Comparison of DNA quality in raw and reconstituted milk during sterilization.

Responses to milk sterilization are usually evaluated only in terms of physicochemical properties and microbial safety, thus undervaluing the importance of DNA quality in an authentication process by methods based on PCR. Because DNA is a heat-sensitive molecule, we hypothesized that the heating process may impair the detection or quantification of DNA in raw fresh milk (FM) or reconstituted milk (RM), and that differences in DNA quality might exist between FM and RM. We thus investigated the effects of sterilization on the quality of DNA extracted from FM or RM; differences in DNA quality between FM and RM were also evaluated. The quality of extracted DNA from FM or RM was assessed by the specific detection of FM or RM composition in goat milk mixtures using primers targeting the bovine 12S gene, as well as by monitoring DNA yield, purity, ratio of mitochondrial (mt) to nuclear (n) DNA, and the level of DNA degradation. Polymerase chain reaction readily detected both untreated and heat-treated FM or RM in cow-goat milk mixtures, and gave a good sensitivity threshold (0.1%) under all sterilization conditions. The DNA yield and mtDNA:nDNA ratio of FM and RM varied significantly during the sterilization process. These results demonstrated that the sterilization altered the quantification of DNA in FM or RM during sterilization, but DNA could still be readily detected in sterilized FM or RM by PCR. Furthermore, we noted significant differences in DNA integrity, yield, and mtDNA:nDNA ratio between FM and RM during sterilization, which may have potential as a means to distinguish FM and RM.

Development of a rapid mitochondrial DNA extraction method for species identification in milk and milk products.

Isolation of mitochondrial DNA (mtDNA) from milk offers an effective way to monitor aspects of quality control and traceability to ensure food safety. A few methods of DNA isolation from milk have been reported, but many of them are time consuming and expensive. Here, we report a rapid, simple, and efficient method of mtDNA extraction from raw and processed milk (pasteurized, retorted, and UHT milk) to generate substrate for analysis using any PCR analysis platform. Various techniques used for the separation of mitochondria were explored and combined with a sodium dodecyl sulfate method for mtDNA extraction from raw and processed milk. The optimized protocol supports the efficient amplification of mtDNA independent of sample origin and is sufficiently straightforward to allow its widespread adoption by industry.

Genotyping spring viraemia of carp virus and other piscine vesiculo-like viruses using reverse hybridisation.

A simple nylon membrane-based DNA macroarray was developed to genotype spring viraemia of carp virus (SVCV) and related viruses. Twenty-six viruses were genotyped using the array, and the results were confirmed by phylogenetic analysis of a 426 bp partial glycoprotein gene sequence. The array was not only capable of discriminating between the 4 main genogroups of cyprinid vesiculo-type viruses described previously, but also accurately sub-type the SVC viruses assigned to Genogroup I. The assay offers a practical solution for diagnostic laboratories that currently lack a sequencing capability to confirm the nature of PCR products generated in suspected SVCV cases.

A new, improved and generalizable approach for the analysis of biological data generated by -omic platforms.

The principles embodied by the Developmental Origins of Health and Disease (DOHaD) view of 'life history' trajectory are increasingly underpinned by biological data arising from molecular-based epigenomic and transcriptomic studies. Although a number of 'omic' platforms are now routinely and widely used in biology and medicine, data generation is frequently confounded by a frequency distribution in the measurement error (an inherent feature of the chemistry and physics of the measurement process), which adversely affect the accuracy of estimation and thus, the inference of relationships to other biological measures such as phenotype. Based on empirical derived data, we have previously derived a probability density function to capture such errors and thus improve the confidence of estimation and inference based on such data. Here we use published open source data sets to calculate parameter values relevant to the most widely used epigenomic and transcriptomic technologies Then by using our own data sets, we illustrate the benefits of this approach by specific application, to measurement of DNA methylation in this instance, in cases where levels of methylation at specific genomic sites represents either (1) a response variable or (2) an independent variable. Further, we extend this formulation to consideration of the 'bivariate' case, in which the co-dependency of methylation levels at two distinct genomic sites is tested for biological significance. These tools not only allow greater accuracy of measurement and improved confidence of functional inference, but in the case of epigenomic data at least, also reveal otherwise cryptic information.

