Monitoring silver diamine fluoride application with optical coherence tomography

The objective of this study was to investigate the use of optical coherence tomography (OCT) for monitoring changes in the structure of caries lesions overtime after treatment with silver diamine fluoride (SDF). Artificial caries lesions were formed on dentin bovine blocks. Each block was partitioned into 5 windows: one lesion was covered by nail varnish as control (LC), one sound window was covered with nail varnish (SC), one sound window was exposed to SDF (SCT), one lesion received 2 applications of SDF (L2), while the other lesion received one application of SDF (L1). Each window was scanned using OCT before SDF application, and every week subsequently, for 12 weeks after initial SDF treatment. Parameters such as mean intensity and the width of the peak of increased reflectivity located at the sample surface and the intensity at a depth of 180-μm were monitored. High-resolution microscopy was also used to for the analysis of selected samples. Changes in the parameters measured showed significant changes on dentin lesions after SDF application. OCT resolved structural changes after SDF application as well as changes overtime. High resolution microscopy images confirm penetration of SDF into the samples. Such changes can potentially be monitored to determine if and when re-application of SDF is needed.

Biological sex influences susceptibility to Acinetobacter baumannii pneumonia in mice

Acinetobacter baumannii (A. baumannii) is an extremely versatile multidrug-resistant pathogen with a very high mortality rate; therefore, it has become crucial to understand the host response during its infection. Given the importance of mice for modeling infection and their role in preclinical drug development, equal emphasis should be placed on the use of both sexes. Through our studies using a murine model of acute pneumonia with A. baumannii, we observed that female mice were more susceptible to infection. Likewise, treatment of male mice with estradiol increased their susceptibility to infection. Analysis of the airway compartment revealed enhanced inflammation and reduced neutrophil and alveolar macrophage numbers compared with male mice. Depletion of either neutrophils or alveolar macrophages was important for bacterial clearance; however, depletion of alveolar macrophages further exacerbated female susceptibility because of severe alterations in metabolic homeostasis. Our data highlight the importance of using both sexes when assessing host immune pathways.

A case of laboratory cross-contamination of Mycobacterium tuberculosis identified using comparative genomics

BACKGROUND

Two false-positive tuberculosis (TB) cases in Yamagata Prefecture, Japan, 2016.

OBJECTIVE

To report the effectiveness of comparative genomics of Mycobacterium tuberculosis for identification of cross-contamination cases.

DESIGN

Case report of laboratory cross-contamination.

RESULTS

Beginning with detection of an identical genotype in two M. tuberculosis strains using variable number of tandem repeat typing, we suspected M. tuberculosis cross-contamination of specimens collected in a mycobacteriology laboratory based on epidemiological investigations. This suspicion was confirmed using comparative genomics of the two M. tuberculosis strains and a strain from an epidemiologically unrelated specimen from the same batch as the two strains in the mycobacteriology laboratory. All strains had an identical genomic sequence with no single nucleotide variants.

CONCLUSION

Comparative genomics, which offers the highest discrimination power, is a potent tool for identifying laboratory cross-contamination using epidemiological investigations.

Nosocomial Mycobacterium tuberculosis transmission by brief casual contact identified using comparative genomics

This paper reports a case of nosocomial transmission of Mycobacterium tuberculosis by brief casual contact. Routine variable number tandem repeat typing in Yamagata Prefecture, Japan found that M. tuberculosis clinical isolates from two patients showed indistinguishable genotypes. The patients had an epidemiological relationship of sharing a waiting room in a hospital on the same day. As comparative genomics detected only two single nucleotide variants between the isolates, it was concluded that recent tuberculosis transmission occurred in the waiting room. These results indicate that the physical separation of infectious tuberculosis patients is an essential control measure for preventing unpredictable nosocomial transmission by casual contact.

HDAC2-dependent Antipsychotic-like Effects of Chronic Treatment with the HDAC Inhibitor SAHA in Mice

Antipsychotic drugs, including both typical such as haloperidol and atypical such as clozapine, remain the current standard for schizophrenia treatment. These agents are relatively effective in treating hallucinations and delusions. However, cognitive deficits are at present essentially either persistent or exacerbated following chronic antipsychotic drug exposure. This underlines the need of new therapeutic approaches to improve cognition in treated schizophrenia patients. Our previous findings suggested that upregulation of histone deacetylase 2 (HDAC2) expression upon chronic antipsychotic treatment may lead to negative effects on cognition and cortical synaptic structure. Here we tested different phenotypes of psychosis, synaptic plasticity, cognition and antipsychotic drug action in HDAC2 conditional knockout (HDAC2-cKO) mice and controls. Conditional depletion of HDAC2 function in glutamatergic pyramidal neurons led to a protective phenotype against behavior models induced by psychedelic and dissociative drugs, such as DOI and MK801, respectively. Immunoreactivity toward synaptophysin, which labels presynaptic terminals of functional synapses, was decreased in the frontal cortex of control mice chronically treated with clozapine - an opposite effect occurred in HDAC2-cKO mice. Chronic treatment with the class I and class II HDAC inhibitor SAHA prevented via HDAC2 the disruptive effects of MK801 on recognition memory. Additionally, chronic SAHA treatment affected transcription of numerous plasticity-related genes in the frontal cortex of control mice, an effect that was not observed in HDAC2-cKO animals. Together, these findings suggest that HDAC2 may represent a novel target to improve synaptic plasticity and cognition in treated schizophrenia patients.

