Synthesis from DNA of a molecule with the connectivity of a cube

A principal goal of biotechnology is the assembly of novel biomaterials for analytical, industrial and therapeutic purposes. The advent of stable immobile nucleic acid branched junctions makes DNA a good candidate for building frameworks to which proteins or other functional molecules can be attached and thereby juxtaposed. The addition of single-stranded 'sticky' ends to branched DNA molecules converts them into macromolecular valence clusters that can be ligated together. The edges of these frameworks are double-helical DNA, and the vertices correspond to the branch points of junctions. Here, we report the construction from DNA of a covalently closed cube-like molecular complex containing twelve equal-length double-helical edges arranged about eight vertices. Each of the six 'faces' of the object is a single-stranded cyclic molecule, doubly catenated to four neighbouring strands, and each vertex is connected by an edge to three others. Each edge contains a unique restriction site for analytical purposes. This is the first construction of a closed polyhedral object from DNA.

Fabrication of solid-state nanopores with single-nanometre precision

Single nanometre-sized pores (nanopores) embedded in an insulating membrane are an exciting new class of nanosensors for rapid electrical detection and characterization of biomolecules. Notable examples include alpha-hemolysin protein nanopores in lipid membranes and solid-state nanopores in Si3N4. Here we report a new technique for fabricating silicon oxide nanopores with single-nanometre precision and direct visual feedback, using state-of-the-art silicon technology and transmission electron microscopy. First, a pore of 20 nm is opened in a silicon membrane by using electron-beam lithography and anisotropic etching. After thermal oxidation, the pore can be reduced to a single-nanometre when it is exposed to a high-energy electron beam. This fluidizes the silicon oxide leading to a shrinking of the small hole due to surface tension. When the electron beam is switched off, the material quenches and retains its shape. This technique dramatically increases the level of control in the fabrication of a wide range of nanodevices.

Atomic structure of graphene on SiO2

We employ scanning probe microscopy to reveal atomic structures and nanoscale morphology of graphene-based electronic devices (i.e., a graphene sheet supported by an insulating silicon dioxide substrate) for the first time. Atomic resolution scanning tunneling microscopy images reveal the presence of a strong spatially dependent perturbation, which breaks the hexagonal lattice symmetry of the graphitic lattice. Structural corrugations of the graphene sheet partially conform to the underlying silicon oxide substrate. These effects are obscured or modified on graphene devices processed with normal lithographic methods, as they are covered with a layer of photoresist residue. We enable our experiments by a novel cleaning process to produce atomically clean graphene sheets.

Vertebrate slit, a secreted ligand for the transmembrane protein roundabout, is a repellent for olfactory bulb axons

The olfactory bulb plays a central role in olfactory information processing through its connections with both peripheral and cortical structures. Axons projecting from the olfactory bulb to the telencephalon are guided by a repulsive activity in the septum. The molecular nature of the repellent is not known. We report here the isolation of vertebrate homologs of the Drosophila slit gene and show that Slit protein binds to the transmembrane protein Roundabout (Robo). Slit is expressed in the septum whereas Robo is expressed in the olfactory bulb. Functionally, Slit acts as a chemorepellent for olfactory bulb axons. These results establish a ligand-receptor relationship between two molecules important for neural development, suggest a role for Slit in olfactory bulb axon guidance, and reveal the existence of a new family of axon guidance molecules.

Intrauterine devices and pelvic inflammatory disease: an international perspective

The risk of pelvic inflammatory disease (PID) associated with use of an intrauterine device (IUD) has been an important concern that has dominated decisions on its use throughout the world, especially in the USA. Early research that suggested such an association led to both a dramatic decline in use of the method and its withdrawal from the US market by two manufacturers. However, factors other than use of an IUD are now thought to be major determinants of PID risk. To address these concerns, we have reviewed the World Health Organisation's IUD clinical trial data to explore the incidence and patterns of PID risk with use of an IUD. The overall rate of PID among 22,908 IUD insertions and during 51,399 woman-years of follow-up was 1.6 cases per 1000 woman-years of use. After adjustment for confounding factors, PID risk was more than six times higher during the 20 days after insertion than during later times (unadjusted rates, 9.7 vs 1.4 per 1000 woman-years, respectively); the risk was low and constant for up to eight years of follow-up. Rates varied according to geographical area (highest in Africa and lowest in China) and were inversely associated with age. PID rates were lower among women who had IUDs inserted more recently. Our findings indicate that PID among IUD users is most strongly related to the insertion process and to background risk of sexually transmissible disease. PID is an infrequent event beyond the first 20 days after insertion. Because of this increased risk with insertion, IUDs should be left in place up to their maximum lifespan and should not routinely be replaced earlier, provided there are no contraindications to continued use and the woman wishes to continue with the device.

