target, attacked her, raped her, cleaned her blood and escaped before they were later arrested. Certainly, the mastery of routine of the victim and the absence of capable guardianship within the precinct of the church made the motivated rapists successful with their victimisation.
Late Uwaila Vera Omozuwa was a 22-year old microbiology student of University of Benin in Edo state. Following the lockdown of higher institutions due to coronavirus 2019 (COVID-19), Uwa had to go back home to her family to continue to hold up while the COVID-19 pandemic is expected to reduce before returning to school. She was studious and a choir of the Church where she was raped and murdered. Due to the lockdown which brought many people home, Uwa had complained about the disturbance of family members to her reading because of their noise and sought to continue using the Church to read. This became a normal way to her. On May 27, she was met inside the church in the pool of her blood. She was raped, beaten and hit with fire extinguisher on her head. She would later die in the hospital. The church security officer had gone to collect the key to the church from its keeper when he was told someone was in the church already. The security officer was to alert them of the incident in the church. The police paraded her killers on August 26, 2020. They confessed to raping and killing Uwa since they understood her movement. They were paid one million naira to kill her by suspected woman ritualist to use white handkerchief to clean her blood. The Police stated that post-mortem showed she was raped. (Vanguard newspaper June 12,020: How 22-year old UNIBEN student was raped inside church, murdered. https://www.vanguardngr.com/2020/06/how-22-year-old-uniben-student-was-raped-in-church-murdered/)
Site of victimisation can be home or outside the home on the street. Pratt and Turanovic [19] posited that it is theoretical to assume that home is a safe location for victimisation. They argue that victimisation such as child abuse, domestic violence, intimate partner violence all occur within the home.
On June 1, 2020, 18-year old student of Federal College of Animal and Production Technology in Ibadan was raped and murdered for suspected ritual purpose. Her father narrated “I was not at home when the incident happened. The victim’s younger sister was not at home too; she went for Quaranic lessons, but when she returned home, she saw Barakat at the back of the house with deep cuts all over her body. She had been raped and killed. Somebody called me on phone that I should come home but he refused to tell me what happened. When I got home, I saw that my daughter had been raped and hacked to death.” The victims’ mother too was not at home while the incident happened. She was the only one at home in an isolated and bushy environment where the incident occurred
In the case of Barakat, the victim was home alone with no one around her. They also live in isolated place where help was far. The house was surrounded by bush. Understanding this terrain, the motivated offender would later attack her, raped her and killed her.
Case 4 presents another dimension to dangerous spaces where motivated offenders lurks and awaits attractive targets before they strike. For sexual predators, timing of attack is vital. What set the capable guardianship apart from the attractive target is the time the guardian is away from the attractive target. Therefore, leaving home to eke out a living on the streets becomes a risky routine which increases the susceptibility of the hawker to be attacked.
A 17-year old sachet and soft drinks hawker was attacked by three hoodlums around 7 pm and raped her. She was threatened with broken bottles and was with them for 45 minutes.
Timing of economic activity contributed to the victimisation. Selling at odd hour in the neighbourhood of anti-social elements presents opportunities for defilement since guardianship and visibility to poor.
The fifth case for our analysis is that which also happened during the lockdown of Lagos state which is the epicentre of Coronavirus 2019 (COVID-19) infections in Nigeria. Children and their parents were restricted to their residence except for those on essential services duty. Schools had started series of online classes to keep their pupils busy learning. The father was at home as a capable guardian, at least with potential to protect her daughter against attacks. However, that the rapists could attack their victim while the father (guardian) rushed to buy fuel for his daughter to continue online learning unpacks and lay credence to the important of routine activity in understanding sexual predation.
A 12-year old girl was defiled while playing alone in her compound. Her parents were not around when the masked men came in to defile her. Her mother narrated that ‘I went to the office and was called (on the phone) and told that my daughter was raped in our house. I learnt she was having her online class when suddenly, there was a power outage. My husband rushed out to get fuel at a filling station so that she could participate in the class seamlessly. Blessing (not her real name) told us that while she was in the compound, four masked men jumped into the house through the fence. They took her inside and took turns to have sex with her, leaving her with multiple injuries. Immediately I received the call, I became so mad. I headed for the hospital where my daughter was rushed to. When I got there, I was told she suffered ‘vaginal trauma’. The underneath of her clitoris was bruised and she had a deep tear that made her bleed severely, She could have passed out if not that her dad got back home early. She lost a lot of blood. The bleeding stopped after the tear was stitched; although, she is still experiencing very severe pain. I do not think we are secure anymore because it seems like we are being monitored. They perpetuated their evil within the few minutes it took my husband to buy fuel. They could not enter through the gate because of an ongoing construction at a building opposite ours. The site was crowded and that made them avoid entering through the front door. They scaled the fence. Some policemen followed us to the house and saw how the attackers scattered our things around
The rapists scaled the fence, avoided where crowd was and violated the underage before the father returned. This rape defilement follows this order: motivated offender, absence of capable guardian, attractive target attack and defilement and disappearance after the defilement. This finding aligns with the Cohen and Felson [18] who explained how dispersion for legitimate activities away from home could lead to the victimisation of valued object or material.
Maume [25] posited that inequality may contribute to rape indirectly through lifestyle. This partly explains the rape of the 12-year old where the father had to rush to buy fuel for generating power. It is assumed that if generating set were to be available without having to wait for a time to buy fuel, victimisation would not have been possible. This undoubtedly contributed to the victimisation since the guardian had to move away from the attractive target of the rapists, his daughter.
In terms of target suitability, Franklin and Menakar [26], p. 2 posited that individual variation in routine activities may enhance or diminish the chances that someone will be viewed as vulnerable and be selected as target. This is useful in explaining Jennifers’ exposure to sexual predatory gang who pulled her away from save zone to their territory. Scholars [27] underscore how women’s selective routine may heighten their victimisation by sexual predators. They list 1) increasing sexual vulnerability through target attractiveness and exposure to would-be perpetrators and 2) decreasing the capacity to avoid unwanted sexual contact by limiting self-guardianship. It follows therefore that self-guardianship is important regulate movement in and to dangerous places. Target suitability, according to Shwartz and Pitts [28] includes availability, vulnerability, intoxication, and friendship or relationship with men who use alcohol to extort sex. Jennifer’s intoxication reduced self-guardianship and paved way for rape. Studies have shown how being present at alcohol events impairs self-guardianship and increases target attractiveness and sexual assault [27]. According to Felson (1993), men would deploy physical force only when other methods fail. This may explain why they lured her to their comfortable space.
Understanding how rape victimisation occurs may be helpful in checking its future occurrence by simply increasing guardianship and neutralising distractions which may displace the guardian from protecting the vulnerable attractive targets. The five cases we examined showed how the mastery of routines by the rapists contributed to successful victimisation of their targets. Home is also not safe where predators are lurking around. Spontaneous behaviour like buying fuel could remove guardianship from a treasured human being who becomes victimised in the absence of the guardianship. It is important that attention is paid to issue of guardianship, self or social guardianship which would be active and capable of dislodging sexual predators from actualising rape victimisation. Mounting capable guardianship may be one of the possible ways of reducing rape victimisation at individual, family, communal and societal levels.
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