Epigenome-wide analysis links SMAD3 methylation at birth to asthma in children of asthmatic mothers.

BACKGROUND: The timing and mechanisms of asthma inception remain imprecisely defined. Although epigenetic mechanisms likely contribute to asthma pathogenesis, little is known about their role in asthma inception. OBJECTIVE: We sought to assess whether the trajectory to asthma begins already at birth and whether epigenetic mechanisms, specifically DNA methylation, contribute to asthma inception. METHODS: We used the Methylated CpG Island Recovery Assay chip to survey DNA methylation in cord blood mononuclear cells from 36 children (18 nonasthmatic and 18 asthmatic subjects by age 9 years) from the Infant Immune Study (IIS), an unselected birth cohort closely monitored for asthma for a decade. SMAD3 methylation in IIS (n = 60) and in 2 replication cohorts (the Manchester Asthma and Allergy Study [n = 30] and the Childhood Origins of Asthma Study [n = 28]) was analyzed by using bisulfite sequencing or Illumina 450K arrays. Cord blood mononuclear cell-derived IL-1ß levels were measured by means of ELISA. RESULTS: Neonatal immune cells harbored 589 differentially methylated regions that distinguished IIS children who did and did not have asthma by age 9 years. In all 3 cohorts methylation in SMAD3, the most connected node within the network of asthma-associated, differentially methylated regions, was selectively increased in asthmatic children of asthmatic mothers and was associated with childhood asthma risk. Moreover, SMAD3 methylation in IIS neonates with maternal asthma was strongly and positively associated with neonatal production of IL-1ß, an innate inflammatory mediator. CONCLUSIONS: The trajectory to childhood asthma begins at birth and involves epigenetic modifications in immunoregulatory and proinflammatory pathways. Maternal asthma influences epigenetic mechanisms that contribute to the inception of this trajectory.

Draft genome sequence of plant growth-promoting rhizobium Mesorhizobium amorphae, isolated from zinc-lead mine tailings.

Here, we describe the draft genome sequence of Mesorhizobium amorphae strain CCNWGS0123, isolated from nodules of Robinia pseudoacacia growing on zinc-lead mine tailings. A large number of metal(loid) resistance genes, as well as genes reported to promote plant growth, were identified, presenting a great future potential for aiding phytoremediation in metal(loid)-contaminated soil.

Genome sequence and mutational analysis of plant-growth-promoting bacterium Agrobacterium tumefaciens CCNWGS0286 Isolated from a zinc-lead mine tailing.

The plant-growth-promoting bacterium Agrobacterium tumefaciens CCNWGS0286, isolated from the nodules of Robinia pseudoacacia growing in zinc-lead mine tailings, both displayed high metal resistance and enhanced the growth of Robinia plants in a metal-contaminated environment. Our goal was to determine whether bacterial metal resistance or the capacity to produce phytohormones had a larger impact on the growth of host plants under zinc stress. Eight zinc-sensitive mutants and one zinc-sensitive mutant with reduced indole-3-acetic acid (IAA) production were obtained by transposon mutagenesis. Analysis of the genome sequence and of transcription via reverse transcriptase PCR (RT-PCR) combined with transposon gene disruptions revealed that ZntA-4200 and the transcriptional regulator ZntR1 played important roles in the zinc homeostasis of A. tumefaciens CCNWGS0286. In addition, interruption of a putative oligoketide cyclase/lipid transport protein reduced IAA synthesis and also showed reduced zinc and cadmium resistance but had no influence on copper resistance. In greenhouse studies, R. pseudoacacia inoculated with A. tumefaciens CCNWGS0286 displayed a significant increase in biomass production over that without inoculation, even in a zinc-contaminated environment. Interestingly, the differences in plant biomass improvement among A. tumefaciens CCNWGS0286, A. tumefaciens C58, and zinc-sensitive mutants 12-2 (zntA::Tn5) and 15-6 (low IAA production) revealed that phytohormones, rather than genes encoding zinc resistance determinants, were the dominant factor in enhancing plant growth in contaminated soil.

Draft genome of Streptomyces zinciresistens K42, a novel metal-resistant species isolated from copper-zinc mine tailings.

A draft genome sequence of Streptomyces zinciresistens K42, a novel Streptomyces species displaying a high level of resistance to zinc and cadmium, is presented here. The genome contains a large number of genes encoding proteins predicted to be involved in conferring metal resistance. Many of these genes appear to have been acquired through horizontal gene transfer.

