Shared changes in gene expression in frontal cortex of four genetically modified mouse models of depression.

This study aimed to identify whether genetic manipulation of four systems implicated in the pathogenesis of depression converge on shared molecular processes underpinning depression-like behaviour in mice. Altered 5HT function was modelled using the 5-HT transporter knock out mouse, impaired glucocorticoid receptor (GR) function using an antisense-induced knock down mouse, disrupted glutamate function using a heterozygous KO of the vesicular glutamate transporter 1 gene, and impaired cannabinoid signalling using the cannabinoid 1 receptor KO mouse. All 4 four genetically modified mice were previously shown to show exaggerated helpless behaviour compared to wild-type controls and variable degrees of anxiety and anhedonic behaviour. mRNA was extracted from frontal cortex and hybridised to Illumina microarrays. Combined contrast analysis was used to identify genes showing different patterns of up- and down-regulation across the 4 models. 1823 genes were differentially regulated. They were over-represented in gene ontology categories of metabolism, protein handling and synapse. In each model compared to wild-type mice of the same genetic background, a number of genes showed increased expression changes of >10%, other genes showed decreases in each model. Most of the genes showed mixed effects. Several previous array findings were replicated. The results point to cellular stress and changes in post-synaptic remodelling as final common mechanisms of depression and resilience.

Statistical mechanics of learning multiple orthogonal signals: asymptotic theory and fluctuation effects.

The learning of signal directions in high-dimensional data through orthogonal decomposition or principal component analysis (PCA) has many important applications in physics and engineering disciplines, e.g., wireless communication, information theory, and econophysics. The accuracy of the orthogonal decomposition can be studied using mean-field theory. Previous analysis of data produced from a model with a single signal direction has predicted a retarded learning phase transition below which learning is not possible, i.e., if the signal is too weak or the data set is too small then it is impossible to learn anything about the signal direction or magnitude. In this contribution we show that the result can be generalized to the case where there are multiple signal directions. Each nondegenerate signal is associated with a retarded learning transition. However, fluctuations around the mean-field solution lead to large finite size effects unless the signal strengths are very well separated. We evaluate the one-loop contribution to the mean-field theory, which shows that signal directions are indistinguishable from one another if their corresponding population eigenvalues are separated by O(N(-tau)) with exponent tau>1/3, where N is the data dimension. Numerical simulations are consistent with the analysis and show that finite size effects can persist even for very large data sets.

The interaction between dam methylation sites and Xba1 restriction digest sites in Escherichia coli O157:H7 EDL933.

AIMS: The aim of this study was to gain a better understanding of the reason for the predicted pulsed-field gel electrophoresis (PFGE) pattern for the sequenced Escherichia coli O157:H7 EDL933 (EDL933) being different from that observed in practice, using the restriction enzyme Xba1. METHODS AND RESULTS: Primers were designed that flanked either side of each of the predicted Xba1 restriction sites, and the resultant PCR products were sequenced. No sequencing errors were found in the published genome. The distribution of dam methylation sites within the genome was investigated, and a new PFGE pattern was predicted by assuming that any Xba1 restriction site that coincided with a dam methylation site would not be cut. The estimated mean band sizes were obtained from six replicate gels. It was found that the observed and predicted PFGE patterns were in good agreement. CONCLUSIONS: The difference between the observed and the predicted PFGE patterns for EDL933, using Xba1, could be accounted for by assuming that the methylated restriction sites were not cut. SIGNIFICANCE AND IMPACT OF THE STUDY: PFGE is commonly used as a subtyping method. This study provides additional information about the basic technique that could enhance the interpretation of PFGE patterns in comparative studies of the E. coli isolates.

Modelling the epidemiology and transmission of Verocytotoxin-producing Escherichia coli serogroups O26 and O103 in two different calf cohorts.

