miRNAs from Inflamed Gingiva Link Gene Signaling to Increased MET Expression

Several array-based microRNA (miRNA) expression studies independently showed increased expression of miRNAs hsa-miR-130a-3p, -142-3p, -144-3p, -144-5p, -223-3p, -17-5p, and -30e-5p in gingiva affected by periodontal inflammation. We aimed to determine direct target genes and signaling pathways regulated by these miRNAs to identify processes relevant to gingival inflammatory responses and tissue homeostasis. We transfected miRNA mimics (mirVana) for each of the 7 miRNAs separately into human primary gingival fibroblasts cultured from 3 different donors. Following RNA sequencing, differential gene expression and second-generation gene set enrichment analyses were performed. miRNA inhibition and upregulation was validated at the transcript and protein levels using quantitative reverse transcriptase polymerase chain reaction, Western blotting, and reporter gene assays. All 7 miRNAs significantly increased expression of the gene MET proto-oncogene, receptor tyrosine kinase (MET). Expression of known periodontitis risk genes CPEB1, ABCA1, and ATP6V1C1 was significantly repressed by hsa-miR-130a-3p, -144-3p, and -144-5p, respectively. The genes WASL, ENPP5, ARL6IP1, and IDH1 showed the most significant and strongest downregulation after hsa-miR-142-3p, -17-5p, -223-3p, and -30e-5p transfection, respectively. The most significantly regulated gene set of each miRNA related to cell cycle (hsa-miRNA-144-3p and -5p [Padj = 4 × 10-40 and Padj = 4 × 10-6], -miR-17-5p [Padj = 9.5 × 10-23], -miR-30e-5p [Padj = 8.2 × 10-18], -miR-130a-3p [Padj = 5 × 10-15]), integrin cell surface interaction (-miR-223-3p [Padj = 2.4 × 10-7]), and interferon signaling (-miR-142-3p [Padj = 5 × 10-11]). At the end of acute inflammation, gingival miRNAs bring together complex regulatory networks that lead to increased expression of the gene MET. This underscores the importance of mesenchymal cell migration and invasion during gingival tissue remodeling and proliferation in restoring periodontal tissue homeostasis after active inflammation. MET, a receptor of the mitogenic hepatocyte growth factor fibroblast secreted, is a core gene of this process.

BACH1 Binding Links the Genetic Risk for Severe Periodontitis with ST8SIA1

Genome-wide association studies identified various loci associated with periodontal diseases, but assigning causal alleles remains difficult. Likewise, the generation of biological meaning underlying a statistical association has been challenging. Here, we characterized the genetic association at the gene ST8SIA1 that increases the risk for severe periodontitis in smokers. We used CRISPR/dCas9 activation and RNA-sequencing to identify genetic interaction partners of ST8SIA1 and to determine its function in the cell. We used reporter gene assays to identify regulatory elements at the associated single-nucleotide polymorphisms (SNPs) and to determine effect directions and allele-specific changes of enhancer activity. Antibody electrophoretic mobility shift assays proved allele-specific transcription factor binding at the putative causal SNPs. We found the reported periodontitis risk gene ABCA1 as the top upregulated gene following ST8SIA1 activation. Gene set enrichment analysis showed highest effects on integrin cell surface interactions (area under the curve [AUC] = 0.85; q = 4.9 × 10-6) and cell cycle regulation (AUC = 0.89; q = 1.6 × 10-5). We identified 2 associated repressor elements in the introns of ST8SIA1 that bind the transcriptional repressor BACH1. The putative causative variant rs2012722 decreased BACH1 binding by 40%. We also pinpointed ST8SIA1 as the target gene of the association. ST8SIA1 inhibits cell adhesion with extracellular matrix proteins, integrins, and cell cycle, as well as enhances apoptosis. Likewise, tobacco smoke reportedly results in an inhibition of cell adhesion and a decrease in integrin-positive cells and cell growth. We conclude that impaired ST8SIA1 repression, independently caused by reduced BACH1 binding at the effect T allele, as well as by tobacco smoke, contributes to higher ST8SIA1 levels, and in smokers who carry the effect T allele, both factors would be additive with damaging effects on the gingival barrier integrity. The activity of ST8SIA1 is also linked with the periodontitis risk gene ABCA1.