Characterization and genomic analysis of chromate resistant and reducing Bacillus cereus strain SJ1.

BACKGROUND: Chromium is a toxic heavy metal, which primarily exists in two inorganic forms, Cr(VI) and Cr(III). Chromate [Cr(VI)] is carcinogenic, mutational, and teratogenic due to its strong oxidizing nature. Biotransformation of Cr(VI) to less-toxic Cr(III) by chromate-resistant and reducing bacteria has offered an ecological and economical option for chromate detoxification and bioremediation. However, knowledge of the genetic determinants for chromate resistance and reduction has been limited so far. Our main aim was to investigate chromate resistance and reduction by Bacillus cereus SJ1, and to further study the underlying mechanisms at the molecular level using the obtained genome sequence. RESULTS: Bacillus cereus SJ1 isolated from chromium-contaminated wastewater of a metal electroplating factory displayed high Cr(VI) resistance with a minimal inhibitory concentration (MIC) of 30 mM when induced with Cr(VI). A complete bacterial reduction of 1 mM Cr(VI) was achieved within 57 h. By genome sequence analysis, a putative chromate transport operon, chrIA1, and two additional chrA genes encoding putative chromate transporters that likely confer chromate resistance were identified. Furthermore, we also found an azoreductase gene azoR and four nitroreductase genes nitR possibly involved in chromate reduction. Using reverse transcription PCR (RT-PCR) technology, it was shown that expression of adjacent genes chrA1 and chrI was induced in response to Cr(VI) but expression of the other two chromate transporter genes chrA2 and chrA3 was constitutive. In contrast, chromate reduction was constitutive in both phenotypic and gene expression analyses. The presence of a resolvase gene upstream of chrIA1, an arsenic resistance operon and a gene encoding Tn7-like transposition proteins ABBCCCD downstream of chrIA1 in B. cereus SJ1 implied the possibility of recent horizontal gene transfer. CONCLUSION: Our results indicate that expression of the chromate transporter gene chrA1 was inducible by Cr(VI) and most likely regulated by the putative transcriptional regulator ChrI. The bacterial Cr(VI)-resistant level was also inducible. The presence of an adjacent arsenic resistance gene cluster nearby the chrIA1 suggested that strong selective pressure by chromium and arsenic could cause bacterial horizontal gene transfer. Such events may favor the survival and increase the resistance level of B. cereus SJ1.

Evolution of lactation: nutrition v. protection with special reference to five mammalian species.

The evolutionary origin of the mammary gland has been difficult to establish because little knowledge can be gained on the origin of soft tissue organs from fossil evidence. One approach to resolve the origin of lactation has compared the anatomy of existing primitive mammals to skin glands, whilst another has examined the metabolic and molecular synergy between mammary gland development and the innate immune system. We have reviewed the physiology of lactation in five mammalian species with special reference to these theories. In all species, milk fulfils dual functions of providing protection and nutrition to the young and, furthermore, within species the quality and quantity of milk are highly conserved despite maternal malnutrition or illness. There are vast differences in birth weight, milk production, feeding frequency, macronutrient concentration, growth rate and length of lactation between rabbits, quokkas (Setonix brachyurus), pigs, cattle and humans. The components that protect the neonate against infection do so without causing inflammation. Many protective components are not unique to the mammary gland and are shared with the innate immune system. In contrast, many of the macronutrients in milk are unique to the mammary gland, have evolved from components of the innate immune system, and have either retained or developed multiple functions including the provision of nourishment and protection of the hatchling/neonate. Thus, there is a strong argument to suggest that the mammary gland evolved from the inflammatory response; however, the extensive protection that has developed in milk to actively avoid triggering inflammation seems to be a contradiction.

Overweight and obesity among youth participants in American football.