What are Canadian primary care physicians prescribing for the treatment of gonorrhea?

BACKGROUND

Cases of Neisseria gonorrhea are on the rise in Canada, which-if undetected or undertreated-can lead to morbidity and infertility. In addition, the number of antimicrobial resistant strains is also increasing creating the risk that N. gonorrhea may become untreatable. In 2013, the Public Health Agency of Canada (PHAC) released Canadian recommendations for the management and treatment of gonorrhea that identified the need for combination therapy to address and minimize antimicrobial resistance. However, the level of awareness and uptake of these guidelines is not well-known.

OBJECTIVES

To assess primary care physicians' prescribing practices for the management and treatment of gonorrhea.

METHODS

After validity testing, two online cross-sectional surveys were conducted with a convenience sample of Canadian physicians. Physicians answered true/false statements and open-ended questions relating to three clinical scenarios: 1) suspected anogenital infection drawing from a population of men who have sex with men (MSM); 2) suspected anogenital infection drawing from a non-MSM population; and, 3) suspected pharyngeal infection drawing from any population. Frequencies of responses were calculated for the statements. Open-ended responses were recoded into treatment categories and frequencies were calculated for each scenario.

RESULTS

A total of 625 physicians completed the survey. Most physicians (60%-95%) accurately identified knowledge statements regarding pharmaceutical management, partner notification and public health reporting. For all clinical scenarios, 30%-35% of physicians did not provide any treatment information, approximately 30% indicated treating with cephalosporin monotherapy, 20%-25% indicated they would prescribe a cephalosporin and azithromycin and a minority of physicians identified other treatment options. When physicians were asked about the purpose of the second antibiotic, azithromycin, 49% indicated it was to provide presumptive treatment for gonorrhea and chlamydia. Forty-one percent indicated it was to provide presumptive treatment for chlamydia only.

CONCLUSION

This convenience sample suggests that although knowledge of pharmaceutical management, partner notification, and public health reporting is high, the use of combination therapy to deter the development of antimicrobial resistant gonorrhea may not be widespread among primary care physicians. In light of both the growing incidence of N. gonorrhea and the rising rates of antimicrobial resistance in Canada, consideration on how to improve awareness and update of best prescribing practices in primary care may be indicated.

Putative classification of clades of enterohemorrhagic Escherichia coli O157 using an IS-printing system

Enterohemorrhagic Escherichia coli O157 (O157) strains can be classified in clades by single nucleotide polymorphisms (SNPs), but this analysis requires significant laboratory effort. As the distribution of insertion sequence (IS) 629 insertions has been reported to be biased among different clades, O157 isolates can be putatively classified in clades by comparison with an IS629 distribution database. A database of the IS629 distribution in O157 strains isolated in Chiba Prefecture and their classification in clades was determined by SNP analysis and IS-printing, an easy and quick analytical tool for IS629 in the O157 genome. The IS629 distribution in O157 strains isolated in Fukuoka and Yamagata Prefectures was determined by IS-printing. These strains were putatively classified in clades by Relative Likelihood calculations that compared the IS-printing data and the IS629 distribution database. Concordance Ratios were calculated, which compared the number of strains putatively classified in a clade by Relative Likelihood to the number of strains classified in that clade by SNP analysis. For the Fukuoka and Yamagata strains, the Concordance Ratios for clades 3, 6 and 8 were 97-100%, for clade 7 about 88%, and for clades 2 and 12 over 90%. In conclusion, O157 clade 2, 3, 6, 7, 8 and 12 strains could be putatively classified by IS-printing.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study demonstrated that enterohemorrhagic E. coli O157 (O157) strains could be putatively classified in clades using an IS-printing system. IS-printing was previously developed as a relatively quick and easy tool for analysis of insertion sequence 629 in the O157 genome. Since most local government public health institutes in Japan carry out IS-printing for early detection of O157 outbreaks, these data should be useful for putative classification of O157 strains in each area.

A review of Human Immunodeficiency Virus (HIV) rapid testing

BACKGROUND

In Canada, it is estimated that 71,300 persons were living with HIV at the end of 2011. Approximately 25% (14,500 to 21,500) of prevalent cases were unaware of their HIV infection. Expanded use of HIV rapid tests may increase the detection of undiagnosed infections, enable earlier treatment and support services and prevent the onward transmission of HIV.

OBJECTIVE

To examine patient acceptability, impact (defined as receipt of test results and linkage to care) and cost-effectiveness of HIV rapid tests.

METHODS

A search was conducted for systematic reviews on HIV rapid testing, with studies from both developed and developing countries, published in English and between 2000 and 2013. The Assessment of Multiple Systematic Review (AMSTAR) tool was used to assess the included systematic reviews for methodological quality. Results were summarized narratively for each of the outcomes.

RESULTS

Eight systematic reviews were included. Acceptability of HIV rapid tests was generally high in medical settings (69% to 98%) especially among pregnant women and youth attending emergency rooms but was lower in non-medical settings (14% to 46%). The percentage of people who obtained their test results was variable. It was high (83% to 93%) in emergency rooms but was low in a rapid care setting with regular business hours (27%). Impact on linkage to care was limited. Only one systematic review examined cost-effectiveness of rapid testing and concluded that HIV rapid tests were cost-effective in comparison to traditional methods; however, results were all based on static models.