Entamoeba gingivalis Exerts Severe Pathogenic Effects on the Oral Mucosa

The protozoan Entamoeba gingivalis colonizes the healthy oral mucosa with a prevalence of 15%. Colonization can be asymptomatic, and it is considered not pathogenic. However, it is able to invade lacerated oral mucosa, where it ingests fragments of live cells, suggesting pathogenous potential. Here, we characterized the transcriptomes of gingival cells after infection with E. gingivalis using RNA sequencing and observed pathogen interaction with the epithelial monolayer barrier by scanning electron microscopy. In epithelial and fibroblast cells, strongest differential expression showed gene set “chemokines and inflammatory molecules in myeloid cells” (area under the curve [AUC] = 0.9, effect size 5.15, adjusted P = 3.1 × 10⁻¹⁹) and “cell cycle and growth arrest” (AUC = 0.91, effect size = 4.56, adjusted P = 4.8 × 10⁻⁹), respectively. The most upregulated genes were TNF (fold change 430) and IL8 (fold change 359) in epithelial cells and ZN331 (fold change 18) in fibroblasts. We showed that E. gingivalis killed live epithelial cells by trogocytosis, demonstrating strong pathogenic potential.

Human immunology studies using organ donors: Impact of clinical variations on immune parameters in tissues and circulation

Organ donors are sources of physiologically healthy organs and tissues for life-saving transplantation, and have been recently used for human immunology studies which are typically confined to the sampling of peripheral blood. Donors comprise a diverse population with different causes of death and clinical outcomes during hospitalization, and the effects of such variations on immune parameters in blood and tissues are not known. We present here a coordinate analysis of innate and adaptive immune components in blood, lymphoid (bone marrow, spleen, lymph nodes), and mucosal (lungs, intestines) sites from a population of brain-dead organ donors (2 months-93 years; n = 291) across eight clinical parameters. Overall, the blood of donors exhibited similar monocyte and lymphocyte content and low serum levels of pro-inflammatory cytokines as healthy controls; however, donor blood had increased neutrophils and serum levels of IL-8, IL-6, and MCP-1 which varied with cause of death. In tissues, the frequency and composition of monocytes, neutrophils, B lymphocytes and T cell subsets in lymphoid or mucosal sites did not vary with clinical state, and was similar in donors independent of the extent of clinical complications. Our results reveal that organ donors maintain tissue homeostasis, and are a valuable resource for fundamental studies in human immunology.

Differential transcriptomic and metabolic profiles of M. africanum- and M. tuberculosis-infected patients after, but not before, drug treatment

The epidemiology of Mycobacterium tuberculosis (Mtb) and M. africanum (Maf) suggest differences in their virulence, but the host immune profile to better understand the pathogenesis of tuberculosis (TB) have not been studied. We compared the transcriptomic and metabolic profiles between Mtb and Maf-infected TB cases to identify host biomarkers associated with lineages-specific pathogenesis and response to anti-TB chemotherapy. Venous blood samples from Mtb- and Maf-infected patients obtained before and after anti-TB treatment were analysed for cell composition, gene expression and metabolic profiles. Prior to treatment, similar transcriptomic profiles were seen in Maf- and Mtb-infected patients. In contrast, post-treatment, over 1600 genes related to immune responses and metabolic diseases were differentially expressed between the groups. Notably, the upstream regulator hepatocyte nuclear factor 4-alpha (HNF4α), which regulated 15% of these genes, was markedly enriched. Serum metabolic profiles were similar in both group pre-treatment, but the decline in pro-inflammatory metabolites post-treatment were most pronounced in Mtb-infected patients. Together, the differences in both peripheral blood transcriptomic and serum metabolic profiles between Maf- and Mtb-infected patients observed over the treatment period, might be indicative of intrinsic host factors related to susceptibility to TB and/or differential efficacy of the standard anti-TB treatment on the two lineages.

Photosensitisation studies of silicone polymer doped with methylene blue and nanogold for antimicrobial applications

2 nm gold nanoparticle (AuNP) and methylene blue (MB) incorporated into medical-grade silicone polymer for antimicrobial applications.

