Genotypic and phenotypic diversity of the noncapsulated Haemophilus influenzae:Adaptation and pathogenesis in the human airways

The human respiratory tract contains a highly adapted microbiota including commensal and opportunistic pathogens. Noncapsulated or nontypable Haemophilus influenzae (NTHi) is a human-restricted member of the normal airway microbiota in healthy carriers and an opportunistic pathogen in immunocompromised individuals. The duality of NTHi as a colonizer and as a symptomatic infectious agent is closely related to its adaptation to the host, which in turn greatly relies on the genetic plasticity of the bacterium and is facilitated by its condition as a natural competent. The variable genotype of NTHi accounts for its heterogeneous gene expression and variable phenotype, leading to differential host-pathogen interplay among isolates. Here we review our current knowledge of NTHi diversity in terms of genotype, gene expression, antigenic variation, and the phenotypes associated with colonization and pathogenesis. The potential benefits of NTHi diversity studies discussed herein include the unraveling of pathogenicity clues, the generation of tools to predict virulence from genomic data, and the exploitation of a unique natural system for the continuous monitoring of long-term bacterial evolution in human airways exposed to noxious agents. Finally, we highlight the challenge of monitoring both the pathogen and the host in longitudinal studies, and of applying comparative genomics to clarify the meaning of the vast NTHi genetic diversity and its translation to virulence phenotypes.

Distinctive Profile of IsomiR Expression and Novel MicroRNAs in Rat Heart Left Ventricle

MicroRNAs (miRNAs) are single-stranded non-coding RNAs that negatively regulate target gene expression through mRNA cleavage or translational repression. There is mounting evidence that they play critical roles in heart disease. The expression of known miRNAs in the heart has been studied at length by microarray and quantitative PCR but it is becoming evident that microRNA isoforms (isomiRs) are potentially physiologically important. It is well known that left ventricular (patho)physiology is influenced by transmural heterogeneity of cardiomyocyte phenotype, and this likely reflects underlying heterogeneity of gene expression. Given the significant role of miRNAs in regulating gene expression, knowledge of how the miRNA profile varies across the ventricular wall will be crucial to better understand the mechanisms governing transmural physiological heterogeneity. To determinine miRNA/isomiR expression profiles in the rat heart we investigated tissue from different locations across the left ventricular wall using deep sequencing. We detected significant quantities of 145 known rat miRNAs and 68 potential novel orthologs of known miRNAs, in mature, mature* and isomiR formation. Many isomiRs were detected at a higher frequency than their canonical sequence in miRBase and have different predicted targets. The most common miR-133a isomiR was more effective at targeting a construct containing a sequence from the gelsolin gene than was canonical miR-133a, as determined by dual-fluorescence assay. We identified a novel rat miR-1 homolog from a second miR-1 gene; and a novel rat miRNA similar to miR-676. We also cloned and sequenced the rat miR-486 gene which is not in miRBase (v18). Signalling pathways predicted to be targeted by the most highly detected miRNAs include Ubiquitin-mediated Proteolysis, Mitogen-Activated Protein Kinase, Regulation of Actin Cytoskeleton, Wnt signalling, Calcium Signalling, Gap junctions and Arrhythmogenic Right Ventricular Cardiomyopathy. Most miRNAs are not expressed in a gradient across the ventricular wall, with exceptions including miR-10b, miR-21, miR-99b and miR-486.

Body-centric ultra-wideband multi-channel characterisation and spatial diversity in the indoor environment

This study presents the findings of an empirical channel characterisation for an ultra-wideband off-body optic fibre-fed multiple-antenna array within an office and corridor environment. The results show that for received power experiments, the office and corridor were best modelled by lognormal and Rician distributions, respectively [for both line of sight (LOS) and non-LOS (NLOS) scenarios]. In the office, LOS measurements for t and tRMS were both described by the Normal distribution for all channels, whereas NLOS measurements for t and t were Nakagami and Weibull distributed, respectively. For the corridor measurements, LOS for t and t were either Nakagami or normally distributed for all channels, with NLOS measurements for t and t being Nakagami and normally distributed, respectively. This work also shows that achievable diversity gain was influenced by both mutual coupling and cross-correlation co-efficients. Although the best diversity gains were 1.8 dB for three-channel selective diversity combining, the authors present recommendations for improving these results. © The Institution of Engineering and Technology 2013.

