20: NASOPHARYNX MICROBIOME COMPOSITION VARIES OVER TIME IN PEDIATRIC ASTHMA

Purpose of Study

The application of next-generation sequencing (NGS) technology has shown that microbial communities in the respiratory airways (i.e., the microbiome) play a significant role in the onset, development and severity of asthma. However, little is known about their temporal dynamics (i.e., microbial succession), which poses a significant obstacle to identifying pulmotypes of disease and assessing inter-patient variation. Here, we couple NGS and 16S rRNA data to characterize the nasopharynx microbiome of children with asthma and determine its stability over time.

Methods Used

We collected nasal washes from 40 children with asthma enrolled in the AsthMaP-2 Project from two consecutive visits, six months apart. Total DNA was extracted and sequenced for the 16S-V4 rRNA gene region (∼250 bp) using the MySeq Illumina platform. Reads were analyzed in Mothur using the SILVAv119 reference database. Alpha diversity metrics and phylogenetic and count-base distance community indexes of beta diversity were compared across samples and time points. PCoA and NJ clustering analysis were used to assess community relatedness. Differences in alpha diversity and OTU abundance between sample pairs across time points were also compared.

Summary of Results

A mean of 27,479 clean 16S sequences corresponding to an average of 173 OTUs were sequenced and detected per sample, respectively. Representatives of Moraxella, Corynebacterium, Prevotella, Staphylococcus, Alloiococcus, Streptococcus, Peptoniphilus, Fusobacterium, and Haemophilus accounted for 36 to 99% of the reads across samples. These genera have been previously found in the nasopharynx of asthmatic and healthy children. A total of 61 OTUs from these genera were present in at least 50% of the samples (i.e., the nasal core microbiome). Significant differences in core microbiome composition were detected between sample pairs, but no directional trend (increase or decrease) was observed across sample pairs. Samples were randomly ordinated and did not cluster together.

Conclusions

Our analysis of nasal microbiomes in 40 asthmatic children revealed significant differences in composition within individuals over six months. Future cross-sectional microbiome studies need to be aware of short span temporal dynamics in nasal microbiota.

ZONE BEHAVIOR OF ENZYMES : ILLUSTRATED BY THE EFFECT OF DISSOCIATION CONSTANT AND DILUTION ON THE SYSTEM CHOLINESTERASE-PHYSOSTIGMINE

1. The kinetics of the reversible combination of one enzyme center with one molecule of a substrate or inhibitor is treated as a true bimolecular instead of a pseudomonomolecular reaction. The general equations describing such a reaction are presented and analyzed algebraically and graphically. 2. A new term, "specific concentration," is introduced to denote the concentration of reactants in units equal to the dissociation constant. Its use makes the kinetic equations universally applicable to all reversible systems of the given type. 3. It is shown that such a system exhibits three "zones" of behavior. Each zone is characterized and shown to exhibit significant differences in the function relating the concentrations of the components of the system at equilibrium. The zone boundaries are rigorously defined in terms of the specific enzyme concentration, for the mathematical error tolerable with a given experimental accuracy; and approximate boundaries for practical use are proposed. 4. The classical treatment of enzyme kinetics is shown to be a limiting case valid only for low specific enzyme concentrations (zone A) and to be inapplicable in a number of systems whose dissociation constants are very small or whose molar enzyme concentrations are very great, and in which, therefore, the specific enzyme concentrations are large. See Table I for a summary of zone differences. 5. In an enzyme system containing substrate or inhibitor, dilution before determination of reaction velocities is shown to be a crucial operation, entailing large changes in the fraction of enzyme in the form of a complex. The changes in fractional activity or inhibition with dilution are shown to be a function of specific enzyme concentration, the dilution factor, and the fraction of enzyme initially in the form of complex. Equations are given permitting the calculation of the state of the system at any concentration. The errors introduced into physiological work by failure to take the dilution effect into account are pointed out. 6. Experimental data are presented showing that the system composed of serum cholinesterase and physostigmine behaves as predicted by the dilution effect equations. 7. Two other conclusions of practical pharmacological importance are drawn from the theory of zone behavior: (a) The finding that a biological response is a linear function of the dose of a drug does not necessarily mean that the reaction is irreversible, but only that if reversible, the reactant with which the drug combines has a high specific concentration. (b) If a tissue enzyme has a high specific concentration, all reversible inhibitors will be equally potent in combining with it, regardless of their relative potency in dilute systems; provided only that their dissociation constants are within certain broad limits. 8. It is shown how the type of analysis here applied to bimolecular reactions can be applied in toto to systems of the type E + nX ⇋ EX_n, where n molecules of substrate or inhibitor unite with one enzyme center. The zone boundaries and the magnitude of the dilution effect change with n, but the general characteristics of the zones are the same for all values of n. 9. Since the analysis is based only on mass law assumptions, it is applicable to any system that is formally analogous to the one here treated.