CONCLUSION

Overall, HIV rapid tests demonstrated generally high acceptability, variability in receiving test results and limited impact on linkage to care. While these findings suggest that HIV rapid tests may be useful, further research is needed to confirm in whom, when and where they are best used and how to ensure better linkage to care.

Analysis of the population genetics of clades of enterohaemorrhagic Escherichia coli O157:H7/H- isolated in three areas in Japan

AIMS

The genetic differences of enterohaemorrhagic Escherichia coli O157 (O157) strains isolated from humans in three widely-separated areas in Japan were analysed to provide information on possible geographic aspects of O157 pathogenicity.

METHODS AND RESULTS

Epidemiologically unlinked O157 strains were isolated in Chiba (300 strains), Fukuoka (260 strains) and Yamagata (81 strains) prefectures. These strains were classified in clades by single nucleotide polymorphism in seven loci and lineage-specific polymorphism assay-6, and differences between the strains in each clade were compared by population genetic analyses using the IS-printing system. Analysis of the clades from the three areas showed linkage disequilibrium of the strains in each clade. Comparison of the genetic differences of strains from the three areas in each clade, from calculated ΦPT values, indicated that the strains in each clade were the same population in all three areas, except possibly the clade 12 strains.

CONCLUSIONS

Population genetics analyses confirmed that the distribution of O157 strains in the clades isolated in three areas in Japan were similar and stable.

SIGNIFICANCE AND IMPACT OF THE STUDY

The pathogenicity of O157 strains infecting humans was comparable due to the similar, stable geographic distribution of O157 clades.

Identification of three residues essential for 5-hydroxytryptamine 2A-metabotropic glutamate 2 (5-HT2A·mGlu2) receptor heteromerization and its psychoactive behavioral function

Serotonin and glutamate G protein-coupled receptor (GPCR) neurotransmission affects cognition and perception in humans and rodents. GPCRs are capable of forming heteromeric complexes that differentially alter cell signaling, but the role of this structural arrangement in modulating behavior remains unknown. Here, we identified three residues located at the intracellular end of transmembrane domain four that are necessary for the metabotropic glutamate 2 (mGlu2) receptor to be assembled as a GPCR heteromer with the serotonin 5-hydroxytryptamine 2A (5-HT(2A)) receptor in the mouse frontal cortex. Substitution of these residues (Ala-677(4.40), Ala-681(4.44), and Ala-685(4.48)) leads to absence of 5-HT(2A)·mGlu2 receptor complex formation, an effect that is associated with a decrease in their heteromeric ligand binding interaction. Disruption of heteromeric expression with mGlu2 attenuates the psychosis-like effects induced in mice by hallucinogenic 5-HT(2A) agonists. Furthermore, the ligand binding interaction between the components of the 5-HT(2A)·mGlu2 receptor heterocomplex is up-regulated in the frontal cortex of schizophrenic subjects as compared with controls. Together, these findings provide structural evidence for the unique behavioral function of a GPCR heteromer.

Astrocyte-derived VEGF-A drives blood-brain barrier disruption in CNS inflammatory disease

In inflammatory CNS conditions such as multiple sclerosis (MS), current options to treat clinical relapse are limited, and more selective agents are needed. Disruption of the blood-brain barrier (BBB) is an early feature of lesion formation that correlates with clinical exacerbation, leading to edema, excitotoxicity, and entry of serum proteins and inflammatory cells. Here, we identify astrocytic expression of VEGF-A as a key driver of BBB permeability in mice. Inactivation of astrocytic Vegfa expression reduced BBB breakdown, decreased lymphocyte infiltration and neuropathology in inflammatory and demyelinating lesions, and reduced paralysis in a mouse model of MS. Knockdown studies in CNS endothelium indicated activation of the downstream effector eNOS as the principal mechanism underlying the effects of VEGF-A on the BBB. Systemic administration of the selective eNOS inhibitor cavtratin in mice abrogated VEGF-A-induced BBB disruption and pathology and protected against neurologic deficit in the MS model system. Collectively, these data identify blockade of VEGF-A signaling as a protective strategy to treat inflammatory CNS disease.

Proapoptotic and antiapoptotic actions of Stat1 versus Stat3 underlie neuroprotective and immunoregulatory functions of IL-11

Current therapies for multiple sclerosis target inflammation but do not directly address oligodendrocyte protection or myelin repair. The gp130 family cytokines ciliary neurotrophic factor, leukemia inhibitory factor, and IL-11 have been identified as oligodendrocyte growth factors, and IL-11 is also strongly immunoregulatory, but their underlying mechanisms of action are incompletely characterized. In this study, we demonstrate that these effects of IL-11 are mediated via differential regulation of apoptosis in oligodendrocytes versus Ag-presenting dendritic cells (DCs), and are dependent on lineage-specific activity of the transcription factors Stat1 versus Stat3. Focal demyelinating lesions induced in cerebral cortices of IL-11Rα(-/-) mice using stereotactic microinjection of lysolecithin were larger than in controls, and remyelination was delayed. In IL-11Rα(-/-) mice, lesions displayed extensive oligodendrocyte loss and axonal transection, and increased infiltration by inflammatory cells including CD11c(+) DCs, CD3(+) lymphocytes, and CD11b(+) phagocytes. In oligodendrocyte progenitor cell (OPC) cultures, IL-11 restricted caspase 9 activation and apoptosis, and it increased myelination in OPC-neuron cocultures. Importantly, siRNA inhibition of Stat1 enhanced the antiapoptotic effects of IL-11 on OPCs, but IL-11 induced apoptosis in the presence of Stat3 silencing. In contrast, IL-11 augmented caspase activation and apoptosis in cultures of CD11c(+) DCs, but not in CD11b(+) or CD3(+) cells. Inhibition of Stat3 exacerbated the proapoptotic effects of IL-11 on DCs, whereas they were ablated in Stat1(-/-) cultures. Collectively, these findings reveal novel mechanisms underlying the actions of a neuroprotective and immunoregulatory member of the gp130 cytokine family, suggesting avenues to enhance oligodendrocyte viability and restrict CNS inflammation in multiple sclerosis.

