| | | | The melting temperatures of the primers are according to the formula 2(A+T) + 4(G+C), or according to the %GC method (values in parentheses).
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| | | | DNA extraction
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| | | | i) | PCR inhibitors were noted by the authors of this method (3) to be present in DNA samples prepared from whole MBV-infected postlartval Penaeus monodon when using the extraction method recommended by Wang et al. (42) for BP, which incorporates proteinase K. However, when hot phenol was used to extract the DNA, this inhibitory effect was removed.
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| | | | ii) | With the hot phenol method, the sample to be tested (postlarvae, shrimp hepatopancreas, faeces) are freeze-dried and ground to a powder in liquid nitrogen with a motor and pestle.
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| | | | iii) | Approximately 300 mg of the resulting material is added immediately to 400 µl of preheated (65°C) lysis buffer (100 mM Tris/HCl, 100 mM ethylene diamine tetra-acetic acid [EDTA], 1% sodium dodecyl sulfate, pH 8.0) and incubated at 65°C for 5-10 minutes.
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| | | | iv) | The resulting suspensison is coarsely homogenised by spot centrifugation and homogenisation with a microfuge tube pestle. Tris/HCl-buffered phenol, pH 8.0 (600 µl) is added and the mixture is incubated for 2 hours at 65°C with occasional inversion.
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| | | | v) | Following centrifugation at 12,000 g for 10 minutes at room temperature, the aqueous layer is transferred to a fresh microfuge tube and extracted twice with an equal volume of phenol/chloroform (1/1). Then, a total of 50 µl of the aqueous layer is transferred to a fresh microfuge tube containing 150 µl dilution buffer and extracted once more with an equal volume of phenol/chloroform (1/1) followed by a straight chloroform extraction.
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| | | | vi) | Ammonium acetate is added to the aqueous layer to a final concentration of 2.5 M, mixed briefly, and two volumes of -20°C ethanol are added with 1 µl of 20 mg/litre glycogen to precipate the DNA.
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| | | | vii) | DNA is precipitated by incubation at -20°C overnight or by incubation at -70°C for 1 hour.
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| | | | viii) | DNA is pelleted at 12,000 g for 15 minutes at 4°C. The resulting DNA pellet is rinsed twice, first with 500 µl 80% cold ethanol and centrifuged at 12000 g for 10 minutes at 4°C, followed by an identical rinse and centrifugation at room temperature.
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| | | | ix) | The final DNA pellet is dried in vacuo, resuspended in 100 µl dilution buffer (10 mM Tris/HCl, pH 8.0, 0.1 mM EDTA, pH 8.0) at room temperature overnight or at 37°C for 2 hours. Following spectrophotometric analysis, and prior to PCR, the DNA is diluted to 50 ng/µl in dilution buffer.
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| | | | Nested PCR method
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| | | | i) | Prior to PCR, the extracted total DNA is denatured in boiling water for 3 minutes followed by followed by quick chilling in ice-water.
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| | | | ii) | A total of 100 ng of extracted DNA is used as template.
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| | | | iii) | Each reaction tube contains 50 mM KCl, 10 mM Tris/HCl, pH 9, 0.1% Triton X-100, 0.2 mM of each dNTP, 1.5 mM MgCl2 , 0.25 µM of each MBV1.4F and MBV1.4R, 2.5 U of Taq, and made up to a final volume of 50 µl.
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| | | | iv) | The reaction mixes are overlaid with mineral oil (as necessary).
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| | | | v) | The conditions for the first round of amplification are: one cycle of 96°C for 5 minutes; 40 cycles of 94°C for 30 seconds, 65°C for 30 seconds, 72°C for 60 seconds; and one cycle of 72°C for 7 minutes.
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| | | | vi) | The second step of the nested PCR is accomplished with 0.5 µl of the primary PCR reaction used as template with the internal primers.
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| | | | vii) | The second round of amplification reaction contains 50 mM KCl, 10 mM Tris/HCl, pH 9.0, 0.1% Triton X-100, 1.5 mM MgCl2, 0.2 mM of each dNTP, 0.25 µM of each of the primers MBV1.4NF and MBV1.4NR, and 2.5 U of Taq, and made up to a final volume of 50 µl.