OBJECTIVE: To estimate the prevalence of overweight and obesity among participants in youth American football 9 to 14 years of age. STUDY DESIGN: Cross-sectional, 653 boys, 8.7 to 14.6 years. Height and weight were measured; body mass index (BMI) was calculated. Overweight and obesity were defined by international (International Obesity Task Force [IOTF]) and United States (Centers for Disease Control [CDC]) criteria. Prevalence and 95% confidence interval were calculated. Player age, height, and weight and midparent height were used to predict mature height; current height was expressed as a percentage of predicted mature height as an estimate of maturity status. RESULTS: Overall 45.0% (41.2% to 48.9%) and 42.6% (38.8% to 46.5%) of players were overweight or obese by CDC and IOTF criteria, respectively. Prevalence was highest in early maturing boys. Based on position-activity at time of injury (n = 180), overweight and obesity were more common among offensive and defensive linemen. CONCLUSION: Overweight and obesity were more prevalent in youth football players than in national samples of American boys. Allowing for limitations of the BMI and the relative stability of the BMI from adolescence into adulthood, a relatively large number of football participants may be at risk for later overweight or obesity, and the risk appears to be greater for offensive and defensive line positions.

Maturity status of youth football players: a noninvasive estimate.

PURPOSE: To estimate the biological maturity status of youth football players 9-14 yr old using a noninvasive method and to compare the body size of players of contrasting status. METHODS: Subjects were members of youth football teams in two central Michigan communities. Height and weight were measured on 653 boys 8.7-14.6 yr. Heights of biological parents of 582 boys were reported and subsequently adjusted for overestimation. Decimal age, height, and weight of the player and midparent height were used to predict mature (adult) height for the boy. Current height of each player was expressed as a percentage of his predicted mature height to provide an estimate of biological maturity status. Percentage of predicted mature height of each boy was expressed as a z-score to classify players into maturity groups. ANCOVA, controlling for age, was used to compare body size in contrasting maturity groups. RESULTS: Mean percentages of predicted mature height of the players matched those of longitudinal reference samples, but there was a trend for higher percentages among older players, suggesting advanced maturation. Overall, 405 boys were classified as on time/average in maturity status (69.6% [95%CI 65.7-73.3]), 154 were classified as early/advanced (25.5% [95%CI 23.0-30.3]), and only 23 were classified as late/delayed (3.9% [95%CI 2.6-6.0]). The gradient for height, weight, and BMI was as follows: early > on time > late, and differences were greater for weight and the BMI than for height. CONCLUSION: Percentage of predicted mature height attained at a given age appears to be a reasonable indicator of maturity status. The method needs to be validated with other more direct indicators (skeletal age, sexual maturation) and applied to other samples.

Enhancing Capabilities in health professions education.

OBJECTIVE: This article documents the results of ongoing summative program evaluation of a suite of postgraduate courses at The University of Western Australia designed to enhance the educational capabilities, academic leadership and scholarly output of health professionals. METHODS: Commencing students were invited to participate in this descriptive, longitudinal study that surveyed students at commencement and subsequently over a seven year period. Data was collected at baseline and follow-up in relation to the respondents' educational leadership responsibilities, promotions, involvement in new educational programs, and recognition for contributions towards student learning, educational scholarly outputs and involvement in training programs. RESULTS: The respondents came from a wide range of health professions and worked in various roles, with a quarter already holding leadership positions. During the follow-up period, half reported receiving a new promotion or moving to new positions requiring educational leadership. Those identifying as being involved with the development of new educational programs doubled and 34% received a new teaching award. Scholarly productivity doubled with 45% giving an oral presentation related to education, 21% publishing and 29% being successful in obtaining funding related to an education project. CONCLUSIONS: These postgraduate courses in health professions education appear to be positively influencing graduates' capabilities, especially in the areas of educational leadership skills and scholarly productivity. For those looking to develop a community of leaders in health professions education, the authors offer some suggestions.

Direct identification of PTEN phosphorylation sites.

The PTEN tumor suppressor gene encodes a phosphatidylinositol 3'-phosphatase that is inactivated in a high percentage of human tumors, particularly glioblastoma, melanoma, and prostate and endometrial carcinoma. Previous studies showed that PTEN is a seryl phosphoprotein and a substrate of protein kinase CK2 (CK2). However, the sites in PTEN that are phosphorylated in vivo have not been identified directly, nor has the effect of phosphorylation on PTEN catalytic activity been reported. We used mass spectrometric methods to identify Ser(370) and Ser(385) as in vivo phosphorylation sites of PTEN. These sites also are phosphorylated by CK2 in vitro, and phosphorylation inhibits PTEN activity towards its substrate, PIP3. We also identify a novel in vivo phosphorylation site, Thr(366). Following transient over-expression, a fraction of CK2 and PTEN co-immunoprecipitate. Moreover, pharmacological inhibition of CK2 activity leads to decreased Akt activation in PTEN+/+ but not PTEN-/- fibroblasts. Our results contrast with previous assignments of PTEN phosphorylation sites based solely on mutagenesis approaches, suggest that CK2 is a physiologically relevant PTEN kinase, and raise the possibility that CK2-mediated inhibition of PTEN plays a role in oncogenesis.