Recent advances towards tuberculosis control: vaccines and biomarkers

Of all infectious diseases, tuberculosis (TB) remains one of the most important causes of morbidity and mortality. Recent advances in understanding the biology of Mycobacterium tuberculosis (Mtb) infection and the immune response of the infected host have led to the development of several new vaccines, a number of which are already undergoing clinical trials. These include pre-exposure prime vaccines, which could replace bacille Calmette-Guérin (BCG), and pre-exposure booster vaccines given in addition to BCG. Infants are the target population of these two types of vaccines. In addition, several postexposure vaccines given during adolescence or adult life, in addition to BCG as a priming vaccine during infancy, are undergoing clinical testing. Therapeutic vaccines are currently being assessed for their potential to cure active TB as an adjunct to chemotherapy. BCG replacement vaccines are viable recombinant BCG or double-deletion mutants of Mtb. All booster vaccines are composed of one or several antigens, either expressed by viral vectors or formulated with adjuvants. Therapeutic vaccines are killed mycobacterial preparations. Finally, multivariate biomarkers and biosignatures are being generated from high-throughput data with the aim of providing better diagnostic tools to specifically determine TB progression. Here, we provide a technical overview of these recent developments as well of the relevant computational approaches and highlight the obstacles that still need to be overcome.

Asymmetric competition in plant populations

Recently there has been much interest in the hypothesis that competition between individual plants is asymmetric or onesided: larger individuals obtain a disproportionate share of the resources (for their relative size) and suppress the growth of smaller individuals. This has important implications for population structure, for the analysis of competition between plants at the individual, population and community levels, and for our understanding of competition as a selective force in the evolution of plant populations.

Safety and tolerability of cladribine tablets in multiple sclerosis: the CLARITY (CLAdRIbine Tablets treating multiple sclerosis orallY) study

BACKGROUND

Cladribine is a synthetic deoxyadenosine analogue in development as an oral multiple sclerosis (MS) therapy.

OBJECTIVE

To report in detail the safety findings from the 96-week, phase III, double-blind CLARITY study, which evaluated treatment with cladribine tablets in relapsing-remitting MS.

METHODS

A total of 1,326 patients were randomized 1:1:1 to two short-course regimens of cladribine tablets (3.5 or 5.25 mg/kg cumulative dose over 96 weeks) or placebo. Safety assessments included monitoring for adverse events (AEs), routine physical and neurologic examinations and frequent laboratory parameter assessments.

RESULTS

Of the randomized patients, 88.6% completed treatment with cladribine tablets versus 86.3% with placebo. Lymphopenia was the most commonly reported AE in patients treated with cladribine tablets and was anticipated based on the mechanism of action. The incidence of infections was 48.3% with cladribine tablets and 42.5% with placebo, with 99.1% and 99.0% rated mild-to-moderate by investigators. Herpes zoster infections developed in 20 (2.3%) cladribine-treated patients; all cases were dermatomal. There were no herpes zoster infections in the placebo group. Nine (1.0%) patients experienced events related to uterine leiomyomas in the cladribine tablets groups versus one (0.2%) with placebo. Three isolated cases of malignancy were reported in cladribine-treated patients during the study; a fourth was reported during post-study surveillance. A pre-malignant cervical carcinoma in situ was also reported. The incidence of malignancies during the study did not exceed the expected rate in a population standardized for country, gender and age.

CONCLUSION

The safety and tolerability profile observed in the CLARITY study together with the reported efficacy support the potential for cladribine tablets as an MS therapy.

Combination of GM-CSF and cytosine in myelodysplasia results in improved neutrophil function

Granulocyte-macrophage colony-stimulating factor (GM-CSF) was given concurrently with low-dose cytosine arabinoside for 3 weeks to patients with myelodysplasia. Neutrophil activation as evidenced by increased chemiluminescence and reduced surface expression of CD16 was consistently seen during therapy. An attendant fall in chemotaxis was also observed. These effects occurred even when neutrophil counts did not rise significantly at lower doses of GM-CSF. Although no improvement in anaemia or thrombocytopenia was observed, the neutrophil counts became normal during therapy without significant expansion of marrow cellularity or colony-forming ability. No major toxicities were observed, even at higher dosages of GM-CSF.