Abnormal reorganization of preplate neurons and their associated extracellular matrix: an early manifestation of altered neocortical development in the reeler mutant mouse.

The formation of the distinct layers of the cerebral cortex begins when cortical plate neurons take up positions within the extracellular matrix (ECM)-rich preplate, dividing it into the marginal zone above and the subplate below. We have analyzed this process in the reeler mutant mouse, in which cortical lamination is severely disrupted. The recent observation that the product of the reeler gene is an ECM-like protein that is expressed by cells of the marginal zone indicates a critical role for ECM in cortical lamination. We have found that preplate cells in normal cortex that are tagged during their terminal division with bromodeoxyuridine (BrdU) are closely associated with chondroitin sulfate proteoglycans (CSPGs), which were identified by immunolabeling; this association is maintained in the marginal zone and subplate after the preplate is divided by cortical plate formation. Cortical plate cells do not aggregate within the preplate in reeler; instead, preplate cells remain as an undivided superficial layer containing abundant CSPGs, and cortical plate neurons accumulate below them. These findings indicate that preplate cells are responsible for the formation of a localized ECM, because the association of CSPGs with preplate cells is maintained even when these cells are in abnormal positions. The failure of cortical plate neurons to aggregate within the framework of the preplate and its associated ECM and to divide it is one of the earliest structural abnormalities detectable in reeler cortex, suggesting that this step is important for the subsequent formation of cortical layers.

Developmental expression of keratan sulfate-like immunoreactivity distinguishes thalamic nuclei and cortical domains.

Proteoglycans influence axonal outgrowth in several experimental paradigms, and their distribution during development suggests a role in axon guidance. We have used a monoclonal antibody, 5D4, that recognizes an epitope on sulfated keratans (KS), to define the distribution of keratan sulfate proteoglycans (KSPGs) in the developing thalamus and cortex of the rat. During development, 5D4 immunolabeling is present on thalamic axons as they grow through the internal capsule and subplate but is not present in the adjacent pathway for cortical efferent axons. Individual thalamic nuclei differ markedly in their expression of KSPGs; these distinctions persist throughout the period of developmentally regulated expression. Major cortical domains also differ in their expression of KSPGs, which are expressed throughout medial (cingulate and retrosplenial) cortex well before neocortex. Immunolabeling for KSPGs diminishes 2 weeks after birth; in the adult it is associated with small glia. The 5D4 epitope is present on several KSPGs (320, 220, and 160 kD) on Western blots during development but only in a broad 200-kD band in adult brain. Immunolabeling is degraded on sections and Western blots by keratanase II but not by keratanase I or chondroitinase ABC, confirming that the antibody recognizes KS. Bands identified by 5D4 on Western blots differ from those identified by antibodies to known KSPGs (aggrecan, claustrin, SV2, ABAKAN, phosphacan-KS), indicating that 5D4 is labeling KSPGs not previously described in the brain. The selective expression of KSPGs during development suggests that they may be a part of the molecular identity of thalamic nuclei and cortical domains that defines their connectivity.

Chondroitin sulfate proteoglycans in the developing cerebral cortex: the distribution of neurocan distinguishes forming afferent and efferent axonal pathways.