Morphometric analysis of corneal endothelial giant cells in normal and traumatized corneas

Corneal endothelial cells from normal and traumatized human, primate, cat and rabbit eyes were studied by specular microscopy. Morphometric analysis was performed on micrographs of corneal endothelium using a semi-automated image analysis system. The results showed that under normal conditions the corneal endothelium of all four species exhibit major morphological similarities (mean cell areas: human 317 +/- 32 microns 2, primate 246 +/- 22 microns2, cat 357 +/- 25 microns 2, rabbit 308 +/- 35 microns 2). The normal corneal endothelium in man was found to be more polymegethous than that of the other species. Trauma to cat, primate and human corneas resulted in a long-term reduction in endothelial cell density and enhanced polymegethism. In contrast, the reparative response of the rabbit ensured the reformation of an essentially normal monolayer following injury. Endothelial giant cells were a normal inclusion in the rabbit corneal endothelium but were only significant in cat, primate and man following trauma. The presence of corneal endothelial giant cells in amitotic corneas may therefore represent a compensatory response in the absence of mitotic potential.

The Role of Growth Trajectories in Classifying Fetal Growth Restriction

OBJECTIVE: To examine the validity of a growth trajectory method to discriminate between pathologically and constitutionally undergrown fetuses using repeated measures of estimated fetal weight.

METHODS: In a prospective, observational, multicenter study in Ireland, 1,116 women with a growth-restricted fetus diagnosed participated with the objective of evaluating ultrasound findings as predictors of pediatric morbidity and mortality. Fetal growth trajectories were based on estimated fetal weight.

RESULTS: Between 22 weeks of gestation and term, two fetal growth trajectories were identified: normal (96.7%) and pathologic (3.3%). Compared with the normal trajectory, the pathologic trajectory was associated with an increased risk for preeclampsia (odds ratio [OR] 8.1, 95% confidence interval [CI] 2.6–23.4), increased umbilical artery resistance at 30 weeks of gestation (OR 12.6, 95% CI 4.6–34.1) or 34 weeks of gestation (OR 28.0, 95% CI 8.9–87.7), reduced middle cerebral artery resistance at 30 weeks of gestation (OR 0.33, 95% CI 0.12–0.96) or 34 weeks of gestation (OR 0.14, 95% CI 0.03–0.74), lower gestational age at delivery (mean 32.02 weeks of gestation compared with 38.02 weeks of gestation; P<.001), and higher perinatal complications (OR 21.5, 95% CI 10.5–44.2). In addition, 89.2% of newborns with pathologic fetal growth were admitted to neonatal intensive care units compared with 25.9% of those with normal growth.

CONCLUSIONS: Fetal growth trajectory analysis reliably differentiated fetuses with a pathologic growth pattern among a group of women with growth-restricted fetuses. With further development, this approach could provide clarity to how we define, identify, and ultimately manage pathologic fetal growth.

LEVEL OF EVIDENCE: II

High population prevalence of cardiac troponin I measured by a high-sensitivity assay and cardiovascular risk estimation: the MORGAM Biomarker Project Scottish Cohort

Aims
Our aim was to test the prediction and clinical applicability of high-sensitivity assayed troponin I for incident cardiovascular events in a general middle-aged European population.

Methods and results
High-sensitivity assayed troponin I was measured in the Scottish Heart Health Extended Cohort (n = 15 340) with 2171 cardiovascular events (including acute coronary heart disease and probable ischaemic strokes), 714 coronary deaths (25% of all deaths), 1980 myocardial infarctions, and 797 strokes of all kinds during an average of 20 years follow-up. Detection rate above the limit of detection (LoD) was 74.8% in the overall population and 82.6% in men and 67.0% in women. Troponin I assayed by the high-sensitivity method was associated with future cardiovascular risk after full adjustment such as that individuals in the fourth category had 2.5 times the risk compared with those without detectable troponin I (P < 0.0001). These associations remained significant even for those individuals in whom levels of contemporary-sensitivity troponin I measures were not detectable. Addition of troponin I levels to clinical variables led to significant increases in risk prediction with significant improvement of the c-statistic (P < 0.0001) and net reclassification (P < 0.0001). A threshold of 4.7 pg/mL in women and 7.0 pg/mL in men is suggested to detect individuals at high risk for future cardiovascular events.