Signaling network of dendritic cells in response to pathogens: a community-input supported knowledgebase

Background

Dendritic cells are antigen-presenting cells that play an essential role in linking the innate and adaptive immune systems. Much research has focused on the signaling pathways triggered upon infection of dendritic cells by various pathogens. The high level of activity in the field makes it desirable to have a pathway-based resource to access the information in the literature. Current pathway diagrams lack either comprehensiveness, or an open-access editorial interface. Hence, there is a need for a dependable, expertly curated knowledgebase that integrates this information into a map of signaling networks.

Description

We have built a detailed diagram of the dendritic cell signaling network, with the goal of providing researchers with a valuable resource and a facile method for community input. Network construction has relied on comprehensive review of the literature and regular updates. The diagram includes detailed depictions of pathways activated downstream of different pathogen recognition receptors such as Toll-like receptors, retinoic acid-inducible gene-I-like receptors, C-type lectin receptors and nucleotide-binding oligomerization domain-like receptors. Initially assembled using CellDesigner software, it provides an annotated graphical representation of interactions stored in Systems Biology Mark-up Language. The network, which comprises 249 nodes and 213 edges, has been web-published through the Biological Pathway Publisher software suite. Nodes are annotated with PubMed references and gene-related information, and linked to a public wiki, providing a discussion forum for updates and corrections. To gain more insight into regulatory patterns of dendritic cell signaling, we analyzed the network using graph-theory methods: bifan, feedforward and multi-input convergence motifs were enriched. This emphasis on activating control mechanisms is consonant with a network that subserves persistent and coordinated responses to pathogen detection.

Conclusions

This map represents a navigable aid for presenting a consensus view of the current knowledge on dendritic cell signaling that can be continuously improved through contributions of research community experts. Because the map is available in a machine readable format, it can be edited and may assist researchers in data analysis. Furthermore, the availability of a comprehensive knowledgebase might help further research in this area such as vaccine development. The dendritic cell signaling knowledgebase is accessible at http://tsb.mssm.edu/pathwayPublisher/DC_pathway/DC_pathway_index.html.

Coregulation mapping based on individual phenotypic variation in response to virus infection

Background

Gene coregulation across a population is an important aspect of the considerable variability of the human immune response to virus infection. Methodology to investigate it must rely on a number of ingredients ranging from gene clustering to transcription factor enrichment analysis.

Results

We have developed a methodology to investigate the gene to gene correlations for the expression of 34 genes linked to the immune response of Newcastle Disease Virus (NDV) infected conventional dendritic cells (DCs) from 145 human donors. The levels of gene expression showed a large variation across individuals. We generated a map of gene co-expression using pairwise correlation and multidimensional scaling (MDS). The analysis of these data showed that among the 13 genes left after filtering for statistically significant variations, two clusters are formed. We investigated to what extent the observed correlation patterns can be explained by the sharing of transcription factors (TFs) controlling these genes. Our analysis showed that there was a significant positive correlation between MDS distances and TF sharing across all pairs of genes. We applied enrichment analysis to the TFs having binding sites in the promoter regions of those genes. This analysis, after Gene Ontology filtering, indicated the existence of two clusters of genes (CCL5, IFNA1, IFNA2, IFNB1) and (IKBKE, IL6, IRF7, MX1) that were transcriptionally co-regulated. In order to facilitate the use of our methodology by other researchers, we have also developed an interactive coregulation explorer web-based tool called CorEx. It permits the study of MDS and hierarchical clustering of data combined with TF enrichment analysis. We also offer web services that provide programmatic access to MDS, hierarchical clustering and TF enrichment analysis.

Conclusions

MDS mapping based on correlation in conjunction with TF enrichment analysis represents a useful computational method to generate predictions underlying gene coregulation across a population.

Antiviral response dictated by choreographed cascade of transcription factors

The dendritic cell (DC) is a master regulator of immune responses. Pathogenic viruses subvert normal immune function in DCs through the expression of immune antagonists. Understanding how these antagonists interact with the host immune system requires knowledge of the underlying genetic regulatory network that operates during an uninhibited antiviral response. To isolate and identify this network, we studied DCs infected with Newcastle disease virus, which is able to stimulate innate immunity and DC maturation through activation of RIG-I signaling, but lacks the ability to evade the human IFN response. To analyze this experimental model, we developed a new approach integrating genome-wide expression kinetics and time-dependent promoter analysis. We found that the genetic program underlying the antiviral cell-state transition during the first 18 h postinfection could be explained by a single convergent regulatory network. Gene expression changes were driven by a stepwise multifactor cascading control mechanism, where the specific transcription factors controlling expression changed over time. Within this network, most individual genes were regulated by multiple factors, indicating robustness against virus-encoded immune evasion genes. In addition to effectively recapitulating current biological knowledge, we predicted, and validated experimentally, antiviral roles for several novel transcription factors. More generally, our results show how a genetic program can be temporally controlled through a single regulatory network to achieve the large-scale genetic reprogramming characteristic of cell-state transitions.