Mathematical models are constructed to investigate the population dynamics of Verocytotoxin-producing Escherichia coli (VTEC) serogroups O26 and O103 in two different calf cohorts. We compare the epidemiological characteristics of these two serogroups within the same calf cohort as well as the same serogroups between the two calf cohorts. The sources of infection are quantified for both calf cohort studies. VTEC serogroups O26 and O103 mainly differ in the rate at which calves acquire infection from sources other than infected calves, while infected calves typically remain infectious for less than 1 week regardless of the serogroups. Fewer than 20% of VTEC-positive samples are the result of calf-to-calf transmission. PFGE typing data are available for VTEC-positive samples to further subdivide the serogroup data in one of the two calf cohort studies. For serogroup O26 but not O103, there is evidence for unequal environmental exposure to infection with different PFGE types.

Molecular characterisation of bovine faecal Escherichia coli shows persistence of defined ampicillin resistant strains and the presence of class 1 integrons on an organic beef farm.

Antimicrobial use is heavily restricted on organic farms; however, few studies have been conducted to investigate the impact this has on the epidemiology of resistance in pathogenic and commensal bacteria. We investigated the persistence of antimicrobial resistant Escherichia coli within an organic beef herd over a period of 28 months. Faecal samples collected monthly from three calf cohorts and annually from adult cattle and environmental samples, were screened for the presence of ampicillin, apramycin and nalidixic acid resistant E. coli. The prevalence of ampicillin resistance ranged from 27.3 to 40.7% in the annual herd and environmental samplings (n=22-55) and was greater in the calf cohorts, with a peak cohort prevalence of >47% in all 3 years (n=16-18). Apramycin and nalidixic acid resistant E. coli were rare. Pulsed-field gel electrophoresis (PFGE) identified 10 main genotype groups within the herd, with evidence of strain transmission between different livestock groups, animal species and years. Multiple resistance was found in >44% of isolates tested, with ampicillin, neomycin, sulphamethoxazole and tetracycline carriage the commonest phenotype identified. PCR detected the presence of class 1 integrons in <5% of resistant isolates, 6/7 of which were of cattle origin. These data demonstrate that ampicillin resistant E. coli was common on the farm despite restricted antimicrobial use, although strain diversity was low. Persistence of defined genotype groups was observed between years, together with the transmission of resistant strains between different animal species on the farm.

Principal-component-analysis eigenvalue spectra from data with symmetry-breaking structure.

Principal component analysis (PCA) is a ubiquitous method of multivariate statistics that focuses on the eigenvalues lambda and eigenvectors of the sample covariance matrix of a data set. We consider p, N-dimensional data vectors xi drawn from a distribution with covariance matrix C. We use the replica method to evaluate the expected eigenvalue distribution rho(lambda) as N--> infinity with p=alphaN for some fixed alpha. In contrast to existing studies we consider the case where C contains a number of symmetry-breaking directions, so that the sample data set contains some definite structure. Explicitly we set C=sigma2I+sigma(2)Sigma(S)(m=1)A(m)B(m)B(T)(m), with A(m)>0 for all m. We find that the bulk of the eigenvalues are distributed as for the case when the elements of xi are independent and identically distributed. With increasing alpha a series of phase transitions are observed, at alpha=A(-2)(m), m=1,2,..., S, each time a single delta function, delta(lambda-lambda(u)(A(m))), separates from the upper edge of the bulk distribution, where lambda(u)(A)=sigma(2)[1+A][1+(alphaA)(-1)]. We confirm the results of the replica analysis by studying the Stieltjes transform of rho(lambda). This suggests that the results obtained from the replica analysis are universal, irrespective of the distribution from which xi is drawn, provided the fourth moment of each element of xi exists.

Transcriptome profiling of a Saccharomyces cerevisiae mutant with a constitutively activated Ras/cAMP pathway.