Conclusion
Troponin I, measured with a high-sensitivity assay, is an independent predictor of cardiovascular events and might support selection of at risk individuals.

Spectroscopic Observations of SN 2012fr: A Luminous Normal Type Ia Supernova with Early High Velocity Features and Late Velocity Plateau

We present 65 optical spectra of the Type Ia supernova SN 2012fr, of which 33 were obtained before maximum light. At early times SN 2012fr shows clear evidence of a high-velocity feature (HVF) in the Si II 6355 line which can be cleanly decoupled from the lower velocity "photospheric" component. This Si II 6355 HVF fades by phase -5; subsequently, the photospheric component exhibits a very narrow velocity width and remains at a nearly constant velocity of v~12,000 km/s until at least 5 weeks after maximum brightness. The Ca II infrared (IR) triplet exhibits similar evidence for both a photospheric component at v~12,000 km/s with narrow line width and long velocity plateau, as well as a high-velocity component beginning at v~31,000 km/s two weeks before maximum. SN 2012fr resides on the border between the "shallow silicon" and "core-normal" subclasses in the Branch et al. (2009) classification scheme, and on the border between normal and "high-velocity" SNe Ia in the Wang et al. (2009a) system. Though it is a clear member of the "low velocity gradient" (LVG; Benetii et al., 2005) group of SNe Ia and exhibits a very slow light-curve decline, it shows key dissimilarities with the overluminous SN 1991T or SN 1999aa subclasses of SNe Ia. SN 2012fr represents a well-observed SN Ia at the luminous end of the normal SN Ia distribution, and a key transitional event between nominal spectroscopic subclasses of SNe Ia.

Distal Deposition of Tephra from the Eyjafjallajökull 2010 Summit Eruption

The 2010 Eyjafjallajökull lasted 39 days and had 4 different phases, of which the first and third (14–18 April and 5–6 May) were most intense. Most of this period was dominated by winds with a northerly component that carried tephra toward Europe, where it was deposited in a number of locations and was sampled by rain gauges or buckets, surface swabs, sticky-tape samples and air filtering. In the UK, tephra was collected from each of the Phases 1–3 with a combined range of latitudes spanning the length of the country. The modal grain size of tephra in the rain gauge samples was 25 um, but the largest grains were 100 um in diameter and highly vesicular. The mass loading was equivalent to 8–218 shards cm2, which is comparable to tephra layers from much larger past eruptions. Falling tephra was collected on sticky tape in the English Midlands on 19, 20 and 21st April (Phase 2), and was dominated by aggregate clasts (mean diameter 85 um, component grains <10 um). SEM-EDS spectra for aggregate grains contained an extra peak for sulphur, when compared to control samples from the volcano, indicating that they were cemented by sulphur-rich minerals e.g. gypsum (CaSO4⋅H2O). Air quality monitoring stations did not record fluctuations in hourly PM10 concentrations outside the normal range of variability during the eruption, but there was a small increase in 24-hour running mean concentration from 21–24 April (Phase 2). Deposition of tephra from Phase 2 in the UK indicates that transport of tephra from Iceland is possible even for small eruption plumes given suitable wind conditions. The presence of relatively coarse grains adds uncertainty to concentration estimates from air quality sensors, which are most sensitive to grain sizes <10 um. Elsewhere, tephra was collected from roofs and vehicles in the Faroe Islands (mean grain size 40 um, but 100 um common), from rainwater in Bergen in Norway (23–91 um) and in air filters in Budapest, Hungary (2–6 um). A map is presented summarizing these and other recently published examples of distal tephra deposition from the Eyjafjallajökull eruption. It demonstrates that most tephra deposited on mainland Europe was produced in the highly explosive Phase 1 and was carried there in 2–3 days.