The first thalamocortical axons to arrive in the developing cerebral cortex traverse a pathway that is separate from the adjacent intracortical pathway for early efferents, suggesting that different molecular signals guide their growth. We previously demonstrated that the intracortical pathway for thalamic axons is centered on the subplate (Bicknese et al. [1994] J. Neurosci. 14:3500-3510), which is rich in chondroitin sulfate proteoglycans (CSPGs; Sheppard et al. [1991] J. Neurosci. 11:3928-3942), whereas efferent axons cross the subplate to exit in a zone containing much less CSPG. To define the molecular composition of the subplate further, we used antibodies against CSPG core proteins and chondroitin sulfate disaccharides in an immunohistochemical analysis of their distribution in the developing neocortex of the rat. Immunolabeling for neurocan, a central nervous system-specific CSPG (Rauch et al. [1992] J. Biol. Chem. 267:19537-19547), and for chondroitin 6-sulfate and unsulfated chondroitin becomes prominent in the subplate before the arrival of thalamic afferents. Immunolabeling is initially sparse in the cortical plate but appears later in maturing cortical layers. A postnatal decline in immunolabeling occurs uniformly for most proteoglycans, but, in the somatosensory cortex, labeling for neurocan, phosphacan, and chondroitin 4- and 6-sulfate declines in the centers of the whisker barrels before the walls. In contrast to neurocan, immunolabeling for other proteoglycans is either uniformly distributed (syndecan-1, N-syndecan, 5F3, phosphacan, chondroitin 4-sulfate), restricted to axons (PGM1), distributed exclusively on nonneuronal elements (2D6, NG2, and CD44), or undetectable (9.2.27, aggrecan, decorin). Thus, neurocan is a candidate molecule for delineating the intracortical pathway of thalamocortical axons and distinguishing it from that of cortical efferents.

Immune destruction of rabbit corneal cells infected with herpes simplex virus: lymphocyte reactivity by antibody-dependent cellular cytotoxicity.

Continuous rabbit cornea cells and cells grown from the stromal layer of corneas excised from New Zealand white rabbits were infected with herpes simplex virus (HSV) strain RE and examined for cytolysis (51Cr release) by antibody-dependent cellular cytotoxicity (ADCC). These sources of lymphocytes from normal animals were used as effector cells: blood, spleen, and lymph nodes. Specific activity was observed in over 75% of rabbits with all three effector cell types, using immune serum from a rabbit a 21 days after infection. Activity was generally weak (less than 30% specific 51Cr release) and was abolished by dilutions of antibody 1:1000 or greater. Effector cells were not active when nonimmune serum was substituted for immune serum. Peritoneal exudate macrophages used as controls exhibited higher levels of release and were active with antibody diluted greater than 1:1000. HSV antibody reactive in ADCC appeared 7 days after intrastromal injection of infectious virus. Lymphocyte ADCC activity obtained from draining lymph nodes of infected animals was similar to that obtained with normal animals. Results indicate a weakly active lymphocyte effector-cell system in normal and infected rabbits.

Extracellular matrix in early cortical development.

Studies of the distribution and production of ECM components during development of the cerebral cortex have suggested several hypotheses regarding their functional role. In the earliest stages of cortical development, fibronectin is produced by cells in the ventricular zone throughout the telencephalic vesicle, where it may serve as a part of the local environment that supports cell division and determines cell fate. Fibronectin is also distributed along radial glial processes. It is closely associated with preplate neurons, as are chondroitin sulfate proteoglycans and several other ECM components. This association continues as preplate cells are divided into the marginal zone and subplate by the invasion of cortical plate neurons, suggesting that ECM, preplate cells and radial glia serve as a scaffold for cortical plate formation. Fibronectin is also produced by migrating neurons, but only by those moving into specific cortical domains, suggesting that it may help neurons destined for specific targets discriminate between adjacent glial guides. A recently defined ECM-like protein, reelin, is absent or abnormal in the reeler mutant mouse in which cortical neurons are severely malpositioned. Reelin is produced by marginal zone cells and is therefore appropriately located to serve as a stop signal for migrating neurons. Axons leaving the cortical plate cross the CSPG-rich subplate, then turn to follow a path containing much less CSPG. In contrast, the cortical trajectory of thalamic axons is centered on the subplate, indicating that CSPGs in the subplate are not a barrier to axon outgrowth and may instead be serving as guidance cues that distinguish afferent from efferent pathways. Neurocan, a CNS-specific CSPG with many molecular features that indicate roles in cell-cell and cell-substrate interactions, is the only CSPG defined to date whose distribution supports a role in distinguishing afferent from efferent pathways.

Thy-1 expression in the retinotectal system of the chick.