In situ multi-level analysis of viscoelastic deformation mechanisms in tendon collagen

Tendon is a hydrated multi-level fibre composite, in which time-dependent behaviour is well established. Studies indicate significant stress relaxation, considered important for optimising tissue stiffness. However, whilst this behaviour is well documented, the mechanisms associated with the response are largely unknown. This study investigates the sub-structural mechanisms occurring during stress relaxation at both the macro (fibre) and nano (fibril) levels of the tendon hierarchy. Stress relaxation followed a two-stage exponential behaviour, during which structural changes were visible at the fibre and fibril levels. Fibril relaxation and fibre sliding showed a double exponential response, while fibre sliding was clearly the largest contributor to relaxation. The amount of stress relaxation and sub-structural reorganisation increased with increasing load increments, but fibre sliding was consistently the largest contributor to stress relaxation. A simple model of tendon viscoelasticity at the fibril and fibre levels has been developed, capturing this behaviour by serially coupling a Voigt element (collagen fibril), with two Maxwell elements (non-collagenous matrix between fibrils and fibres). This multi-level analysis provides a first step towards understanding how sub-structural interactions contribute to viscoelastic behaviour. It indicates that nano- and micro-scale shearing are significant dissipative mechanisms, and the kinetics of relaxation follows a two-stage exponential decay, well fitted by serially coupled viscoelastic elements.

Interferon-beta pretreatment of conventional and plasmacytoid human dendritic cells enhances their activation by influenza virus

Influenza virus produces a protein, NS1, that inhibits infected cells from releasing type I interferon (IFN) and blocks maturation of conventional dendritic cells (DCs). As a result, influenza virus is a poor activator of both mouse and human DCs in vitro. However, in vivo a strong immune response to virus infection is generated in both species, suggesting that other factors may contribute to the maturation of DCs in vivo. It is likely that the environment in which a DC encounters a virus would contain multiple pro-inflammatory molecules, including type I IFN. Type I IFN is a critical component of the viral immune response that initiates an antiviral state in cells, primarily by triggering a broad transcriptional program that interferes with the ability of virus to establish infection in the cell. In this study, we have examined the activation profiles of both conventional and plasmacytoid dendritic cells (cDCs and pDCs) in response to an influenza virus infection in the context of a type I IFN-containing environment. We found that both cDCs and pDCs demonstrate a greater activation response to influenza virus when pre-exposed to IFN-β (IFN priming); although, the priming kinetics are different in these two cell types. This strongly suggests that type I IFN functions not only to reduce viral replication in these immune cells, but also to promote greater DC activation during influenza virus infections.

Influenza infection leads to a serious respiratory infection of the lung epithelium. Lying directly below the epithelial cells are immune system sentinels known as dendritic cells. These cells interact with the virus and carry parts of the virus to draining lymph nodes to activate killer T cells. In order to effectively carry out this function, DCs must perceive the presence of a virus using receptors specially adapted for this function. However, when DCs are mixed with influenza virus in the laboratory, no activation occurs because the virus produces a protein called NS1 that blocks the receptors. Yet, patients infected with influenza virus develop a strong adaptive response that leads to recovery from infection. This observation suggests that additional factors must be present that contribute to the activation of the DCs. The most likely contributor is type I interferon, a ubiquitous protein released from many cells upon exposure to virus. In this study, we mixed influenza virus with DCs in the presence of type I interferon and found that this greatly enhanced their activation. Treatment with interferon allowed the DC to bypass the block in activation mediated by the influenza NS1 protein. Our data suggest that the production of type I interferon within an infected patient may endow the DCs with the ability to fully respond to influenza virus.

The fragile X mental retardation protein binds and regulates a novel class of mRNAs containing U rich target sequences

Fragile X syndrome is a common form of inherited mental retardation caused by the absence of the fragile X mental retardation protein (FMRP). It has been hypothesized that FMRP is involved in the processing and/or translation of mRNAs. Human and mouse target-mRNAs, containing purine quartets, have previously been identified. By using cDNA-SELEX (systematic evolution of ligands by exponential enrichment), we identified another class of human target-mRNAs which contain U rich sequences. This technique, in contrast to oligonucleotide-based SELEX, allows the identification of FMRP targets directly from mRNA pools. Many of the proteins encoded by the identified FMRP targets have been implicated in neuroplasticity. Steady state levels of target-mRNAs were unchanged in the brain of fragile X mice. However, levels of two target-encoded proteins, an L-type calcium channel subunit and MAP1B, were downregulated in specific brain regions suggesting a defect in the expression of target-encoded proteins in fragile X syndrome.