Often changes in gene expression levels have been considered significant only when above/below some arbitrarily chosen threshold. We investigated the effect of applying a purely statistical approach to microarray analysis and demonstrated that small changes in gene expression have biological significance. Whole genome microarray analysis of a pde2Delta mutant, constructed in the Saccharomyces cerevisiae reference strain FY23, revealed altered expression of approximately 11% of protein encoding genes. The mutant, characterized by constitutive activation of the Ras/cAMP pathway, has increased sensitivity to stress, reduced ability to assimilate nonfermentable carbon sources, and some cell wall integrity defects. Applying the Munich Information Centre for Protein Sequences (MIPS) functional categories revealed increased expression of genes related to ribosome biogenesis and downregulation of genes in the cell rescue, defense, cell death and aging category, suggesting a decreased response to stress conditions. A reduced level of gene expression in the unfolded protein response pathway (UPR) was observed. Cell wall genes whose expression was affected by this mutation were also identified. Several of the cAMP-responsive orphan genes, upon further investigation, revealed cell wall functions; others had previously unidentified phenotypes assigned to them. This investigation provides a statistical global transcriptome analysis of the cellular response to constitutive activation of the Ras/cAMP pathway.

The immune response of regional lymph nodes during the early stages of Fasciola hepatica infection in cattle.

In this study we examined regional immune responses to Fasciola hepatica infection in the natural ruminant host. Naïve cattle and those pre-exposed to a drug-abbreviated infection were subsequently challenged and lymph nodes extracted at slaughter. In vitro proliferation and cytokine production by mononuclear cells isolated from hepatic and mesenteric lymph nodes were measured after culture with whole fluke antigen (WFA). Hepatic lymph node cells had a significantly greater response to parasite antigen than mesenteric lymph node cells (P < 0.02), although there was no difference in the magnitude of the proliferative response between naïve and pre-exposed challenged cattle. Mononuclear cells from hepatic lymph nodes produced interferon gamma, interleukin 2 and interleukin 4 after culture with parasite antigen, indicative of a mixed, T helper type 0, response. Comparison of the hepatic node response to a variety of F. hepatica antigens showed that proliferation was lower after culture with cathepsin-L, than with a high molecular weight fraction, WFA or excretory-secretory antigen. Cell culture supernatant fluid from unstimulated hepatic lymph node cells showed an IgG1 response to antigens of 48, 52-70, 82, 96 and 120-190 kDa on Western blot in pre-exposed, but not naïve, challenged animals.

Factors affecting the errors in the estimation of evolutionary distances between sequences.

Phylogenetic methods that use matrices of pairwise distances between sequences (e.g., neighbor joining) will only give accurate results when the initial estimates of the pairwise distances are accurate. For many different models of sequence evolution, analytical formulae are known that give estimates of the distance between two sequences as a function of the observed numbers of substitutions of various classes. These are often of a form that we call "log transform formulae". Errors in these distance estimates become larger as the time t since divergence of the two sequences increases. For long times, the log transform formulae can sometimes give divergent distance estimates when applied to finite sequences. We show that these errors become significant when t approximately 1/2 |lambda(max)|(-1) logN, where lambda(max) is the eigenvalue of the substitution rate matrix with the largest absolute value and N is the sequence length. Various likelihood-based methods have been proposed to estimate the values of parameters in rate matrices. If rate matrix parameters are known with reasonable accuracy, it is possible to use the maximum likelihood method to estimate evolutionary distances while keeping the rate parameters fixed. We show that errors in distances estimated in this way only become significant when t approximately 1/2 |lambda(1)|(-1) logN, where lambda(1) is the eigenvalue of the substitution rate matrix with the smallest nonzero absolute value. The accuracy of likelihood-based distance estimates is therefore much higher than those based on log transform formulae, particularly in cases where there is a large range of timescales involved in the rate matrix (e.g., when the ratio of transition to transversion rates is large). We discuss several practical ways of estimating the rate matrix parameters before distance calculation and hence of increasing the accuracy of distance estimates.

Pre-exposure of cattle to drug-abbreviated Fasciola hepatica infections: the effect upon subsequent challenge infection and the early immune response.

