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A large variety of methods has been proposed in the literature for microarray data analysis. The aim of this paper was to present techniques used by the EADGENE (European Animal Disease Genomics Network of Excellence) WP1.4 participants for data quality control, normalisation and statistical methods for the detection of differentially expressed genes in order to provide some more general data analysis guidelines. All the workshop participants were given a real data set obtained in an EADGENE funded microarray study looking at the gene expression changes following artificial infection with two different mastitis causing bacteria: Escherichia coli and Staphylococcus aureus. It was reassuring to see that most of the teams found the same main biological results. In fact, most of the differentially expressed genes were found for infection by E. coli between uninfected and 24 h challenged udder quarters. Very little transcriptional variation was observed for the bacteria S. aureus. Lists of differentially expressed genes found by the different research teams were, however, quite dependent on the method used, especially concerning the data quality control step. These analyses also emphasised a biological problem of cross-talk between infected and uninfected quarters which will have to be dealt with for further microarray studies

The aim of this paper was to describe, and when possible compare, the multivariate methods used by the participants in the EADGENE WP1.4 workshop. The first approach was for class discovery and class prediction using evidence from the data at hand. Several teams used hierarchical clustering (HC) or principal component analysis (PCA) to identify groups of differentially expressed genes with a similar expression pattern over time points and infective agent (E. coli or S. aureus). The main result from these analyses was that HC and PCA were able to separate tissue samples taken at 24 h following E. coli infection from the other samples. The second approach identified groups of differentially co-expressed genes, by identifying clusters of genes highly correlated when animals were infected with E. coli but not correlated more than expected by chance when the infective pathogen was S. aureus. The third approach looked at differential expression of predefined gene sets. Gene sets were defined based on information retrieved from biological databases such as Gene Ontology. Based on these annotation sources the teams used either the GlobalTest or the Fisher exact test to identify differentially expressed gene sets. The main result from these analyses was that gene sets involved in immune defence responses were differentially expressed.

Objective. To examine the effects of intraarticular induction of interleukin-1 (IL-1) expression in adult mice. Methods. We used somatic mosaic analysis in a novel transgenic mouse with an inducible IL-1 transcription unit. Transgene activation was induced by Cre recombinase in the temporomandibular joints (TMJs) of adult transgenic mice (conditional knockin model). The effects of intraarticular IL-1 induction were subsequently evaluated at the cellular, histopathologic, and behavioral levels. Results. We developed transgenic mice capable of germline transmission of a dormant transcription unit consisting of the mature form of human IL-1 as well as the reporter gene -galactosidase driven by the rat procollagen 1A1 promoter. Transgene activation by a feline immunodeficiency virus Cre vector resulted in histopathologic changes, including articular surface fibrillations, cartilage remodeling, and chondrocyte cloning. We also demonstrated up-regulation of genes implicated in arthritis (cyclooxygenase 2, IL-6, matrix metalloproteinase 9). There was a lack of inflammatory cells in these joints. Behavioral changes, including increased orofacial grooming and decreased resistance to mouth opening, were used as measures of nociception and joint dysfunction, respectively. The significant increase in expression of the pain-related neurotransmitter calcitonin gene-related peptide (CGRP) in the sensory ganglia as well as the auxiliary protein CGRP receptor component protein of the calcitonin-like receptor in the brainstem further substantiated the induction of pain. Conclusion. Induction of IL-1 expression in the TMJs of adult mice led to pathologic development, dysfunction, and related pain in the joints. The somatic mosaic model presented herein may prove useful in the preclinical evaluation of existing and new treatments for the management of joint pathologic changes and pain, such as in osteoarthritis.