Temperature dependence of the mid-infrared dielectric function of YBCO in the ab plane

We have excited mid-infrared surface plasmons in two YBCO thin films of contrasting properties using attenuated total reflection of light and found that the imaginary part of the dielectric function decreases linearly with reduction in temperature. This result is in contrast with the commonly reported conclusion of infrared normal reflectance studies. If sustained it may clarify the problem of understanding the normal state properties of YBCO and the other cuprates. The dielectric function of the films, epsilon = epsilon(1) + i epsilon(2), was determined between room temperature and 80K: epsilon(1) was found to be only slightly temperature dependent but somewhat sample dependent, probably as a result of surface and grain boundary contamination. The imaginary part, epsilon(2), (and the real part of the conductivity, sigma(1),) decreased linearly with reduction in temperature in both films. Results obtained were: for film 1: epsilon(1) = - 14.05 - 0.0024T and epsilon(2) - 4.11 + 0.086T and for film 2: epsilon(1) = - 24.09 + 0.0013T and epsilon(2) = 7.66 + 0.067T where T is the temperature in Kelvin. An understanding of the results is offered in terms of temperature-dependent intrinsic intragrain inelastic scattering and temperature-independent contributions: elastic and inelastic grain boundary scattering and optical interband (or localised charge) absorption. The relative contribution of each is estimated. A key conclusion is that the interband (or localised charge) absorption is only similar to 10%. Most importantly, the intrinsic scattering rate, 1/tau, decreases linearly with fall in temperature, T, in a regime where current theory predicts dependence on frequency, omega, to dominate. The coupling constant, lambda, between the charge carriers and the thermal excitations has a value of 1.7, some fivefold greater than the far infrared value. These results imply a need to restate the phenomenology of the normal state of high temperature superconductors and seek a corresponding theoretical understanding.

Next-generation sequencing of the mitochondrial genome and association with IgA nephropathy in a renal transplant population

Kidneys are highly aerobic organs that are critically dependent on the normal functioning of mitochondria. Genetic variations disrupting mitochondrial function are associated with multifactorial disorders including kidney disease. This study sequenced the entire mitochondrial genome in a renal transplant cohort of 64 individuals, using next-generation sequencing, to evaluate the association of genetic variants with IgA nephropathy and end-stage renal disease (ESRD, n = 100).

On the scaling behavior of electric conductivity in [C(4)mim][NTf2]

In this work we examine, for the first time, the molar conductivity behavior of the deeply supercooled room temperature ionic liquid [C₄mim][NTf₂] in the temperature, pressure and volume thermodynamic space in terms of density scaling (TV^γ)⁻¹ combined with the equation of state (EOS). The exponent γ_σ determined from the Avramov model analysis is compared with the coefficient obtained from the viscosity studies carried out at moderate temperatures. Therefore, the experimental results presented herein provide the answer to the long-standing question regarding the validity of thermodynamic scaling of ionic liquids over a wide temperature range, i.e. from the normal liquid state to the glass transition point. Finally, we investigate the relationship between the dynamic and thermodynamic properties of [C₄mim][NTf₂] represented by scaling exponent γ and Grüneisen constant γ_G, respectively.

BRCA1--conductor of the breast stem cell orchestra:the role of BRCA1 in mammary gland development and identification of cell of origin of BRCA1 mutant breast cancer

Breast cancer treatment has been increasingly successful over the last 20 years due in large part to targeted therapies directed against different subtypes. However, basal-like breast cancers still represent a considerable challenge to clinicians and scientists alike since the pathogenesis underlying the disease and the target cell for transformation of this subtype is still undetermined. The considerable similarities between basal-like and BRCA1 mutant breast cancers led to the hypothesis that these cancers arise from transformation of a basal cell within the normal breast epithelium through BRCA1 dysfunction. Recently, however, a number of studies have called this hypothesis into question. This review summarises the initial findings which implicated the basal cell as the cell of origin of BRCA1 related basal-like breast cancers, as well as the more recent data which identifies the luminal progenitor cells as the likely target of transformation. We compare a number of key studies in this area and identify the differences that could explain some of the contradictory findings. In addition, we highlight the role of BRCA1 in breast cell differentiation and lineage determination by reviewing recent findings in the field and our own observations suggesting a role for BRCA1 in stem cell regulation through activation of the p63 and Notch pathways. We hope that through an increased understanding of the BRCA1 role in breast differentiation and the identification of the cell(s) of origin we can improve treatment options for both BRCA1 mutant and basal-like breast cancer subgroups.