In this study we examined whether juvenile liver flukes are capable of stimulating protective immune responses in cattle. Four experimental groups of cattle were studied as follows: group A, a positive control, received a primary infection on day 0 and a secondary infection 28 days later; group B also received two infections but the primary infection was terminated by drug treatment on day 5; group C, received infections on days 0, 5 and 10 which were terminated by drug treatments on days 1, 6 and 11 and then a secondary infection on day 28; group D received an infection only on day 28. Juvenile flukes appear to induce protective responses because: (a) group B animals had significantly lower levels of gamma-GT (P<0.05) than group D; (b) both groups B and C exhibited lower parenchymal phase GLDH levels (P=0.006 and 0.041, respectively); and (c) both groups B and C had lower secondary phase eosinophilia (P=0.002 and 0.02, respectively) than those in group D. Sera taken from groups A-C contained antibodies reacting to a variety of proteins in adult fluke somatic antigen and excretory-secretory preparations, particularly to proteins of 52-60, 68-72 and 82-96 kDa. After secondary challenge the antibody responses of group A to these proteins declined while reactivity to proteins of 28-30 kDa increased. Antibody responses to the 28-30 kDa proteins were not detected in groups B-D until 3 weeks later than those observed in group A. Antibody responses to Fasciola hepatica cathepsin L proteases, which are known to induce protection, were monophasic, of the IgG1 isotype only and were not observed prior to secondary challenge in any of the four groups. In contrast, the response to another protective antigen fraction, a high molecular sized haem protein, was of a mixed IgG1/IgG2 nature and was detected within 14 days of primary infection. However, no significant difference in antibody titres to either protein preparation was observed after the secondary infection when groups B and C were compared to group D.

RNA sequence evolution with secondary structure constraints: comparison of substitution rate models using maximum-likelihood methods.

We test models for the evolution of helical regions of RNA sequences, where the base pairing constraint leads to correlated compensatory substitutions occurring on either side of the pair. These models are of three types: 6-state models include only the four Watson-Crick pairs plus GU and UG; 7-state models include a single mismatch state that combines all of the 10 possible mismatches; 16-state models treat all mismatch states separately. We analyzed a set of eubacterial ribosomal RNA sequences with a well-established phylogenetic tree structure. For each model, the maximum-likelihood values of the parameters were obtained. The models were compared using the Akaike information criterion, the likelihood-ratio test, and Cox's test. With a high significance level, models that permit a nonzero rate of double substitutions performed better than those that assume zero double substitution rate. Some models assume symmetry between GC and CG, between AU and UA, and between GU and UG. Models that relaxed this symmetry assumption performed slightly better, but the tests did not all agree on the significance level. The most general time-reversible model significantly outperformed any of the simplifications. We consider the relative merits of all these models for molecular phylogenetics.

The natural history of syphilis. Implications for the transmission dynamics and control of infection.

BACKGROUND: Syphilis remains a significant cause of morbidity in many developing countries and in some areas within North America and Europe. Mathematical models of the transmission dynamics of sexually transmitted infections have provided insights of relevance both to the interpretation of observed epidemiological patterns and to the design of control programs. Their use for the study of syphilis has been limited to date. GOALS AND STUDY DESIGN: The authors investigated the transmission dynamics of syphilis against a template based on the natural history of infection in individual patients with the aim of (1) identifying gaps in our understanding of the biology of infection, and (2) providing insights of relevance to the design of control policies. RESULTS: Analyses reveal that Treponema pallidum has a moderate to high probability of transmission during contact between susceptible and infectious sexual partners. This, combined with questions over the existence of any immunity to reinfection, helps to ensure the long-term persistence of syphilis within "core" activity groups. Patterns of treatment in North America are shown to have significantly altered the relative frequency of individuals in the different stages of disease. CONCLUSIONS: The analyses emphasize the benefits to be gained from treating infected people early in the primary stage of infection to reduce the effective period during which infected people can transmit to others. This form of treatment is beneficial for both the individual and the community. Treatment has greatly altered the incidence of different disease stages, but the full implications of treatment depend on whether immunity is present.

Alteration of cell cycle timing and induction of surface instability in starfish blastomeres microinjected with antibodies to spectrin.