THE MECHANISM OF ENZYME-INHIBITOR-SUBSTRATE REACTIONS : ILLUSTRATED BY THE CHOLINESTERASE-PHYSOSTIGMINE-ACETYLCHOLINE SYSTEM

The mechanism of enzyme-inhibitor-substrate reactions has been analyzed from a theoretical standpoint and illustrated by data from the system cholinesterase-physostigmine-acetylcholine. This treatment is by no means limited to a single system but should be generally applicable to others of similar type. Competitive enzyme-inhibitor-substrate systems show the same characteristic "zones of behavior" already demonstrated for non-competitive systems by Straus and Goldstein. These zones, three in number, determine the mathematical function which relates activity of an enzyme to concentration of an added substrate or inhibitor or both. The effects of suboptimal substrate concentration in such systems have been considered, and the errors arising from various common simplifications of the descriptive equations have been pointed out. The zone behavior phenomenon has been shown to be useful in determining the number of molecules of substrate or inhibitor combining reversibly with a single enzyme center. The kinetics of competitive inhibition, dilution effect, combination of inhibitor or substrate with enzyme, and destruction of inhibitor or substrate by enzyme have been analyzed and experimentally verified, and absolute velocity constants have been determined. Theoretical conclusions have been discussed from the standpoint of their physiological significance. Specifically, it has been shown that: 1. The inhibition of cholinesterase by physostigmine is competitive. A single molecule of physostigmine or acetylcholine combines with one center of cholinesterase—n = 1; and the mechanism n = 2 has been. excluded. Numerical values of the constants for this system are as follows: K_I = 3.11 x 10^–8k₁ (combination) = 8.3 x 10⁵k₂ (dissociation) = 0.026 K_S = 1.25 x 10^–3k₃ (combination) = 260 k₄ (dissociation) = 0.32 2. No definitive value can be assigned to E, the molar concentration of enzyme centers, but in 4.54 per cent dog serum, E < 1.8 x 10^–8 (E_I' < 0.58). The system therefore operates in (or nearly in) zone A at this concentration. 3. Competitive displacement of inhibitor by substrate and vice versa introduces considerable error in the usual 20 minute determination of the activity of an inhibited enzyme, unless properly corrected for. 4. Dissociation of the enzyme-inhibitor complex on dilution proceeds moderately slowly so that the full corrections for dilution cannot be applied unless time has been allowed for full dissociation. 5. Combination of physostigmine with cholinesterase is slow at all but large concentrations of inhibitor. 6. The destruction of physostigmine or acetylcholine by cholinesterase follows the predicted curve; k_D for the destruction of physostigmine is found to be > 0.00182; k_D for acetylcholine destruction is > 3500. There is no reason to assume inhibition of destruction by excess substrate or inhibitor. 7. The common assumption that enzymatic activity follows (or nearly follows) a monomolecular course is true only under limited conditions, which have been here defined. It is not valid, as a rule, for the enzymatic destruction of an inhibitor (e.g., physostigmine) and its application to such a case may lead to erroneous conclusions about the reaction mechanism.

Expanding CEP290 mutational spectrum in ciliopathies

Ciliopathies are an expanding group of rare conditions characterized by multiorgan involvement, that are caused by mutations in genes encoding for proteins of the primary cilium or its apparatus. Among these genes, CEP290 bears an intriguing allelic spectrum, being commonly mutated in Joubert syndrome and related disorders (JSRD), Meckel syndrome (MKS), Senior-Loken syndrome and isolated Leber congenital amaurosis (LCA). Although these conditions are recessively inherited, in a subset of patients only one CEP290 mutation could be detected. To assess whether genomic rearrangements involving the CEP290 gene could represent a possible mutational mechanism in these cases, exon dosage analysis on genomic DNA was performed in two groups of CEP290 heterozygous patients, including five JSRD/MKS cases and four LCA, respectively. In one JSRD patient, we identified a large heterozygous deletion encompassing CEP290 C-terminus that resulted in marked reduction of mRNA expression. No copy number alterations were identified in the remaining probands. The present work expands the CEP290 genotypic spectrum to include multiexon deletions. Although this mechanism does not appear to be frequent, screening for genomic rearrangements should be considered in patients in whom a single CEP290 mutated allele was identified.