Translocation of double-strand DNA through a silicon oxide nanopore

We report double-strand DNA translocation experiments using silicon oxide nanopores with a diameter of about 10 nm . By monitoring the conductance of a voltage-biased pore, we detect molecules with a length ranging from 6557 to 48 500 base pairs. We find that the molecules can pass the pore both in a straight linear fashion and in a folded state. Experiments on circular DNA further support this picture. We sort the molecular events according to their folding state and estimate the folding position. As a proof-of-principle experiment, we show that a nanopore can be used to distinguish the lengths of DNA fragments present in a mixture. These experiments pave the way for quantitative analytical techniques with solid-state nanopores.

Stimulation of 92-kDa gelatinase B promoter activity by ras is mitogen-activated protein kinase kinase 1-independent and requires multiple transcription factor binding sites including closely spaced PEA3/ets and AP-1 sequences

The 92-kDa type IV collagenase (92-kDa gelatinase B also referred to as MMP-9), which plays a critical role in extracellular matrix degradation, is regulated by growth factors that mediate their effects through the ras proto-oncogene. The current study was undertaken to determine the transcriptional requirements for the induction of 92-kDa gelatinase B expression by an activated ras oncogene. Transfection of OVCAR-3 cells with an expression vector encoding an activated Ha-ras increased 92-kDa gelatinolytic activity and stimulated (over 10-fold) the activity of a CAT reporter driven by 670 nucleotides of 5' flanking sequence of the 92-kDa gelatinase B gene. Transient assays using a CAT reporter driven by 5' deleted fragments of the 92-kDa gelatinase B promoter indicated that a region spanning -634 to -531 was required for optimal induction of the promoter. The individual deletion, or mutation, of a PEA3/ets (-540) motif, AP-1 sites (-533, -79), a NF-kappa B (-600) consensus sequence, and a GT box (-52) substantially reduced the activation of the promoter by ras. An expression vector encoding the PEA3 transcription factor caused a 3-fold stimulation of the wild type but not the PEA3/ets-deleted 92-kDa gelatinase B promoter. Coexpression of a dominant negative c-jun antagonized the ras-dependent stimulation of the 92-kDa gelatinase B promoter-driven CAT reporter. The signaling pathway mediating the induction of 92-kDa gelatinase B promoter activity by ras was examined. The expression of a phosphatase (CL100) which inactivates multiple mitogen-activate protein kinase members abrogated the stimulation of 92-kDa gelatinase B promoter activity by ras. However, the expression of a kinase-deficient mitogen-activated protein kinase kinase 1 (MEK1) did not prevent activation of the 92-kDa gelatinase B promoter by ras and a constitutively activated c-raf expression vector was insufficient for 92-kDa gelatinase B promoter activation. Thus, the stimulation of the 92-kDa gelatinase B promoter by ras requires multiple elements including closely spaced PEA3/est and AP-1 sites and is MEK1-independent.

The mouse SLIT family: secreted ligands for ROBO expressed in patterns that suggest a role in morphogenesis and axon guidance

The Slit gene encodes a secreted molecule essential for neural development in Drosophila embryos. Here we report the identification of three Slit homologues in the mouse. We demonstrate that the mouse SLIT1 protein can bind ROBO1, a transmembrane receptor implicated in axon guidance. Both whole-mount and section in situ hybridization studies reveal unique and complementary patterns of expression of the three mouse Slit genes and of Robo1, both within the central nervous system and in other developing tissues. The complementary expression patterns of Slit and Robo1 and their in vitro interaction suggest a ligand-receptor relationship. The expression of all three Slit genes in the floor plate suggests that they are likely to share the same functional properties with their Drosophila homologue in midline neural development and axon guidance. The complementary expression of Slit and Robo1 in different subdivisions of the somites suggests their possible function in axon pathfinding and neural crest cell migration. The unique expression pattern in limb and other organs indicates additional potential functions of the Slit gene family.