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| | | | viii) | The reaction mixes are overlaid with mineral oil (as necessary).
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| | | | ix) | The conditions for the second round of amplification are: one cycle of 96°C for 5 minutes; 35 cycles of 94°C for 30 seconds, 60°C for 30 seconds, 72°C for 60 seconds; and one cycle of 72°C for 7 minutes.
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| | | | x) | Demonstration of the PCR products (533 bp first step and 361 bp second step) is accomplished by adding 1 µl of gel-loading buffer (0.25% [w/v] bromophenol blue, 15% [w/v] Ficoll-type 400, 100 mM EDTA, pH 8.0) to 10 µl of each reaction mixture and electrophoresis through a 0.8% agarose gel in TAE buffer (40 mM Tris-acetate, 1 mM EDTA, pH 8.0) containing 0.5 g/litre ethidium bromide.
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| 2. | Diagnostic Methods for Confirmatory Tests
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| | Confirmation of infection by MBV may be accomplished with any of the methods listed in Section 1 (i.e. wet-mounts of hepatopancreas tissue squashes or of faecal strands, or by PCR). The other methods available for confirmatory diagnosis of MBV include: autofluorescence with phloxine, and routine histological methods (4-6, 19, 20, 23, 36).
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| | 2.1. | Autofluorescence method with phloxine stain
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| | | Another method for detecting MBV occlusion bodies is based on the fluorescence of phloxine-stained occlusion bodies (5, 20, 36). Aqueous 0.001% phloxine may be added to tissue squash preparations to make wet-mounts of hepatopancreas or faeces for direct examination. Histological sections stained with routine haematoxylin and eosin (H& E) containing 0.005% phloxine, are also suitable for this procedure. MBV occlusions in wet-mounts of tissue squashes, in faeces, or in histological sections fluoresce bright yellow-green against a pale green background under epi-fluorescence (barrier filter of 0-515 nm and a 490 nm exciter filter). Other objects in the tissues and insect baculovirus occlusion bodies do not fluoresce with this method. Hence, the method can provide a rapid and specific diagnosis.
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| | 2.2. | Histological methods
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| | | Histology may be used to provide a definitive diagnosis of MBV infection. Because 10% buffered formalin and other fixatives provide, at best, only fair fixation of the shrimp hepatopancreas (the principal target organ for MBV), the use of Davidson's fixative (containing 33% ethyl alcohol [95%], 20% formalin [approximately 37% formaldehyde], 11.5% glacial acetic acid and 33.5% distilled or tap water) is highly recommended for all routine histological studies of shrimp (4, 20). To obtain the best results, dead shrimp should not be used. Only live, moribund, or compromised shrimp should be selected for fixation and histological examination. Selected shrimp are killed by injection of fixative directly into the hepatopancreas; the cuticle over the cephalothorax and abdomen just lateral to the dorsal midline is opened with fine-pointed surgical scissors to enhance fixative penetration (the abdomen may be removed and discarded), the whole shrimp (or cephalothorax less the abdomen) is immersed in fixative for 24-48 hours, and then transferred to 70% ethyl alcohol for storage. After transfer to 70% ethyl alcohol, fixed specimens may be transported by wrapping in cloth or a paper towel saturated with 70% ethyl alcohol and packed in leak-proof plastic bags. To begin histological processing, fixed shrimp are 'cut-in' (see ref. 4 for a photographic guide to this procedure) to facilitate eventual sectioning of the hepatopancreas and midgut. After dehydration, the specimens are embedded in paraffin and sections of 5-7 µm thickness are cut. Routine histological stains such as Mayer-Bennett's or Harris H& E, Giemsa stains, and Gram tissue-staining methods may be used for the demonstration of MBV diagnostic spherical occlusion bodies in hepatopancreatocytes, gut epithelial cells, or gut lumen (5, 6, 10, 20, 24). Typically, MBV-infected hepatopancreatic (or occasionally midgut) cells will present markedly hypertrophied nuclei with single or, more often, multiple occlusion bodies, chromatin diminution and margination. Occlusion bodies may be stained bright red with H& E stains, and intensely, but variably, with Gram's tissue stains. Brown and Brenn's histological Gram stain, although not specific for baculovirus occlusion bodies, tends to stain occlusions more intensely (either red or purple, depending on section thickness, time of decolouration, etc.) than the surrounding tissue, aiding in demonstrating their presence in low-grade infections (19, 20, 23).