Spectrin has been implicated in a variety of different processes during late embryogenesis, after transcription of the zygotic genome has been activated. However, relatively little is known about the role of maternally derived spectrin during the early cleavage divisions that give rise to a multicellular embryo. To investigate the role of spectrin in early development, we have microinjected anti-spectrin antibodies into Patiria miniata starfish embryos to inhibit the activity of the maternal pool of spectrin. Microinjection of affinity-purified anti-spectrin antibody, or low to moderate doses of F(ab) fragments, into one blastomere of a two-cell-stage embryo caused a dose-dependent, progressive increase in the length of the cell cycle compared to the uninjected control blastomere. The progeny of injected blastomeres were unable to participate in the formation of a blastula epithelium, instead forming a loose aggregate of cells that eventually stopped dividing. When division stopped, the cells formed surface protrusions and became motile. At high doses of either whole antibody or F(ab) fragments, cells initiated, but failed to complete, cytokinesis. Blastomeres injected with high doses of F(ab) fragments also failed to reform nuclei and underwent variable periods of cell cycle arrest up to 12 hr. Injected embryos stained with BODIPY-phallacidin exhibited extensive disruption of the cortical actin cytoskeleton. These results support previous studies implicating spectrin in stabilizing the cell surface and maintaining the organization of the cortical cytoskeleton. They further suggest that spectrin is not required for the initiation or contraction of the cleavage furrow, but functions in the completion of cytokinesis. Most surprisingly, however, the results demonstrate that inhibition of spectrin function alters cell cycle timing, suggesting that disruption of the actin cytoskeleton inhibits progression through the cell cycle.

Stimulation of cortical actin polymerization in the sea urchin egg cortex by NH4Cl, procaine and urethane: elevation of cytoplasmic pH is not the common mechanism of action.

Previous studies have demonstrated that the penetrating weak base NH4Cl and the anesthetics procaine and urethane disrupt the normal attachment of cortical granules to the cortex of the sea urchin egg. Hylander and Summers (1981: Dev. Biol. 86:1-11) hypothesized that this effect may be caused by a pH-induced polymerization of cortical actin. We have tested this hypothesis by measuring the intracellular pH of eggs of the sea urchins S. purpuratus and A. punctulata treated with NH4Cl, procaine, or urethane, and determining the effects of these agents on the organization of cortical actin. Intracellular pH was determined by the ratiometric measurement of the fluorescent dye BCECF, and filamentous actin organization was examined by confocal laser scanning microscopy of BODIPY-phallocidin stained eggs. Treatment of eggs with either NH4Cl or procaine resulted in a rapid and reversible increase in cytoplasmic pH of up to 1 pH unit and a dose-dependent increase in the intensity of fluorescent staining of the cortex, indicating an increase in the content of filamentous actin. While urethane also induced a dramatic polymerization of cortical actin, no effect on cytoplasmic pH could be detected. These results demonstrate that NH4Cl, procaine and urethane all induce an increase in the amount of filamentous actin in the sea urchin egg cortex that may participate in the detachment of cortical granules. However, these compounds do not share a common mechanism of action based on the elevation of cytoplasmic pH.

Activation of the ATP-ubiquitin-proteasome pathway in skeletal muscle of cachectic rats bearing a hepatoma.

Rats implanted with Yoshida ascites hepatoma (YAH) show a rapid and selective loss of muscle protein due mainly to a marked increase (63-95%) in the rate of protein degradation (compared with rates in muscles of pair-fed controls). To define which proteolytic pathways contribute to this increase, epitrochlearis muscles from YAH-bearing and control rats were incubated under conditions that modify different proteolytic systems. Overall proteolysis in either group of rats was not affected by removal of Ca2+ or by blocking the Ca(2+)-dependent proteolytic system. Inhibition of lysosomal function with methylamine reduced proteolysis (-12%) in muscles from YAH-bearing rats, but not in muscles of pair-fed rats. When ATP production was also inhibited, the remaining accelerated proteolysis in muscles of tumor-bearing rats fell to control levels. Muscles of YAH-bearing rats showed increased levels of ubiquitin-conjugated proteins and a 27-kDa proteasome subunit in Western blot analysis. Levels of mRNA encoding components of proteolytic systems were quantitated using Northern hybridization analysis. Although their total RNA content decreased 20-38%, pale muscles of YAH-bearing rats showed increased levels of ubiquitin mRNA (590-880%) and mRNA for multiple subunits of the proteasome (100-215%). Liver, kidney, heart, and brain showed no weight loss and no change in these mRNA species. Muscles of YAH-bearing rats also showed small increases (30-40%) in mRNA for cathepsins B and D, but not for calpain I or heat shock protein 70. Our findings suggest that accelerated muscle proteolysis and muscle wasting in tumor-bearing rats result primarily from activation of the ATP-dependent pathway involving ubiquitin and the proteasome.