Oncogenic role of DDX3 in breast cancer biogenesis

Benzo[a]pyrene diol epoxide (BPDE), the active metabolite of benzo[a]pyrene present in tobacco smoke, is a major cancer-causing compound. To evaluate the effects of BPDE on human breast epithelial cells, we exposed an immortalized human breast cell line, MCF 10A, to BPDE and characterized the gene expression pattern. Of the differential genes expressed, we found consistent activation of DDX3, a member of the DEAD box RNA helicase family. Overexpression of DDX3 in MCF 10A cells induced an epithelial-mesenchymal-like transformation, exhibited increased motility and invasive properties, and formed colonies in soft-agar assays. Besides the altered phenotype, MCF 10A-DDX3 cells repressed E-cadherin expression as demonstrated by both immunoblots and by E-cadherin promoter-reporter assays. In addition, an in vivo association of DDX3 and the E-cadherin promoter was demonstrated by chromatin immunoprecipitation assays. Collectively, these results demonstrate that the activation of DDX3 by BPDE, can promote growth, proliferation and neoplastic transformation of breast epithelial cells.

Validation of diffusion tensor magnetic resonance axonal fiber imaging with registered manganese-enhanced optic tracts

Noninvasive mapping of white matter tracts using diffusion tensor magnetic resonance imaging (DTMRI) is potentially useful in revealing anatomical connectivity in the human brain. However, a gold standard for validating DTMRI in defining axonal fiber orientation is still lacking. This study presents the first validation of the principal eigenvector of the diffusion tensor in defining axonal fiber orientation by superimposing DTMRI with manganese-enhanced MRI of optic tracts. A rat model was developed in which optic tracts were enhanced by manganese ions. Manganese ion (Mn(2+)) is a potent T1-shortening agent and can be uptaken and transported actively along the axon. Based on this property, we obtained enhanced optic tracts with a T1-weighted spin-echo sequence 10 h after intravitreal injection of Mn(2+). The images were compared with DTMRI acquired with exact spatial registration. Deviation angles between tangential vectors of the enhanced tracts and the principal eigenvectors of the diffusion tensor were then computed pixel by pixel. We found that under signal-to-noise (SNR) of 30, the variance of deviation angles was (13.27 degrees). In addition, the dependence of this variance on SNR obeys stochastic behavior if SNR is greater than 10. Based on this relation, we estimated that an rms deviation of less than 10 degrees could be achieved with DTMRI when SNR is 40 or greater. In conclusion, our method bypasses technical difficulties in conventional histological approach and provides an in vivo gold standard for validating DTMRI in mapping white matter tracts.

Gender differences in the effects of bereavement-related psychological distress in health outcomes

BACKGROUND

This study examined whether traumatic grief, depressive and anxiety symptoms formed three distinct factors for widows and widowers. In addition, we examined whether high symptom levels of traumatic grief, depression and anxiety predicted different mental and physical health outcomes for widows and widowers.

METHOD

Ninety-two future widows and 58 future widowers were interviewed at the time of their spouse's hospital admission and then at 6 weeks, 6, 13 and 25 month follow-ups. Principal axis factor analyses tested the distinctiveness of traumatic grief, depressive and anxiety symptoms, by gender. Repeated measures ANOVA tested for gender differences and changes over time in mean symptom levels of traumatic grief, depression and anxiety. Linear and logistic regression models estimated the effects of high symptom levels of traumatic grief, depression and anxiety at 6 months on health outcomes at 13 and 25 months post-intake by gender.