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| | 2.3. | Molecular methods
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| | | Nonradioactive DIG-labelled gene probes to MBV have been developed (20, 23, 26-28, 33). Gene probe and PCR methods may provide greater diagnostic sensitivity in detecting low-grade infections than do more traditional wet-mount or histological techniques. Furthermore, PCR methods (see Section 1.3.) have the added advantage of being applicable to nonlethal testing of faecal samples collected from valuable broodstock shrimp.
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| | | DIG-labelled DNA probes for representative strains of BP and MBV are commercially available as ShrimProbeTM kits from DiagXotics (Wilton, Connecticut, USA). The probes are labelled with a nonradioactive label, digoxigenin-11-dUTP (DIG). These probes only work well with the in-situ hybridisation method with histological sections because there are substances present in the hepatopancreas and faeces of shrimp that provide both false-positive and false-negative results with samples that are blotted directly and not extracted prior to probing.
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| | | . | 2.3.1. Dot-blot hybridisation procedure for MBV
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| | | | While specific DNA probes for MBV are available, their application to dot-blot hybridisation procedures is not recommended for most routine diagnostic applications. Pigments present in the hepatopancreas leave a coloured spot on the hybridisation membrane that can result in the masking of a positive test or in the false interpretation of a negative test. Likewise, bits of chitin (which nonspecifically bind DNA probes), pigments, and other materials present in the faecal sample may also result in false-positive or false-negative dot-blot hybridisation tests. Extraction of DNA from the hepatopancreas or faeces prior to blotting or the use of chemiluminescent or radioactively labelled probes may circumvent these problems, but the adequacy of other test methods (i.e. direct wet-mounts, histology, or PCR) has not indicated a need for the further refinement and application of the dot-blot method (20).
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| | | . | 2.3.2. In-situ hybridisation procedure
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| | | | The in-situ hybridisation protocol given in detail in Section 1.2. of Chapter 4.1.6. Infectious hypodermal and haematopoietic necrosis virus (IHHNV) uses the GeniusTM System developed by Boehringer Mannheim Biochemicals (now Roche Molecular Biochemicals) and was adapted from the Boehringer Mannheim's Nonradioactive In Situ Hybridization Application Manual. An additional step is required for the in-situ hybridisation test for MBV. Follow steps i-vi of Section 1.2., in-situ hybridisation procedure for IHHNV, in Chapter 4.1.6. For MBV substitute the following modifications to step vii before proceeding with steps viii-xvii as given for IHHNV:
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| | | | i) | (Modified step vii): Boil the DIG-labelled probe for 10 minutes and quench on ice; spin briefly in the cold (~4-10°C) using a refrigerated centrifuge or a chilled microcentrifuge) to bring all the liquid down to the base of the microcentrifuge tube; keep on ice. Dilute the probe to 50 ng/ml in prehybridisation solution and cover the tissue with 500 µl of the solution. Denature the double-stranded viral DNA in the tissue of the histological section by placing the slides on a 85°C heat block (or on aluminium foil that is placed over a boiling water bath) for 6-10 minutes. Quench the slides on ice for 5 minutes. Incubate the slides overnight at 42°C in a humid chamber. Drain the fluid on to blotting paper. During this incubation step, keep the wash buffers at 37°C to prewarm them.
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| | | | ii) | Proceed with steps viii-xvii as given for IHHNV.
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| | | | With DIG-labelled probes, accumulations of MBV viral DNA within infected cell nuclei, in cytoplasmic phagosomes, or in necrotic tissue debris are stained blue to a dark blue-black. Although they contain virus, occlusion bodies do not normally react with DIG-labelled DNA probes because the occlusion body protein crystalline matrix does not permit penetration of the probe (20).
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