Thymosin beta4 enhances endothelial cell differentiation and angiogenesis

When human umbilical vein endothelial cells (HUVEC) differentiate into capillary-like tubes, there is a five-fold upregulation of the mRNA for thymosin beta4 (Tbeta4) (Grant et al. J Cell Sci 1995; 108: 3685-94 [1]) and this endogenous expression plays an important role in endothelial cell attachment to and spreading on matrix components. We now show that exogenous addition of thymosin beta4 (in the ng-microg range) to HUVEC in culture can induce several biological responses. These responses include increased tube formation in vitro. Additionally, exogenous thymosin beta4 enhances vascular sprouting in the coronary artery ring angiogenesis assay. Measurements of these vascular sprouts show a doubling of the vessel area (via increased branching) with as little as 100 ng of synthetic thymosin beta4. These processes appear to involve the binding of thymosin beta4 to an unknown cell surface receptor and internalization of the protein. This cell surface-binding appears not to be mediated through the thymosin beta4-actin binding domain LKTET. An increase in thymosin beta4 cytoplasmic staining in HUVEC exposed 10 microg of the peptide appears to occur without increased mRNA translation. In summary Tbeta4 induces an increase in cell-matrix attachment, proliferation, tube formation, internalization of the peptide and rearrangement of the actin cytoskeleton. The data now defines both an autocrine and paracrine role for thymosin beta4 in vessel formation.

Three-Dimensional Ultrastructural Karyotype Analysis from the Meiotic Parthenogenetic Nematode Heterodera betulae

Meiotic chromosome structure and function are described in the plant-parasitic nematode Heterodera betulae. Twelve synaptonemal complexes (SCs) were reconstructed from pachytene nuclei; therefore, n=12 is predicted for this species. Morphologically distinct sex chromosomes were not observed. Only one end of the SC is attached to the nuclear envelope, and there is no bouquet arrangement at pachytene. The structure of the SC in this meiotic parthenogenetic nematode was different than in other nematodes that reproduce via amphimixis; a striated central element with transverse filaments was not observed. Multiple SCs, or polycomplexes, were present in the nucleus. Recombination nodules were not observed. The centrioles were comprised of nine doublet microtubules connected by a ring, which is a distinct modification from the typical nine triplet microtubules without any interconnecting structure.

Meiotic Structures in the Animal-Parasitic Nematode Ascaris megalocephala: Synaptonemal Complexes, Recombination Nodules, and Centrioles

Two synaptonemal complexes (SCs) were present in the pachytene nuclei of Ascaris megalocephala. The SC was tripartite and comprised of two lateral elements (25 nm) with a striated central element (25 nm) and a central region of 65 nm. Spherical recombination nodules were observed to be associated only with the central element, although they are non-existent in the related A. lumbricoides var. suum (Goldstein, 1977). The SCs were attached to the nuclear envelope at only one end, while the other end was free in the nucleoplasm. This lack of bouquet formation of the chromosomes is consistent with all other nematodes studied. Morphologically distinct sex chromosomes were not observed, which differs from the presence of five Y-chromosomes present in A. lumbricoides var. suum (Goldstein and Moens, 1976). Centrioles (0.2 microm wide) reproduced by budding off the parental centriole. The centrioles consisted of nine singlet microtubules connected by an electron-dense proteinaceous ring. This structure is consistent with centrioles described in other nematodes, yet distinctly different from the centriole structure observed in most organisms in which it consists of nine triplet microtubules without any connecting ring. Multiple synaptonemal complexes, or polycomplexes, are found in A. megalocephala and A. lumbriocoides var. suum. They appear as stacked SC and are present inside the nucleus during zygotene and in the cytoplasm at pachytene.

Lymphoid apoptosis and myeloid hyperplasia in CCAAT displacement protein mutant mice

CCAAT displacement protein (cux/CDP) is an atypical homeodomain protein that represses expression of several developmentally regulated lymphoid and myeloid genes in vitro, including gp91-phox, immunoglobulin heavy chain, the T-cell receptor beta and gamma chains, and CD8. To determine how this activity affects cell development in vivo, a hypomorphic allele of cux/CDP was created by gene targeting. Homozygous mutant mice (cux/CDP(Delta HD/Delta HD)) demonstrated a partial neonatal lethality phenotype. Surviving animals suffered from a wasting disease, which usually resulted in death between 2 and 3 weeks of age. Analysis of T lymphopoiesis demonstrated that cux/CDP(Delta HD/Delta HD) mice had dramatically reduced thymic cellularity due to enhanced apoptosis, with a preferential loss of CD4(+)CD8(+) thymocytes. Ectopic CD25 expression was also observed in maturing thymocytes. B lymphopoiesis was also perturbed, with a 2- to 3-fold reduction in total bone marrow B-lineage cells and a preferential loss of cells in transition from pro-B/pre-BI to pre-BII stages due to enhanced apoptosis. These lymphoid abnormalities were independent of effects related to antigen receptor rearrangement. In contrast to the lymphoid demise, cux/CDP(Delta HD/Delta HD) mice demonstrated myeloid hyperplasia. Bone marrow reconstitution experiments identified that many of the hematopoietic defects were linked to microenvironmental effects, suggesting that underexpression of survival factors or overexpression of death-inducing factors accounted for the phenotypes observed. Tumor necrosis factor (TNF) levels were elevated in several tissues, especially thymus, suggesting that TNF may be a target gene for cux/CDP-mediated repression. These data suggest that cux/CDP regulates normal hematopoiesis, in part, by modulating the levels of survival and/or apoptosis factors expressed by the microenvironment.