RESULTS

Three distinct symptom clusters (i.e. traumatic grief, depressive and anxiety symptoms) were found to emerge for both widows and widowers. Widows had higher mean levels of traumatic grief, depressive and anxiety symptoms. High symptom levels of traumatic grief measured at 6 months predicted a physical health event (e.g. cancer, heart attack) at 25 months post-intake for widows. High symptom levels of anxiety measured at 6 months predicted suicidal ideation at 25 months for widowers.

CONCLUSIONS

The results suggest that there are gender differences in the levels of psychological symptoms resulting from bereavement and in their effects on subsequent mental and physical health for widows and widowers.

Rapid interferon gamma-dependent clearance of influenza A virus and protection from consolidating pneumonitis in nitric oxide synthase 2-deficient mice

Viral infection often activates the interferon (IFN)-gamma-inducible gene, nitric oxide synthase 2 (NOS2). Expression of NOS2 can limit viral growth but may also suppress the immune system and damage tissue. This study assessed each of these effects in genetically deficient NOS2(-/-) mice after infection with influenza A, a virus against which IFN-gamma has no known activity. At inocula sufficient to cause consolidating pneumonitis and death in wild-type control mice, NOS2(-/-) hosts survived with little histopathologic evidence of pneumonitis. Moreover, they cleared influenza A virus from their lungs by an IFN-gamma-dependent mechanism that was not evident in wild-type mice. Even when the IFN-gamma-mediated antiviral activity was blocked in NOS2(-/-) mice with anti-IFN-gamma mAb, such mice failed to succumb to disease. Further evidence that this protection was independent of viral load was provided by treating NOS2(+/+) mice with the NOS inhibitor, Nomega-methyl-L-arginine (L-NMA). L-NMA prevented mortality without affecting viral growth. Thus, host NOS2 seems to contribute more significantly to the development of influenza pneumonitis in mice than the cytopathic effects of viral replication. Although NOS2 mediates some antiviral effects of IFN-gamma, during influenza infection it can suppress another IFN-gamma-dependent antiviral mechanism. This mechanism was observed only in the complete absence of NOS2 activity and appeared sufficient to control influenza A virus growth in the absence of changes in cytotoxic T lymphocyte activity.

Poor maternal nutrition followed by accelerated postnatal growth leads to telomere shortening and increased markers of cell senescence in rat islets

Low birth weight (LBW) followed by accelerated postnatal growth is associated with increased risk of developing age-associated diseases such as type 2 diabetes. Gestational protein restriction in rats causes LBW, beta-cell dysfunction, and reduced longevity. These effects may be mediated by accelerated cellular aging. This study tested the hypothesis that LBW followed by rapid postnatal catch-up growth leads to islet telomere shortening through alterations in antioxidant defense capacity, stress/senescence marker proteins, and DNA repair mechanisms at the gene expression level. We used our rat model of gestational protein restriction (recuperated offspring) and control offspring. Southern blotting revealed shorter (P<0.001) islet telomeres in recuperated animals compared to controls. This was associated with increased expression of peroxiredoxin 1 (P<0.05), peroxiredoxin 3 (P<0.01), and heme oxygenase-1 (HO-1) (P<0.05), which are up-regulated under stress conditions. MnSOD expression was significantly (P<0.05) decreased in recuperated offspring, suggesting partial impairment of mitochondrial antioxidant defenses. Markers of cellular senescence p21 and p16 were also increased (P<0.01 and P<0.05, respectively) in the recuperated group. We conclude that maternal diet influences expression of markers of cellular stress and telomere length in pancreatic islets. This may provide a mechanistic link between early nutrition and growth and type 2 diabetes.

The product of the c-fms proto-oncogene: a glycoprotein with associated tyrosine kinase activity

The c-fms proto-oncogene is a member of a gene family that has been implicated in tumorigenesis. Glycoproteins encoded by c-fms were identified in cat spleen cells by means of an immune-complex kinase assay performed with monoclonal antibodies to v-fms-coded epitopes. The major form of the normal cellular glycoprotein has an apparent molecular weight of 170,000 and, like the product of the viral oncogene, serves as a substrate for an associated tyrosine-specific protein kinase activity in vitro. The results suggest that the transforming glycoprotein specified by v-fms is a truncated form of a c-fms-coded growth factor receptor.