Brain inflammation in GM2 gangliosidosis has been recently realized as a key factor in disease development. The aim of this study was to investigate the effects of a FIV beta-hexosaminidase vector in the brain of HexB-deficient (Sandhoff disease) mice following intraperitoneal administration to pups of neonatal age. Since brain inflammation, lysosomal storage and neuromuscular dysfunction are characteristics of HexB deficiency, these parameters were employed as experimental outcomes in our study. The ability of the lentiviral vector FIV(HEX) to infect murine cells was initially demonstrated with success in normal mouse fibroblasts and human Tay-Sachs cells in vitro. Furthermore, systemic transfer of FIV(HEX) to P2 HexB-/- knockout pups lead to transduction of peripheral and central nervous system tissues. Specifically, beta-hexosaminidase expressing cells were immunolocalized in periventricular areas of the cerebrum as well as in the cerebellar cortex. FIV(HEX) neonatal treatment resulted in reduction of GM2 storage along with attenuation of the brain inflammation and amelioration of the attendant neuromuscular deterioration. In conclusion, these results demonstrate the effective transfer of a beta-hexosaminidase lentiviral vector to the brain of Sandhoff mice and resolution of the GM2 gangliosidosis after neonatal intraperitoneal administration.

Gene therapy is emerging as a novel treatment method for the management of temporomandibular joint disorders. The aim of this investigation was to study the effects of lentiviral vectors on the temporomandibular joint. Consequently, we injected into the articular joint space a defective feline immunodeficiency virus capable of infecting dividing as well as terminally differentiated cells with the reporter gene lacZ, the expression of which was studied by means of PCR, X-gal histochemistry, and β-galactosidase immunocytochemistry. Our results showed successful transduction of hard and soft tissues of the temporomandibular joint. Interestingly, a subset of primary sensory neurons of the ipsilateral trigeminal ganglion also stained positive for the reporter gene, presumably following uptake of the lentiviral vector by peripheral nerve fibers and retrograde transport to the nucleus. These findings suggest that lentiviral vectors can potentially serve as a platform for the transfer of anti-nociceptive genes for the management of temporomandibular joint pain.

Sucessful intestinal adaptation after massive enterectomy is dependent on increased efficiency of nutrient transport. However, midgut resection (MGR) in rabbits induces an initial decrease in sodium-dependent brush border neutral amino acid transport, whereas parenteral epidermal growth factor (EGF) and growth hormone (GH) reverse this downregulation. We investigated intestinal amino acid transporter B0 (ATB0) and oligopeptide transporter 1 (PEPT 1) mRNA expression after resection and in response to EGF and/or GH.Rabbits underwent anesthesia alone (control) or proximal, midgut, and distal resections. Full-thickness intestine was harvested from all groups on postoperative day (POD) 7, and on POD 14 from control and MGR rabbits. A second group of MGR rabbits received EGF and/or GH for 7 days, beginning 7 days after resection. ATB0 and PEPT 1 mRNA levels were determined by Northern blot analysis.In control animals, ileal ATB0 mRNA abundance was three times higher than jejunal mRNA, whereas PEPT 1 mRNA expression was similar. By 7 and 14 days after MGR, jejunal ATB0 mRNA abundance was decreased by 50% vs control jejunum. A 50% decrease in jejunal PEPT 1 message was delayed until 14 days after MGR. Treatment with EGF plus GH did not alter ATB0 mRNA expression but doubled PEPT 1 mRNA in the jejunum.The site of resection, time postresection, and growth factors treatment differentially influence ATB0 and PEPT 1 mRNA expression. Enhanced sodium-dependent brush border neutral amino acid transport with GH plus EGF administration is independent of increased ATB0 mRNA expression in rabbit small intestine after enterectomy.