High-frequency response of subwavelength-structured metals in the petahertz domain

Electromagnetic plane waves, incident on and reflecting from a dielectric-conductor interface, set up a standing wave in the dielectric with the B-field adjacent to the conductor. It is shown here how the harmonic time variation of this B-field induces an E-field and a conduction current J (c) within the skin depth of a real metal; and that at frequencies in the visible and near-infrared range, the imaginary term sigmai of the complex conductivity sigma = sigma(r) + isigma(i) dominates the optical response. Continuity conditions of the E-field through the surface together with the in-quadrature response of the conductivity determine the phase relation between the incident E-M field and J(c). If slits or grooves are milled into the metal surface, a displacement current in the dielectric gap and oscillating charge dipoles at the structure edges are established in quadrature phase with incident field. These dipoles radiate into the aperture and launch surface waves from the edges. They are the principle source of light transmission through the apertures.

The effects of density, spatial pattern, and competitive symmetry on size variation in simulated plant populations

Patterns of size inequality in crowded plant populations are often taken to be indicative of the degree of size asymmetry of competition, but recent research suggests that some of the patterns attributed to size-asymmetric competition could be due to spatial structure. To investigate the theoretical relationships between plant density, spatial pattern, and competitive size asymmetry in determining size variation in crowded plant populations, we developed a spatially explicit, individual-based plant competition model based on overlapping zones of influence. The zone of influence of each plant is modeled as a circle, growing in two dimensions, and is allometrically related to plant biomass. The area of the circle represents resources potentially available to the plant, and plants compete for resources in areas in which they overlap. The size asymmetry of competition is reflected in the rules for dividing up the overlapping areas. Theoretical plant populations were grown in random and in perfectly uniform spatial patterns at four densities under size-asymmetric and size-symmetric competition. Both spatial pattern and size asymmetry contributed to size variation, but their relative importance varied greatly over density and over time. Early in stand development, spatial pattern was more important than the symmetry of competition in determining the degree of size variation within the population, but after plants grew and competition intensified, the size asymmetry of competition became a much more important source of size variation. Size variability was slightly higher at higher densities when competition was symmetric and plants were distributed nonuniformly in space. In a uniform spatial pattern, size variation increased with density only when competition was size asymmetric. Our results suggest that when competition is size asymmetric and intense, it will be more important in generating size variation than is local variation in density. Our results and the available data are consistent with the hypothesis that high levels of size inequality commonly observed within crowded plant populations are largely due to size-asymmetric competition, not to variation in local density.

Phase shifts and interference in surface plasmon polariton waves

A pi phase shift between the incident wave and surface Plasmon polariton (SPP) waves launched from a one-dimensional (slit or groove) subwavelength structure has been found in numerical simulations and invoked to explain recent measurements of optical transmission in slit arrays. Although groove launchers exhibit an overall phase shift that depends on the groove depth, it is shown here how magnetic field induction at the incident surface, and oscillating dipoles from the accumulated charge at the slit or groove edges on the entrance facet lead to an intrinsic pi phase shift, independent of the groove or slit depth. Destructive interference between the pi-shifted surface wave and the incident wave explains the observed transmission minima when the pitch of an array of slits becomes equal to an integer multiple of the SPP wavelength.

Surface-wave interferometry on single subwavelength slit-groove structures fabricated on gold films

We apply the technique of far-field interferometry to measure the properties of surface waves generated by two-dimensional (2D) single subwavelength slit-groove structures on gold films. The effective surface index of refraction n(surf) measured for the surface wave propagating over a distance of more than 12 mum is determined to be n(surf) = 1.016+/-0.004, to within experimental uncertainty close to the expected bound surface plasmon-polariton (SPP) value for a Au/Air interface of n (spp) = 1.018. We compare these measurements to finite-difference-time-domain (FDTD) numerical simulations of the optical field transmission through these devices. We find excellent agreement between the measurements and the simulations for n(surf). The measurements also show that the surface wave propagation parameter k(surf) exhibits transient behavior close to the slit, evolving smoothly from greater values asymptotically toward k (spp) over the first 2-3 mum of slit-groove distance x(sg). This behavior is confirmed by the FDTD simulations.