The RNA binding domain of Jerky consists of tandemly arranged helix-turn-helix/homeodomain-like motifs and binds specific sets of mRNAs

A deficit in the Jerky protein in mice causes recurrent seizures reminiscent of temporal lobe epilepsy. Jerky is present in mRNA particles in neurons. We show that the N-terminal 168 amino acids of Jerky are necessary and sufficient for mRNA binding. The binding domain is similar to the two tandemly arranged homeodomain-like helix-turn-helix DNA binding motifs of centromere binding protein B. The putative helix-turn-helix motifs of Jerky can also bind double-stranded DNA and represent a novel mammalian RNA/DNA binding domain. Microarray analysis identified mRNAs encoding proteins involved in ribosome assembly and cellular stress response that specifically bound to the RNA binding domain of Jerky both in vitro and in vivo. These data suggest that epileptogenesis in Jerky-deficient mice most likely involves pathways associated with ribosome biogenesis and neuronal survival and/or apoptosis.

IGF-I-induced apoptosis in LM2d6 cultured at a low concentration of fetal bovine serum

We examined the effects of IGF-I (1-1000 ng/ml) on cell proliferation in LM2d6 mouse fibroblast cells at 0.1, 1.0 and 5.0% fetal bovine serum (FBS). In medium containing 0.1% FBS, treatment of LM2d6 cells with IGF-I significantly reduced the cell number in a dose- and time-dependent manner, whereas no effects were seen at 1 or 5% FBS. Treatment of the cells with 0.1% FBS for 72 h caused DNA laddering and nuclear condensation. However, Scatchard analysis for IGF-I binding sites on the cells revealed that both the number and the affinity of IGF-I receptors were not greater than that of Balb/3T3 cells. Furthermore, the apoptotic action of Long (R(3))-IGF-I, an analogue of IGF-I that has a reduced affinity for IGF binding proteins, was not greater than that of IGF-I. Taken together, we conclude that IGF-I reduces cell proliferation at low levels of FBS due to the induction of apoptosis. This effect is probably not caused by an excess production of IGF binding proteins in LM2d6 cells.

Jerky, a protein deficient in a mouse epilepsy model, is associated with translationally inactive mRNA in neurons

Temporal lobe epilepsy (TLE) is a common seizure disorder, but the underlying molecular mechanisms are unknown. We reported previously that inactivation of the jerky gene in mice causes recurrent limbic seizures highly similar to TLE. Electrophysiological studies showed abnormal firing in hippocampal neurons in these mice, but it is not known how a deficiency in the Jerky protein leads to neuronal hyperexcitability. Here we show that Jerky is a brain-specific protein with a high expression level in neurons. Jerky binds mRNAs with high affinity, and it is a component of messenger ribonucleoprotein complexes in vivo. However, Jerky is not associated with ribosomes and actively translating mRNAs. These data suggest that Jerky may regulate mRNA use in neurons, and its deficiency could lead to perturbations in the regulated use of preexisting mRNAs.

Avoidance responding following amphetamine-induced dopamine depletion

The effect of an amphetamine-induced depletion of striatal dopamine on active and passive avoidance responding of rats was examined. Sixteen animals received two sets of 4 injections each of 15 mg/kg d-amphetamine, administered at 2 hr intervals with each set delivered one week apart. One week after the last injection, animals were given 50 consecutive active avoidance trials in a shuttle box. Animals treated with amphetamine exhibited a 50%, depletion of striatal dopamine and showed a slower learning curve, as evidenced by significantly fewer avoidances and a slower escape latency during trials 21-30. Both groups demonstrated a 90% avoidance rate by trials 41-50. A separate group of rats was treated as above and trained for several weeks on the active avoidance procedure. Haloperidol (0.01-0.10 mg/kg intraperitoneally) dose-dependently decreased avoidance number and increased avoidance and escape latency in both groups, an effect that was exaggerated in those animals previously treated with amphetamine. Finally, these animals were tested in the same apparatus using a passive avoidance procedure. The amphetamine treatment produced a significantly higher mean number of avoidances in this procedure compared to saline-treated animals during trials 1-20. These results suggest that the impairment in conditioned avoidance following amphetamine treatment is due to a motoric, rather than a cognitive deficit.

Infection of bovine immunodeficiency virus and bovine leukemia virus in water buffalo and cattle populations in Pakistan

A survey of antibodies to bovine immunodeficiency virus (BIV) known as bovine lentivirus and bovine leukemia virus (BLV) was conducted with samples from water buffalo and cattle populations in Pakistan. A total of 370 water buffaloes and 76 cattle were tested, and 10.3% and 15.8%, respectively, were found positive for anti-BIV p26 antibodies determined by Western blotting, while 0.8% of water buffaloes and no cattle were positive for anti-BLV antibodies determined by immunodiffusion test. BIV-seropositive water buffaloes and cattle were found to have BIV proviral DNA in the peripheral blood mononuclear cells determined by nested polymerase chain reaction. This is the first report of BIV infections in water buffaloes.

Effects of NTE-122, an acyl-CoA:cholesterol acyltransferase inhibitor, on cholesterol esterification and lipid secretion from CaCo-2 cells, and cholesterol absorption in rats

The effect of NTE-122 (trans-1,4-bis[[1-cyclohexyl-3-(4-dimethylamino phenyl)ureido]methyl]cyclohexane), an acyl-CoA:cholesterol acyltransferase (ACAT) inhibitor, on cholesterol absorption was investigated. NTE-122 inhibited whole-cell ACAT activity in CaCo-2 cells, a human intestinal cell line, with an IC50 value of 4.7 nM. In CaCo-2 cells cultured on a membrane filter, NTE-122 pronouncedly inhibited the basolateral secretion of newly synthesized cholesteryl esters, and significantly reduced the basolateral secretion of newly synthesized triglycerides without influencing the cellular triglyceride synthesis. Furthermore, NTE-122 (1 mg/kg, p.o.) inhibited [14C]cholesterol absorption in rats. These results suggest that NTE-122 is capable of exhibiting anti-hyperlipidemic effects by reducing the absorption of dietary cholesterol.