Previous investigations into the occurrence of Thy-1 in the chick retina have not clearly defined when the antigen first appears and have not adequately described its expression during the relatively early phases of retinal ontogeny. We have investigated these issues, using improved immunohistochemical procedures and show that Thy-1 is associated with the retinal ganglion cells from the time they begin to differentiate by extending their axonal projections. In addition, we have found that its expression reflects the growth of the optic fibre layer and the elaboration of the ganglion cell dendritic processes into the inner plexiform layer. For the first time we describe the appearance and the developmental expression of Thy-1 in the chick tectum. We have found that Thy-1 is associated with retinal axons from the time of their arrival at the tectum and that its expression reflects the elaboration of the stratum opticum. Within the tectum proper Thy-1 appears first in 3 distinct layers all of which are plexiform in nature. By the time that tectal histogenesis is essentially complete the antigen is expressed by all the layers of the tectum. The implications of these findings are discussed in terms of the development of the individual tissues and with respect to the elaboration of the retinotectal pathway.

The developmental appearance of Thy-1 in the avian cerebellum.

The cellular localization of the Thy-1 antigen during development of the chick cerebellum has been investigated using a monoclonal antibody SB1-20.11. Improved cellular morphology and retention of both membrane and intracellular antigenicity was achieved by the immunohistochemical labelling of polyester wax sections using an indirect peroxidase visualization protocol. A parallel histological investigation was carried out using a modified silver staining procedure based on that of Bodian. Immunoreactivity was found throughout development in the soma and dendritic tree of the Purkinje cell, in the internal granular layer, white matter and elements of the deep cerebellar nuclei. The antigen's expression closely correlates to the morphological maturation of Purkinje cell population. Furthermore, it appears to reflect the formation of glomeruli and the basket cell interaction with the Purkinje cell. An association of Thy-1 with climbing fibres, as reported previously in rodent species, cannot be unambiguously shown in the chick because of the high levels of Thy-1 expressed throughout development on the Purkinje cell dendrites in the molecular layer. The spatial and temporal pattern of expression in the chick cerebellum suggests that Thy-1 contributes to the definition of synaptic fields.

Neural membrane glycoproteins associated with chicken Thy-1: an anti-idiotypic antibody study.

In order to investigate the possible binding of Thy-1 to other neuronal cell surface proteins, anti-idiotypic antibodies were raised using a panel of anti-Thy-1 monoclonal antibodies. Anti-idiotypic antibodies were selected for their ability to bind to day-old chick brain membrane components in enzyme-linked immunosorbent assays (ELISA), and to bind to membrane glycoproteins as determined by Western transfer immunoblotting assays. The 5 monoclonal anti-idiotypic antibodies bind to a membrane glycoprotein component of 70 kDa, and one of the antibodies also binds to 3 higher molecular weight components of 160 kDa, 120 kDa and 90 kDa. These antibodies bind to areas of the chicken cerebellum known to be rich in Thy-1. It is postulated that these molecules are associated with Thy-1, and that the role of Thy-1 on the neuronal cell surface, may be to form complexes with, and/or to stabilise these higher molecular weight glycoproteins during synaptic development.

Characterisation of a novel glycoprotein (AvGp50) in the avian nervous system, with a monoclonal antibody.

A size fractionated lentil lectin-positive fraction derived from a deoxycholate extract of 1-day-old chick forebrain membranes was used to generate a series of monoclonal antibodies (Mabs) against neural antigens. One of these, MabSA1.7 recognises a glycoprotein which is enriched in synaptic plasma membranes, designated AvGp50. Polyacrylamide gel electrophoresis and Western blots show that AvGp50 is comprised of at least two glycoforms, with M(r)s of 53 kDa and 49 kDa respectively. AvGp50 is nervous system specific and most abundantly expressed in the forebrain, tecta and cerebellum where its pattern of expression is developmentally regulated. Immunohistochemical data localises AvGp50 to regions characterised by highly concentrated synapses, in particular, the molecular and granule cell layers of the cerebellum and in the inner and outer plexiform layers in the retina. Solubilization of the protein with the detergent Triton X-100 shows that AvGp50 is predominantly a cytoskeletally associated glycoprotein. However, when a synaptic plasma membrane fraction was treated with Triton X-114, AvGp50 partitioned into the detergent phase. Digestion of the protein with N-glycanase cleaved five N-linked carbohydrate side chains and reduced the molecular weight to approximately 34 and 31 kDa. Removal of the carbohydrate side chains led to an almost complete loss of recognition of the 34 kDa glycoform by the MabSA1.7, suggesting that the monoclonal antibody recognises a carbohydrate rather than peptide epitope.