Surface quality and surface waves on subwavelength-structured silver films

We analyze the physical-chemical surface properties of single-slit, single-groove subwavelength-structured silver films with high-resolution transmission electron microscopy and calculate exact solutions to Maxwell's equations corresponding to recent far-field interferometry experiments using these structures. Contrary to a recent suggestion the surface analysis shows that the silver films are free of detectable contaminants. The finite-difference time-domain calculations, in excellent agreement with experiment, show a rapid fringe amplitude decrease in the near zone (slit-groove distance out to 3-4 wavelengths). Extrapolation to slit-groove distances beyond the near zone shows that the surface wave evolves to the expected bound surface plasmon polariton (SPP). Fourier analysis of these results indicates the presence of a distribution of transient, evanescent modes around the SPP that dephase and dissipate as the surface wave evolves from the near to the far zone.

One billion years of bZIP transcription factor evolution: conservation and change in dimerization and DNA-binding site specificity

The genomic era has revealed that the large repertoire of observed animal phenotypes is dependent on changes in the expression patterns of a finite number of genes, which are mediated by a plethora of transcription factors (TFs) with distinct specificities. The dimerization of TFs can also increase the complexity of a genetic regulatory network manifold, by combining a small number of monomers into dimers with distinct functions. Therefore, studying the evolution of these dimerizing TFs is vital for understanding how complexity increased during animal evolution. We focus on the second largest family of dimerizing TFs, the basic-region leucine zipper (bZIP), and infer when it expanded and how bZIP DNA-binding and dimerization functions evolved during the major phases of animal evolution. Specifically, we classify the metazoan bZIPs into 19 families and confirm the ancient nature of at least 13 of these families, predating the split of the cnidaria. We observe fixation of a core dimerization network in the last common ancestor of protostomes-deuterostomes. This was followed by an expansion of the number of proteins in the network, but no major dimerization changes in interaction partners, during the emergence of vertebrates. In conclusion, the bZIPs are an excellent model with which to understand how DNA binding and protein interactions of TFs evolved during animal evolution.

All-optical atom surface traps implemented with one-dimensional planar diffractive microstructures

We characterize the loading, containment and optical properties of all-optical atom traps implemented by diffractive focusing with one-dimensional (1D) microstructures milled on gold films. These on-chip Fresnel lenses with focal lengths of the order of a few hundred microns produce optical-gradient-dipole traps. Cold atoms are loaded from a mirror magneto-optical trap (MMOT) centered a few hundred microns above the gold mirror surface. Details of loading optimization are reported and perspectives for future development of these structures are discussed.

Surface wave generation and propagation on metallic subwavelength structures measured by far-field interferometry

Transmission spectra of metallic films or membranes perforated by arrays of subwavelength slits or holes have been widely interpreted as resonance absorption by surface plasmon polaritons. Alternative interpretations involving evanescent waves diffracted on the surface have also been proposed. These two approaches lead to divergent predictions for some surface wave properties. Using far-field interferometry, we have carried out a series of measurements on elementary one-dimensional subwavelength structures with the aim of testing key properties of the surface waves and comparing them to predictions of these two points of view.

Specialty care by child neurologists: a workforce analysis

OBJECTIVE

To provide a current profile of the practice of child neurology, report the attitudes of child neurologists toward practice, and analyze the supply of child neurologists.

METHODS

In March 2002, a questionnaire was sent to all active members of the Child Neurology Society (n = 1,051) and to nonmember physicians under age 70 who listed child neurology as a primary or secondary specialty on the American Medical Association Masterfile (n = 433). The response rate was 65%. Eligibility criteria were then applied to arrive at the sample of main specialty in child neurology working at least 20 hours per week in patient care. The final population was 604. Differences in practice characteristics were tested by practice type, and the number of full-time patient care child neurologists was projected by extrapolating to nonrespondents.

RESULTS

There are 904 full-time patient care child neurologists in the United States and 1.27 per 100,000 children. Career satisfaction is 90%, yet no growth in the supply is projected over the next 20 years. Wait times for an appointment average 53 and 44 days for a new and return visit, with longer wait times in university settings. Average annual income is 151,000 dollars.