The compensatory hypertrophy that develops after massive enterectomy is rarely adequate to prevent the development of short bowel syndrome. Trophic hormones such as epidermal growth factor (EGF) and neurotensin (NT) may be useful in improving and accelerating this adaptive response. This study delineates the effects of NT and EGF on remnant small bowel at the microvillus cellular level, which is the prime determinant of surface area. New Zealand white rabbits (2 kg) underwent midgut transection (sham) or 70% jejunoileal resection. Alzet pumps containing saline solution (control), EGF (1.5 microg /kg/hr), or NT (900 microg/kg/day) were implanted in resected animals after which they underwent 1 week of infusion. A second group of EGF animals was killed 2 weeks after infusion completion to assess delayed effects (EGF-delayed). Proximal jejunum was fixed for light and electron microscopy; villus and microvillus parameters were read in a blinded fashion. EGF (2.17+/-0.05 microm), EGF-delayed (2.26+/-1.5 microm, and NT (1.96+/-0.02 microm) animals had significantly increased microvillus heights compared to the control group (1.49+/-0.04 microm). Calculated brush-border surface areas were increased in a similar fashion. EGF and NT failed to elicit increases in jejunal gross villus heights. EGF and NT induce enterocyte microvillus hypertrophy and increase absorptive surface area in remnant bowel after massive enterectomy. In addition, the trophic effects of EGF persist after cessation of infusion. These peptides may be useful in accelerating small bowel adaption and preventing the development of short gut syndrome.

Background. The use of enteral nutrition in patients with nonocclusive splanchnic hypoperfusion is controversial. This study aims to quantitate enterocyte nutrient transport and correlate function with morphology during intestinal ischemia. Methods: New Zealand White rabbits were randomized to control (celiotomy only) 60-minute infrarenal aortic clamp (IRC) or 60-minute supraceliac aortic clamp (SCC). Small intestinal brush border membrane vesicles (BBMVs) were prepared by magnesium precipitation and serial differential centrifugation. Sodium-dependent uptake of glucose, glutamine, alanine, leucine, and arginine into BBMVs was quantitated by rapid mixing and filtration. Histologic examination of the intestine was performed by a pathologist blinded to groups. Data are reported as mean values ± SEM, with significance determined by analysis of variance at p

A combination of epidermal growth factor (EGF) and human growth hormone (hGH) after massive enterectomy induces a 400% increase in arginine transport in the remnant distal small intestine. The kinetic mechanism(s) responsible for enhanced arginine transport under these conditions is unknown.New Zealand White rabbits underwent 70% midjejunoileal resection. After a 1-week recovery period, animals received hGH (0.2 mg/kg/d IM), EGF (1.5 microg/kg/h SC), hGH + EGF, or vehicle (equal volume) for 7 days. Transport of tritiated arginine into brush border membrane vesicles prepared from distal remnant small intestinal mucosa was quantified in the presence and absence of a sodium gradient over a range of arginine concentrations (25 to 5000 micromol/L).Eadie-Hofstee transformation of the kinetic data demonstrates two sodium-dependent arginine transport systems, comprising a high-capacity, low-affinity system and a low-capacity, high-affinity system. A combination of EGF and hGH significantly upregulates both the high-capacity (685%) and low-capacity (350%) maximum transport velocity (Vmax). Additionally, EGF alone significantly upregulates Vmax by 200% in the low-capacity system. There were no significant changes in transport affinity (Km) in either system.There are two quiescent sodium-dependent arginine transport systems in the distal small intestine. A combination of EGF and hGH after massive enterectomy increase arginine transport by Vmax upregulation in both the high-capacity/low-affinity and low-capacity/high-affinity systems.