Effects of NTE-122, a novel acyl-CoA:cholesterol acyltransferase inhibitor, on cholesterol esterification and secretions of apolipoprotein B-containing lipoprotein and bile acids in HepG2

We studied the effect of NTE-122 (trans-1,4-bis[[1-cyclohexyl-3-(4-dimethylamino phenyl) ureido]methyl]cyclohexane), a novel acyl-CoA:cholesterol acyltransferase (ACAT) inhibitor, on intracellular cholesterol esterification and the secretion of apolipoprotein B100 (apoB)-containing lipoprotein and bile acids in the human hepatoma cell line HepG2. NTE-122 markably inhibited [3H]oleate incorporation into cholesteryl esters in HepG2 cells incubated with 5 microg/ml 25-hydroxycholesterol as a stimulus for ACAT (IC50=6.0 nM). On the other hand, NTE-122 did not affect [3H]oleate incorporation into triglycerides and phospholipids and [14C]acetate incorporation into cholesterol. The stimulation of ACAT by 25-hydroxycholesterol caused significant increases in the secretion of radiolabeled cholesteryl esters, radiolabeled triglycerides and apoB mass. NTE-122 pronouncedly inhibited the secretion of radiolabeled cholesteryl esters in proportion to the inhibition of cellular cholesterol esterification, and it significantly reduced the secretion of radiolabeled triglycerides and apoB mass in HepG2 cells incubated with 25-hydroxycholesterol. Furthermore, NTE-122 increased the secretion of bile acids synthesized from [14C]-cholesterol. These results suggest that NTE-122 is capable of exhibiting anti-hyperlipidemic effects by reducing both the cholesterol content and the amount of secreted very low-density lipoprotein and enhancing the excretion of bile acid from the liver.

Snapshot of a large dynamic replicon in a halophilic archaeon: megaplasmid or minichromosome?

Extremely halophilic archaea, which flourish in hypersaline environments, are known to contain a variety of large dynamic replicons. Previously, the analysis of one such replicon, pNRC100, in Halobacterium sp. strain NRC-1, showed that it undergoes high-frequency insertion sequence (IS) element-mediated insertions and deletions, as well as inversions via recombination between 39-kb-long inverted repeats (IRs). Now, the complete sequencing of pNRC100, a 191,346-bp circle, has shown the presence of 27 IS elements representing eight families. A total of 176 ORFs or likely genes of 850-bp average size were found, 39 of which were repeated within the large IRs. More than one-half of the ORFs are likely to represent novel genes that have no known homologs in the databases. Among ORFs with previously characterized homologs, three different copies of putative plasmid replication and four copies of partitioning genes were found, suggesting that pNRC100 evolved from IS element-mediated fusions of several smaller plasmids. Consistent with this idea, putative genes typically found on plasmids, including those encoding a restriction-modification system and arsenic resistance, as well as buoyant gas-filled vesicles and a two-component regulatory system, were found on pNRC100. However, additional putative genes not expected on an extrachromosomal element, such as those encoding an electron transport chain cytochrome d oxidase, DNA nucleotide synthesis enzymes thioredoxin and thioredoxin reductase, and eukaryotic-like TATA-binding protein transcription factors and a chromosomal replication initiator protein were also found. A multi-step IS element-mediated process is proposed to account for the acquisition of these chromosomal genes. The finding of essential genes on pNRC100 and its property of resistance to curing suggest that this replicon may be evolving into a new chromosome.

Complete genomic sequence and analysis of the prion protein gene region from three mammalian species

The prion protein (PrP), first identified in scrapie-infected rodents, is encoded by a single exon of a single-copy chromosomal gene. In addition to the protein-coding exon, PrP genes in mammals contain one or two 5'-noncoding exons. To learn more about the genomic organization of regions surrounding the PrP exons, we sequenced 10(5) bp of DNA from clones containing human, sheep, and mouse PrP genes isolated in cosmids or lambda phage. Our findings are as follows: (1) Although the human PrP transcript does not include the untranslated exon 2 found in its mouse and sheep counterparts, the large intron of the human PrP gene contains an exon 2-like sequence flanked by consensus splice acceptor and donor sites. (2) The mouse Prnpa but not the Prnpb allele found in 44 inbred lines contains a 6593 nucleotide retroviral genome inserted into the anticoding strand of intron 2. This intracisternal A-particle element is flanked by duplications of an AAGGCT nucleotide motif. (3) We found that the PrP gene regions contain from 40% to 57% genome-wide repetitive elements that independently increased the size of the locus in all three species by numerous mutations. The unusually long sheep PrP 3'-untranslated region contains a "fossil" 1.2-kb mariner transposable element. (4) We identified sequences in noncoding DNA that are conserved between the three species and may represent biologically functional sites.