CONCLUSION

The practice characteristics of child neurologists suggest that the specialty will be challenged to meet patient demands.

The evolution of domain arrangements in proteins and interaction networks

Proteins are composed of domains, which are conserved evolutionary units that often also correspond to functional units and can frequently be detected with reasonable reliability using computational methods. Most proteins consist of two or more domains, giving rise to a variety of combinations of domains. Another level of complexity arises because proteins themselves can form complexes with small molecules, nucleic acids and other proteins. The networks of both domain combinations and protein interactions can be conceptualised as graphs, and these graphs can be analysed conveniently by computational methods. In this review we summarise facts and hypotheses about the evolution of domains in multi-domain proteins and protein complexes, and the tools and data resources available to study them.

The nature of alkanethiol self-assembled monolayer adsorption on sputtered gold substrates

A detailed study of the self-assembly and coverage by 1-nonanethiol of sputtered Au surfaces using molecular resolution atomic force microscopy (AFM) and scanning tunneling microscopy (STM) is presented. The monolayer self-assembles on a smooth Au surface composed predominantly of [111] oriented grains. The domains of the alkanethiol monolayer are observed with sizes typically of 5-25 nm, and multiple molecular domains can exist within one Au grain. STM imaging shows that the (4 x 2) superlattice structure is observed as a (3 x 2) structure when imaged under noncontact AFM conditions. The 1-nonanethiol molecules reside in the threefold hollow sites of the Au[111] lattice and aligned along its [112] lattice vectors. The self-assembled monolayer (SAM) contains many nonuniformities such as pinholes, domain boundaries, and monatomic depressions which are present in the Au surface prior to SAM adsorption. The detailed observations demonstrate limitations to the application of 1-nonanethiol as a resist in atomic nanolithography experiments to feature sizes of approximately 20 nm.

Transcription profiles of the bacterium Mycoplasma pneumoniae grown at different temperatures

Applying microarray technology, we have investigated the transcriptome of the small bacterium Mycoplasma pneumoniae grown at three different temperature conditions: 32, 37 and 32 degrees C followed by a heat shock for 15 min at 43 degrees C, before isolating the RNA. From 688 proposed open-reading frames, 676 were investigated and 564 were found to be expressed (P < 0.001; 606 with P < 0.01) and at least 33 (P < 0.001; 77 at P < 0.01) regulated. By quantitative real-time PCR of selected mRNA species, the expression data could be linked to absolute molecule numbers. We found M.pneumoniae to be regulated at the transcriptional level. Forty-seven genes were found to be significantly up-regulated after heat shock (P < 0.01). Among those were the conserved heat shock genes like dnaK, lonA and clpB, but also several genes coding for ribosomal proteins and 10 genes of unassigned functions. In addition, 30 genes were found to be down-regulated under the applied heat shock conditions. Further more, we have compared different methods of cDNA synthesis (random hexamer versus gene-specific primers, different RNA concentrations) and various normalization strategies of the raw microarray data.

Ischaemic heart disease among livestock and agricultural workers

BACKGROUND

Agricultural workers are exposed to organic dust containing endotoxins, mites, and moulds.

AIMS

To compare the occurrence of ischaemic heart disease (IHD) among male and female livestock and agricultural workers with gainfully employed men and women in Sweden.

METHODS

Male and female livestock and agricultural workers were identified in the Swedish National Censuses of 1970 and 1990 and were followed until the end of 1995. The IHD mortality among the livestock and agricultural workers was compared with that of gainfully employed men and women. Information of smoking habits was gathered from a previous national survey.

RESULTS

Male as well as female livestock workers had slightly higher standardised mortality ratios (SMR) regarding IHD compared with all gainfully employed men and women in Sweden. The SMR for male workers was 1.06 (95% CI 0.95 to 1.18). The SMR for female workers was 1.10 (95% CI 0.98 to 1.23). Agricultural workers had lower SMRs. Adjustments for smoking habits would further increase the SMRs by about 9% in male workers and about 5% in female workers.

CONCLUSION

The present data suggest a slightly increased risk for IHD among both male and female livestock workers, which may be the result of organic dust exposure.