Background. After massive enterectomy (ME), remnant intestine undergoes compensatory adaptation. Epidermal growth factor (EGF) and human growth hormone (hGH) have each been shown to enhance total length small intestine nutrient transport after ME. This study aims to determine the differential effects of EGF and hGH on proximal and distal small intestinal remnants after ME. Methods. New Zealand white rabbits underwent 70% mid-jejunoileal resection. After 1 week, animals received hGH (0.2 mg/kg/day), EGF (1.5 μg/kg/hr), hGH + EGF, or vehicle (equal volume) for 7 days. Sodium-dependent uptake of glucose, glutamine, alanine, leucine, and arginine into brush border membrane vesicles was quantitated. Serum insulin-like growth factor-I concentrations as well as proximal and distal villus and microvillus heights were measured. IGF binding protein-3 and -4 mRNA expression was determined in full-thickness proximal and distal gut remnants. Results. Concomitant hGH and EGF treatment up-regulates glucose (100%), glutamine (80%), and leucine (60%) transport in the proximal remnant; alanine (150%) and arginine (400%) transport in the distal remnant; and microvillus height (25% to 35%) both proximally and distally. Serum IGF-I levels and gross villus heights were not different among groups. Conclusions. Co-infusion of hGH and EGF accelerates intestinal adaptation after ME in an additive, nutrient-dependent, and site-specific fashion via enhanced nutrient transport as well as microvillus hypertrophy.

Background: After massive enterectomy, remnant intestine undergoes compensatory adaptation. A combination of human growth hormone (hGH) and a glutamine-enriched modified diet induces further adaptation in patients with short bowel syndrome (SBS) on long-term total parenteral nutrition. The specific actions of each component, however, are not well-defined. Methods: New Zealand White rabbits were randomized to control, sham operation, or SBS (70% midjejunoileal resection) groups and treated with either hGH or saline. Sodium-dependent uptake of glucose, glutamine, alanine, leucine, and arginine into brush border membrane vesicles was quantitated. Serum insulin-like growth factor-I (IGF-I) levels were determined by immunoradiometric assay. Mucosal mRNA expression of IGF-I and IGF binding protein 4 (IGFBP-4) was evaluated by Northern blot analysis using rat cDNA probes. Results: Glutamine and leucine transports were 33 and 39% greater, respectively, in the hGH-treated versus saline-treated SBS group (P < 0.05), supporting induction of system B amino acid transport. This upregulation was due, in part, to an 88% increase in glutamine carrier capacity (V max ) with no change in carrier affinity (K m ). Both hGH treatment and SBS increased serum IGF-I levels without direct correlation with increased nutrient transport. IGFBP-4 mRNA expression in small bowel mucosa of saline-treated SBS animals was significantly greater than saline-treated unoperated control values. Mucosal IGFBP-4 mRNA was not significantly altered from control in the other study groups. IGF-I mRNA expression was not detected in mucosa, but weak hybridization was noted in rabbit liver. Conclusions: Human growth hormone accelerates early adaptation in SBS by upregulation of system B carrier capacity. Serum IGF-I levels and mucosal IGF-I and IGFBP-4 mRNA expression did not directly correlate with this enhanced nutrient transport, suggesting that hGH might exert its adaptive effects by mechanisms that are independent from the IGF system in this model.

Background Octreotide (SMS) is a somatostatin analogue utilized in patients with short bowel syndrome (SBS) to decrease output. It may inhibit small bowel adaptation by blocking the secretion of trophic hormones such as epidermal growth factor (EGF). This study delineates the effects of SMS and EGF on nutrient transport in SBS. Methods One week after 70% jejunoileal resection, 20 New Zealand White rabbits (2 kg) received subcutaneous infusions of saline or EGF (1.5 μg/kg/hr) and injections of saline or SMS s.q. b.i.d. The study groups were EGF/saline, saline/saline, saline/SMS, and EGF/SMS. After 7 days of infusion, intestinal brush border membrane vesicles were prepared and nutrient transport measured. Results SMS reduced active nutrient transport. Kinetics confirmed this was secondary to a reduction in functional carriers in the brush border membrane, without a change in carrier affinity. The coinfusion of EGF ameliorated this effect. On an individual basis, EGF alone did not significantly increase nutrient transport, but when taken as a group, nutrients transport was upregulated 26%. Conclusions SMS is detrimental to small bowel adaptation. EGF reverses this effect and may benefit patients with SBS who require SMS to control high intestinal output.