Comparison of body weight and height of Israeli schoolchildren with the Tanner and Centers for Disease Control and Prevention growth charts

OBJECTIVE

To examine the suitability of the growth charts that are currently used in Israel and consider their replacement with a recent standard. In a sample of schoolchildren, the current Tanner and Whitehouse standards were compared with the new growth charts from the Centers for Disease Control and Prevention (CDC).

METHOD

A total of 746 Israeli healthy children (368 boys and 378 girls) aged 6 to 14 years were sampled from 2 super-regional schools (from the Jewish population). Height was measured using the Leicester height measure, and weight was measured using scales calibrated by the researchers.

RESULTS

In height, 75% of the boys and 81% of the girls fell in the 10th to 90th percentile range of the Tanner standards. In weight, 71% of the boys and 81% of the girls were in the 10th to 90th percentile range. Israeli boys were taller (chi2(1) = 30.53) and heavier (chi2(1) = 29.39), and girls were taller (chi2(1) = 13.81) than predicted by the Tanner standards. The CDC 10th to 90th percentile range included 81% of the boys and 83% of the girls for height and 78% of the boys and 81% of the girls for weight. The girls in our sample were slightly shorter (chi2(1) = 11.87) and lighter (chi2(1) = 9.52) than predicted from the CDC charts. Nevertheless, neither boys' nor girls' body mass index measures (kg/h2) differed from the CDC charts.

CONCLUSIONS

Our data suggest that the CDC growth charts are adequate for assessing Israeli children and slightly better than the current standard. Thus, in the absence of local standards, we recommend the use of the revised CDC growth charts, which include the additional body mass index measure.

A comparison of upper vs. lower and right vs. left visual fields using lexical decision

A series of experiments using the lexical decision task was conducted in order to investigate the functional differences between the upper and lower visual fields (UVF, LoVF) in word recognition. Word-nonword discrimination was swifter and more accurate for word stimuli presented in the UVF. Changing the eccentricity did not affect the UVF advantage over the LoVF. UVF superiority over LoVF was found to be equivalent for both right and left visual hemifield (RVF, LVF). In general, presenting related word primes enhanced all visual field differences in a similar manner (UVF over LoVF and RVF over LVF). However, primes consisting of semantically constraining sentences enhanced the RVF advantage over the LVF, but did not affect the UVF and LoVF differentially. The argument is made that UVF superiority cannot be due to perceptual or attentional differences alone, but must also reflect top-down information flow.

Hydrophone spatial averaging corrections from 1 to 40 MHz

The purpose of this study was to develop and experimentally verify a practical spatial averaging model for frequencies up to 40 MHz. The model is applicable to focused sources of circular geometry, accounts for the effects of hydrophone probe finite aperture, and allows calibration by substitution to be performed when the active elements of reference and tested hydrophone probes differ significantly. Several broadband sources with focal numbers between 3 and 20 were used to produce ultrasound fields with frequencies up to 40 MHz. The effective diameters of the ultrasonic hydrophone probes calibrated in the focal plane of the sources ranged from 150 to 500 microm. Prior to application of the spatial averaging corrections, the hydrophones with diameters smaller than that of the reference hydrophone exhibited experimentally determined absolute sensitivities higher than the true ones. This discrepancy increased with decreasing focal numbers and increasing frequency. It was determined that the error was governed by the cross-section of the beam in the focal plane and the ratio of the effective diameters of the reference and tested hydrophone probes. In addition, the error was found to be reliant on the frequency-dependent effective hydrophone radius. After applying the spatial averaging correction, the overall uncertainty in the hydrophone calibration was on the order of +/-1 dB. The model developed is being extended to be applicable to frequencies beyond 40 MHz, which are becoming increasingly important in diagnostic ultrasound imaging applications.