MADD, a novel death domain protein that interacts with the type 1 tumor necrosis factor receptor and activates mitogen-activated protein kinase

The death domain of the type 1 tumor necrosis factor receptor (TNFR1) mediates interactions with several proteins involved in signaling the downstream effects of TNF. We have used the yeast interaction trap to isolate a protein, MADD, that associates with the death domain of TNFR1 through its own C-terminal death domain. MADD interacts with TNFR1 residues that are critical for signal generation and coimmunoprecipitates with TNFR1, implicating MADD as a component of the TNFR1 signaling complex. Importantly, we have found that overexpression of MADD activates the mitogen-activated protein (MAP) kinase extracellular signal-regulated kinase (ERK), and expression of the MADD death domain stimulates both the ERK and c-JUN N-terminal kinase MAP kinases and induces the phosphorylation of cytosolic phospholipase A2. These data indicate that MADD links TNFR1 with MAP kinase activation and arachidonic acid release and provide further insight into the mechanisms by which TNF exerts its pleiotropic effects.

A cAMP-regulated chloride channel in lymphocytes that is affected in cystic fibrosis

A defect in regulation of a chloride channel appears to be the molecular basis for cystic fibrosis (CF), a common lethal genetic disease. It is shown here that a chloride channel with kinetic and regulatory properties similar to those described for secretory epithelial cells is present in both T and B lymphocyte cell lines. The regulation of the channels by adenosine 3',5'-monophosphate (cAMP)-dependent protein kinase in transformed B cells from CF patients is defective. Thus, lymphocytes may be an accessible source of CF tissue for study of this defect, for cloning of the chloride channel complex, and for diagnosis of the disease.

A perspective on medical infrared imaging

Since the early days of thermography in the 1950s, image processing techniques, sensitivity of thermal sensors and spatial resolution have progressed greatly, holding out fresh promise for infrared (IR) imaging techniques. Applications in civil, industrial and healthcare fields are thus reaching a high level of technical performance. The relationship between body temperature and disease was documented since 400 bc. In many diseases there are variations in blood flow, and these in turn affect the skin temperature. IR imaging offers a useful and non-invasive approach to the diagnosis and treatment (as therapeutic aids) of many disorders, in particular in the areas of rheumatology, dermatology, orthopaedics and circulatory abnormalities. This paper reviews many usages (and hence the limitations) of thermography in biomedical fields.

Parental occupation and childhood cancer: review of epidemiologic studies

Parental occupational exposures might affect childhood cancer in the offspring through genetic changes in the ovum or sperm or through transplacental carcinogenesis. The 24 published epidemiologic studies of this association have all used case-control designs, with controls generally selected from birth certificates or from general population sampling. Occupational exposures were inferred from job titles on birth certificates or through interviews. A large number of occupation-cancer associations have been reported, many of which were not addressed or not confirmed in other studies. Several associations have been found with consistency: paternal exposures in hydrocarbon-associated occupations, the petroleum and chemical industries, and especially paint exposures have been associated with brain cancer; paint exposures have also been linked to leukemias. Maternal exposures have received much less attention, but studies have yielded strongly suggestive results linking a variety of occupational exposures to leukemia and brain cancer. The primary limitations in this literature are the inaccuracy inherent in assigning exposure based on job title alone and imprecision due to limited study size. Although no etiologic associations have been firmly established by these studies, the public health concerns and suggestive data warrant continued research.

Controlled trial of acupuncture for disabling breathlessness

In a randomised controlled trial, twelve matched pairs of patients with chronic obstructive pulmonary disease received traditional Chinese acupuncture or placebo acupuncture. After three weeks' treatment the traditional-acupuncture group showed significantly greater benefit in terms of subjective scores of breathlessness and six-minute walking distance. Objective measures of lung function were unchanged in either group. Whether these differences are mediated by endogenous opiate and/or peptide release remains speculative.

Effect of different etching periods on the bond strength of a composite resin to a machinable porcelain

OBJECTIVES

The purpose of this study was to evaluate microstructure changes of Cerec 2 Vitablocs Mark II porcelain etched by a 5% hydrofluoric acid and examine the effect of different etching times on the bond strength between the porcelain and a composite resin.