Mothers' intention, age, education and the duration and management of breastfeeding.

The authors examined the breastfeeding duration and management of two groups of mothers with different exposures to services of a Certified Lactation Consultant (CLC). One group of mothers, at hospital H1 (n = 46), had access to a CLC, while mothers at hospital H2 (n = 115) did not. Results showed that: (a) mothers at H1 had significantly (t = 2.33, p < .02) longer durations of breastfeeding (M = 3.1 months, SD = 1.2) than peers at H2 (M = 2.4 months, SD = 1.2); (b) a significantly greater proportion of mothers at H1 attained their intended duration of breastfeeding compared to mothers at H2 (Mann-Whitney U, one-tailed test, Z = 1.94, p < .05); and (c) in a stepwise multiple regression analysis, intended length of breastfeeding accounted for 18% of the variance in duration of breastfeeding, mothers' age 9%, and mothers' education 3%. The results support the theory of reasoned action and the theory of patient education.

PIP: The beneficial impact of certified lactation consultants on the duration of breast feeding was demonstrated in a hospital-based study conducted in the southwestern US. These consultants help new mothers to achieve their desired duration of breast feeding and to overcome technical problems through home visits and telephone contact. Compared were the breast feeding histories of 46 new mothers who delivered at a hospital that employed the services of a lactation consultant and the experiences of 115 new mothers who delivered at a hospital in the same community that lacked such a resource. In both hospitals, the majority of mothers were White and married. As hypothesized, the mean duration of breast feeding was significantly longer among mothers provided with the services of a lactation consultant (3.1 months) than among those who did not receive this service (2.4 months). In addition, 71% of the former mothers compared to only 54% of the latter mothers achieved or exceeded their originally intended breast feeding duration.

Intraexaminer, interexaminer, and interdevice comparability of leg length measurements obtained with measuring tape and metrecom.

Leg length inequalities result from a variety of clinical abnormalities. The purpose of this study was to compare repeated leg length measurements taken by two examiners with two devices during a single session. The two devices that were used were a standard tape measure and a Metrecom. Since reliability coefficients do not fully describe the comparability of measurements, ANOVAs were used to describe differences, and Pearson correlations were used to describe relationships between measurements of leg length obtained by the two examiners using the two instruments. Results of the study showed that although reliability and correlation coefficients are high between testers and devices, significant differences in measurements exist between both testers and devices. The measures found to be most comparable were those taken by one examiner using one device. The authors concluded that for clinical purposes, the tape measure may be the more practical device based on its price. It was theorized, however, that in cases of asymmetry or orthopaedic deformity, the accuracy of the Metrecom may be superior. J Orthop Sports Phys Ther 1991;14(6):263-268.

Antepartal uterine hypercontractility secondary to nipple stimulation.

An alarming result was noted in conjunction with a nipple stimulation contraction stress test. In a 42-week pregnant woman with suspected postmaturity, gentle self-stimulation of the right nipple through the clothing for one to 1.5 minutes caused the sudden onset of uterine hypercontractility, increased uterine tone, and severe fetal bradycardia. The bradycardia persisted for approximately five minutes despite supportive measures. Operative delivery was being considered when the fetal heart rate returned to a normal baseline. Ultimately, the patient delivered vaginally without further significant complication. This experience demonstrated that carefully controlled breast stimulation may result in unpredictable uterine hyperstimulation with fetal bradycardia.