Thy-1 antigen is specific to ganglion cells in chicks.

The cellular localization of Thy-1 in the chick retina was investigated by selectively destroying certain populations of neurons with toxins. In control retinae four weeks after intravitreal injection of vehicle, there was strong immunoreactivity for Thy-1 in the nerve fibre layer, ganglion cell layer and inner plexiform layer. By contrast, 4 weeks after intraocular injection with 1.25 nmol of colchicine, virtually all ganglion cells had been destroyed, but most amacrine cells remained. Very little Thy-1 immunoreactivity was evident in these retinae. Four weeks after intraocular injection of 2 mumol of N-methyl-D-aspartic acid (NMDA), a large proportion of amacrine cells had been destroyed, but most ganglion cells remained. In these retinae Thy-1 immunoreactivity was present in the nerve fibre, ganglion cell and inner plexiform layers, in the latter with greater intensity than in controls. We conclude that in chicks the Thy-1 antigen is principally, if not exclusively restricted to ganglion cells.

Antibody mediated destruction of keratocytes infected with herpes simplex virus.

The ability of complement-dependent antibody to mediate destruction of rabbit corneal cells infected with the RE and KOS strains of HSV-1 was examined. Three sources of target cells were used: BHK-21, a monitor of surface antigen expression and cell lysis; SIRC, a continuous cell line of rabbit corneal origin; stromal keratocytes, grown from the middle layer of excised rabbit corneas. Rabbits were infected intrastromally with the RE strain, which causes a high incidence of stromal keratitis, and sacrificed at designated times. Results showed that all three cell types, infected with either HSV strain, expressed surface antigens and were susceptible to lysis by antibody produced during the course of stromal disease. 51Cr-release assays showed that cytolytic antibody appeared as early as 5 days postinfection and reached maximum by day 14-20. Findings suggest a direct relationship between the in vitro demonstration of complement dependent cytolysis of infected stromal cells and the disease process in experimental animals.

Nucleotide sequence analysis of the glycoprotein gene of putative spring viraemia of carp virus and pike fry rhabdovirus isolates reveals four genogroups.

RT-PCR methods have been applied to the detection and sequencing of the glycoprotein gene of putative spring viraemia of carp viruses (SVCV) and pike fry rhabdoviruses (PFRV), including isolates from tench, grass carp, roach, bream and false harlequin, sheatfish and orfe. Phylogenetic analysis of a 550 nucleotide (nt) region of the glycoprotein gene identified 4 groups, I to IV. Significantly, the majority of viruses previously identified as PFRV formed a distinct cluster (Genogroup IV) which shared <80% nucleotide identity with the PFRV reference strain (Genogroup III). The similarity between another PFRV-like virus isolated from grass carp and representatives of Genogroups III and IV was also <80%, indicating that this virus belonged to a third group (Genogroup II). All of the putative SVC viruses were assigned to a 4th group (Genogroup I), sharing <61% nucleotide identity with viruses in Genogroups II to IV.

The application of a model of glucose and insulin dynamics to explain an observed effect of leptin administration in reversal of developmental programming.