METHODS

Six different etching times (0, 5, 30, 60, 120 and 180 s) were used to etch the surfaces of the porcelain, respectively. Etched relief patterns were observed by means of a scanning electron microscope and the bond strength was determined between a dual-cured composite luting agent and the porcelain.

RESULTS

The results showed that composite resin did not bond to unetched porcelain but bonded to etched porcelain, the 120 s etch giving the highest bond strength.

CONCLUSION

The bond strength values corresponded well to the microstructure changes caused by etching.

Anti-biofilm effect of dental adhesive with cationic monomer

The incorporation of polymerizable cationic monomers has been attempted to generate dental resinous materials with antibacterial activity. This study tested the hypothesis that a dental adhesive containing a cationic monomer, methacryloxylethyl cetyl dimethyl ammonium chloride (DMAE-CB), would influence biofilm formation and gtf gene expression of Streptococcus mutans. The effect of the photo-polymerized DMAE-CB-incorporated adhesive on in vitro biofilm accumulation was investigated with spectrophotometry and scanning electron microscopy. The relative level of gtf gene expression by Streptococcus mutans in the biofilm was quantified by real-time reverse-transcription polymerase chain-reaction. The DMAE-CB-incorporated adhesive significantly decreased bio-film accumulation on its surface (P < 0.05), and suppressed the expression of gtfB and gtfC of Streptococcus mutans in the biofilm (P < 0.05). The results suggest that the cured DMAE-CB-incorporated adhesive may hamper biofilm accumulation via selective down-regulation of the expression of gtf genes in Streptococcus mutans.

Barrier contraceptives and sexually transmitted diseases in women: a comparison of female-dependent methods and condoms

INTRODUCTION

Most efforts at sexually transmitted disease (STD) protection center on condom use, but little is known about how condoms compare with other barrier methods, particularly those controlled by women.

METHODS

To evaluate the effect of different barrier contraceptives on the prevalence of STDs and other vaginal infections, we retrospectively studied 5681 visits by women to an urban STD clinic.

RESULTS

As compared with women using no contraceptive or with tubal ligations, women using the contraceptive sponge or diaphragm had at least 65% lower rates of infection with Neisseria gonorrhoeae and Trichomonas vaginalis, while condom users had 34% and 30% lower rates, respectively. For Chlamydia trachomatis, the reduction was 13% among sponge users, 72% among diaphragm users, and 3% among condom users, although these differences were not significant. When compared with women using condoms, women using female-dependent methods (sponge or diaphragm) had significantly lower rates of both gonorrhea and trichomoniasis. Vaginal candidiasis was more common among women using diaphragms but not other barrier methods, while rates of bacterial vaginosis were similar among all groups.

CONCLUSIONS

Women using the contraceptive sponge or diaphragm experience protection from STDs to a greater extent than those relying on condoms. Female-dependent barrier contraceptives should receive more attention in STD risk-reduction programs.

Chronic cerebral hypoperfusion elicits neuronal apoptosis and behavioral impairment

Chronic reductions in cerebral blood flow associated with aging and progressive neurodegenerative disorders can precipitate cognitive failure. To assess whether chronic cerebrovascular insufficiency elicits neuronal apoptosis, apoptotic cell death in the hippocampus was quantitated in a rat model of permanent carotid occlusion. Bilateral carotid artery occlusion (2VO) was shown to induce apoptotic morphology and DNA strand breaks in hippocampal neurons 2 and 27 weeks after ligation. The rate of pyramidal cell apoptosis was higher at chronic (27 weeks) compared to sub-chronic (2 weeks) time points. 2VO-induced apoptosis resulted in a decrease in total pyramidal cell number at 27 weeks but not at earlier time points, indicating progressive neuronal loss. Working and reference memory errors in the radial arm maze were strongly correlated with the number of apoptotic neurons in CA1 but not CA3 pyramidal cell fields. These data provide the first indication that apoptotic loss of pyramidal neurons may play a role in memory impairment associated with clinical conditions of chronic cerebrovascular insufficiency.