Microphysiological modeling of the reproductive tract: A fertile endeavor

Preclinical toxicity testing in animal models is a cornerstone of the drug development process, yet it is often unable to predict adverse effects and tolerability issues in human subjects. Species-specific responses to investigational drugs have led researchers to utilize human tissues and cells to better estimate human toxicity. Unfortunately, human cell-derived models are imperfect because toxicity is assessed in isolation, removed from the normal physiologic microenvironment. Microphysiological modeling often referred to as 'organ-on-a-chip' or 'human-on-a-chip' places human tissue into a microfluidic system that mimics the complexity of human in vivo physiology, thereby allowing for toxicity testing on several cell types, tissues, and organs within a more biologically relevant environment. Here we describe important concepts when developing a repro-on-a-chip model. The development of female and male reproductive microfluidic systems is critical to sex-based in vitro toxicity and drug testing. This review addresses the biological and physiological aspects of the male and female reproductive systems in vivo and what should be considered when designing a microphysiological human-on-a-chip model. Additionally, interactions between the reproductive tract and other systems are explored, focusing on the impact of factors and hormones produced by the reproductive tract and disease pathophysiology.

High-affinity NO3 --H+ cotransport in the fungus Neurospora:Induction and control by pH and membrane voltate

High-affinity nitrate transport was examined in intact hyphae of Neurospora crassa using electrophysiological recordings to characterize the response of the plasma membrane to NO₃ ^- challenge and to quantify transport activity. The NO₃ ^--associated membrane current was determined using a three electrode voltage clamp to bring membrane voltage under experimental control and to compensate for current dissipation along the longitudinal cell axis. Nitrate transport was evident in hyphae transferred to NO₃ ^--free, N-limited medium for 15 hr, and in hyphae grown in the absence of a nitrogen source after a single 2-min exposure to 100 μM NO₃ ^-. In the latter, induction showed a latency of 40-80 min and rose in scalar fashion with full transport activity mensurable approx. 100 min after first exposure to NO₃ ^-; it was marked by the appearance of a pronounced sensitivity of membrane voltage to extracellular NO₃ ^- additions which, after induction, resulted in reversible membrane depolarizations of (+)54-85 mV in the presence of 50 μM NO₃ ^-; and it was suppressed when NH₄ ⁺, was present during the first, inductive exposure to NO₃ ^-. Voltage clamp measurements carried out immediately before and following NO₃ ^- additions showed that the NO₃ ^--evoked depolarizations were the consequence of an inward-directed current that appeared in parallel with the depolarizations across the entire range of accessible voltages -400 to +100 mV). Measurements of NO₃ ^- uptake using NO₃ ^--selective macroelectrodes indicated a charge stoichiometry for NO₃ ^- transport of 1(+):1(NO₃ ^-) with common K(m) and J(max) values around 25 μM and 75 pmol NO₃ ^- cm^-2sec^-1, respectively, and combined measurements of pH(o) and [NO₃ ^-](o) showed a net uptake of approx. 1 H⁺ with each NO₃ ^- anion. Analysis of the NO₃ ^- current demonstrated a pronounced voltage sensitivity within the normal physiological range between -300 and -100 mV as well as interactions between the kinetic parameters of membrane voltage, pH(o) and [NO₃ ^-](o). Increasing the bathing pH from 5.5 to 8.0 reduced the current and the associated membrane depolarizations 2- to 4-fold. At a constant pH(o) of 6.1, driving the membrane voltage from -350 to -150 mV resulted in an approx. 3-fold reduction in the maximum current and a 5-fold rise in the apparent affinity for NO₃ ^-. By contrast, the same depolarization effected an approx. 20% fall in the K(m) for transport as a function in [H⁺](o). These, and additional results are consistent with a charge-coupling stoichiometry of 2(H⁺) per NO anion transported across the membrane, and implicate a carrier cycle in which NO binding is kinetically adjacent to the rate-limiting step of membrane charge transit. The data concur with previous studies demonstrating a pronounced voltage-dependence to high-affinity NO₃ ^- transport system in Arabidopsis, and underline the importance of voltage as a kinetic factor controlling NO₃ ^- transport; finally, they distinguish metabolite repression of NO₃ ^- transport induction from its sensitivity to metabolic blockade and competition with the uptake of other substrates that draw on membrane voltage as a kinetic substrate.