A dynamical model describing the glucose-insulin physiological system was applied to an experiment on the administration of the adipokine leptin between neonatal days 3 and 13 to rats whose dams were subject to different levels of nutrition during gestation. The effect of leptin treatment on the glucose-insulin equilibrium point and on the levels of other associated metabolites showed a significant change in direction that depended on the level of prenatal nutrition. Leptin has been shown to affect two factors that affect the equilibrium levels of glucose and insulin, gluconeogenesis and insulin sensitivity. Each effect is described by a parameter in the dynamical model. Mathematical analysis shows that changes in these parameters in the manner promoted by leptin would indeed increase or decrease the glucose-insulin equilibria depending on their initial equilibrium levels which might be induced by the level of prenatal nutrition. This analysis explains the results of the leptin experiment in the context of the dynamics of the glucocorticoid system. It also proposes a physiological mechanism for the expression of plasticity in the organism based on the status of the glucose and insulin equilibria.

Activity of rabbit monocytes, macrophages, and neutrophils in antibody-dependent cellular cytotoxicity of herpes simplex virus-infected corneal cells.

Rabbit phagocytes were examined for their ability to kill target cells infected with herpes simplex virus by antibody-dependent cellular cytotoxicity. Two sources of rabbit corneal cells were used as targets: Staaten Seruminstitut Rabbit Cornea (a continuous cell line) and stromal keratocytes from the middle layer of corneas excised from New Zealand white rabbits. Peritoneal exudate and alveolar macrophages were found to be the most active effector cells, followed by blood neutrophils and monocytes. Peritoneal exudate and alveolar macrophages killed target cells with dilutions of antibody as high as 1:10,000. Monocyte antibody-dependent cellular cytotoxicity activity was absent in over one-third of the rabbits tested and was only weakly active in positive rabbits. In vitro aging of monocytes did not enhance activity. Antibody reactive with peritoneal exudate macrophages, alveolar macrophages, and blood neutrophil effector cells appeared 7 days after intracorneal injection of infectious herpes simplex virus. Results of these studies show that in vitro assays with a complete rabbit system (effectors cells, antibody, and target cells) can be developed to monitor herpetic disease and suggest an active role for rabbit phagocytes in cytotoxicity of herpes simplex virus-infected cells.

Changes in the distribution of extracellular matrix components accompany early morphogenetic events of mammalian cortical development.

As a step in defining the molecular environment for development of the mammalian cerebral cortex, we have used immunohistochemistry to analyze the distribution and remodeling of three major extracellular matrix (ECM) components, fibronectin, chondroitin sulfate proteoglycan (CSPG), and tenascin, during embryonic and early postnatal stages in the mouse. Fibronectin and CSPG are distributed throughout the proliferative zone that initially comprises the thin wall of the telencephalic vesicle, but their distribution changes as newly generated cells form the preplate just beneath the pia. Immunolabeling for CSPG becomes most prominent in the preplate, and fibronectin becomes restricted to that layer. Just after this change occurs, processes of preplate neurons, visualized with antibodies to neurofilaments, become evident within the matrix-rich preplate zone. The association of fibronectin and CSPG with preplate cells persists as cortical plate neurons divide the preplate; both ECM components are now most prominent in the marginal zone and subplate, the layers above and below the cortical plate that are preplate derived. Within the preplate and its derivatives, immunolabeling of fibronectin is punctate and closely associated with radial glial processes, while labeling of CSPG is more intense and diffuse. Labeling of fibronectin and CSPG declines rapidly as the cortical plate begins to differentiate into cortex; labeling for tenascin first appears at this stage in the most mature layers, the marginal zone and subplate, then gradually becomes widespread throughout all of cortex and subcortical white matter. In early postnatal life, tenascin is eliminated from the hollows of the vibrissal barrels in the somatosensory region; it then declines rapidly throughout cortex. The association of both fibronectin and CSPG with preplate cells and the distribution of fibronectin along radial glia during early cortical development suggest that one or both of these transient cell types might produce specific ECM components or induce their local deposition. The spatial and temporal distribution of fibronectin and CSPG suggests a role in defining a destination for migrating neurons that form the cortical plate and in delineating the pathway for early axonal extension. In contrast, the relatively late appearance of tenascin correlates best with the formation of astrocytes and their processes rather than with the establishment of cortical layers or major axonal pathways. These events are well underway before labeling of tenascin is evident.