Prevention of hydrogen peroxide damage by soybean saponins to mouse fibroblasts

Soybean saponin is one of several soybean glycosides. Recently, new soybean saponins which possess the DDMP (2,5-dihydroxy-6-methyl-2,3-dihydro-4H-pyran-4-one) moiety have been detected. Soyasaponin beta g of these new soybean saponins was shown to inhibit hydrogen peroxide damage to mouse fibroblast cells. Not only the new saponin but also soyasaponin I, which has lost the DDMP moiety from soyasaponin beta g, was tested and showed higher inhibition in this assay. In order to investigate the relationship between the effect and chemical structure, glycyrrhizin, which has a similar chemical structure to soyasaponin I, was also tested and exhibited the same effect as soyasaponins beta g and I. Soyasaponin Ab, a major authentic bisdesmosidic saponin that exists only in the soybean hypocotyl, was also tested and exhibited the highest inhibition of hydrogen peroxide damage among the four saponins. It was concluded that water-soluble soybean saponins protected the cells from damage by hydrogen peroxide.

Rapid purification of fluorescent dye-labeled products in a 96-well format for high-throughput automated DNA sequencing

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DMSO resolves certain compressions and signal dropouts in fluorescent dye labeled primer-based DNA sequencing reactions

Automated base calling algorithms are more sensitive to the quality of the DNA sequencing data than are the labor intensive visual methods of base calling. To improve this quality, data from DNA sequencing reactions have been compared in order to determine the effects of the inclusion of dimethyl sulfoxide (DMSO). Inclusion of 10% DMSO into the reaction cocktail resolves at least one type of sequence compression. This compression may be due to the lack of ability in T7 DNA polymerase to read through certain sequences correctly. The poor quality of these data is seen as radioactive bands or fluorescent signal peaks that have an abnormal alignment, either in the wrong order or as single bands/peaks. The inclusion of DMSO also resolves sequences where the peak signal is absent or severely diminished, leading to a "gap" in the chromatogram profile. DMSO is better than deaza-dITP for resolving certain compressions. Addition of DMSO is a cheaper and more efficient method for high-throughput DNA sequencing than repeating reactions with base analogs.

Organization, sequence, and function of 34.5 kb of genomic DNA encompassing several murine T-cell receptor alpha/delta variable gene segments

A cosmid-bearing murine genomic DNA, encompassing several T-cell receptor variable alpha/delta gene segments, has been sequenced using shotgun DNA cloning methodology coupled with fluorescence-based high-through-put DNA sequencing technology. This region, spanning 34.5 kb, contains a pseudogene V alpha gene segment (psi V alpha 16.1), a V delta gene segment (V delta 2), and a variable gene segment that has been reported to be expressed with both C alpha (V alpha 6) and C delta (V delta 3). Therefore, this cosmid is the ideal vehicle for examining the possible control sequences that may be involved in determining whether a V gene segment associates with either C alpha or C delta. Polymerase chain reaction experiments demonstrate that the two functional variable gene segments (V delta and V alpha/delta) are expressed individually with both C alpha and C delta genes as mRNA, indicating a permissiveness in their expression patterns. In addition, a variety of genomic sequence-related features have been identified.

Intragenic and intergenic recombination between temperature-sensitive mutants of vaccinia virus

The frequency of recombination for a complete set of two-factor crosses between vaccinia virus mutations separated by distances of between 54 and 10692 bp was determined. The results show that in intragenic crosses there is a linear relationship between the recombination frequency observed and distances between the mutations of up to 700 bp. However, no length dependence of the recombination frequency in intergenic crosses with a distance between mutations of 328 to greater than 10000 bp is observed. We attribute this lack of dependence to the high rate of viral DNA interchange, which makes some step other than the cross-over event rate-limiting. Furthermore, we believe that the observed difference in recombination frequency between inter- and intragenic recombination is due to complementation between temperature-sensitive mutants at the permissive temperature.

Phosphorescent zinc sulfide is a nonradioactive alternative for marking autoradiograms

Phosphorescent zinc sulfide is a nonradioactive alternative for making orientation and identification markings on autoradiograms. Measurements with a luminometer show that light emission is linear with respect to ZnS concentration. A minimum activation time of 5 s has been determined, using an incandescent lamp as a light source. Emission decay kinetics show light emissions reached background levels within minutes, depending on the ZnS concentration. This time period is sufficient for X-ray films to be permanently marked. Because of its efficiency and nontoxicity, this autoradiogram marker could be extremely useful in many protocols, including high-throughput radioactive DNA sequencing. This nonradioactive marker will also be useful in protocols utilizing nonradioactive detection systems, such as those calling for biotinylated and chemiluminescent probes.

Superinfection exclusion of vaccinia virus in virus-infected cell cultures

Vaccinia virus-infected BSC 40 cells do not permit the replication of superinfecting vaccinia virus. The extent of superinfecting virus propagation depends on the time of superinfection; there is 90% exclusion by 4 hr after the initial infection, and more than 99% by 6 hr. When superinfection is attempted at 6 hr after infection, the superinfecting virus is incapable of carrying out DNA replication or early gene transcription, demonstrating that an early event in the virus life cycle is inhibited. The rate of adsorption of the superinfecting virus is unaltered which shows that exclusion is affected at a point between adsorption and early gene transcription. In order to exclude superinfection, the primary infecting virus does not require replication of its DNA or expression of its late genes but it must express one or more early genes.