Characterization and genomic analysis of a highly chromate resistant and reducing bacterial strain Lysinibacillus fusiformis ZC1.

Lysinibacillus fusiformis ZC1 isolated from chromium (Cr) contaminated wastewater of a metal electroplating factory displayed high chromate [Cr(VI)] resistance with a minimal inhibitory concentration (MIC) of 60mM in R2A medium. L. fusiformis ZC1 showed resistances to multiple metals (Cu, Ni, Co, Hg, Cd and Ag) and a metalloid (As). This bacterium exhibited an extremely rapid Cr(VI) reduction capability. It almost completely reduced 1mM K(2)CrO(4) in 12h. The Cr(VI) reduction ability of L. fusiformis ZC1 was enhanced by sodium acetate and NADH. By whole genome sequence analysis, strain ZC1 was found to contain large numbers of metal(loid) resistance genes. Specifically, a chrA gene encoding a putative chromate transporter conferring chromate resistance was identified. The chromate resistance was constitutive in both phenotypic and gene expression analyses. Furthermore, we found a yieF gene and several genes encoding reductases that were possibly involved in chromate reduction. Expression of adjacent putative chromate reduction related genes, nitR and yieF, was found to be constitutive. The large numbers of NADH-dependent chromate reductase genes may be responsible for the rapid chromate reduction in order to detoxify Cr(VI) and survive in the harsh wastewater environment.

Genome analysis and characterization of zinc efflux systems of a highly zinc-resistant bacterium, Comamonas testosteroni S44.

A novel and multiple metal(loid)-resistant strain Comamonas testosteroni S44 with a high Zn(2+) resistance level (10 mM) was isolated. To understand the molecular basis for the high zinc resistance, whole genome sequencing was performed and revealed a large number of genes encoding putative metal(loid) resistance proteins, mobile genetic elements (MGEs) and horizontal gene transfer (HGT) events that may have occurred to adapt to a metal(loid)-contaminated environment. In particular, 9 putative Zn(2+) transporters [4 znt operons encoding putative Zn(2+)-translocating P-type ATPases and 5 czc operons encoding putative RND-driven (resistance, nodulation, cell division protein family)] tripartite protein complexes were identified. Real-time RT-PCR analysis revealed that the four zntA-like genes were all induced by Zn(2+), while czcA genes were either Zn(2+)-induced or downregulated by Zn(2+). Furthermore, a zntR1A1 operon encoding a ZntR-type regulator and a P-type ATPase was studied in detail. The zntR1 deletion strain (S44ΔzntR1) displayed intermediate resistance to Zn(2+) (6 mM) and accumulated more intracellular Zn(2+). Reporter gene expression assays indicated that ZntR1 responded to Zn(2+), Cd(2+) and Pb(2+), with Zn(2+) being the best inducer. Gene transcription analysis indicated that ZntR1 was a regulator for transcription of zntA1, while other putative ZntR-type regulators may also regulate the transcription expression of zntA1.

Incidence and player risk factors for injury in youth football.

OBJECTIVE: To estimate the incidence of injuries in youth football and to assess the relationship between player-related risk factors (age, body size, biological maturity status) and the occurrence of injury in youth football. DESIGN: Prospective over two seasons. SETTING: Two communities in central Michigan. PARTICIPANTS: Subjects were 678 youth, 9-14 years of age, who were members of 33 youth football teams in two central Michigan communities in the 2000 and 2001 seasons. METHODS: Certified athletic trainers (ATCs) were on site to record the number of players at all practices and home games (exposures) and injuries as they occurred. A reportable injury (RI) was defined by the criteria used in the National Athletic Trainers' Association (NATA) survey of several high school sports. Estimated injury rates (95% confidence intervals) per athlete exposures (AE) and per number of athletes were calculated for practices and games by grade. Player risk factors included age, height, weight, BMI and estimated maturity status. MAIN OUTCOME MEASURE: Estimated injury rates and relative risks of injury during practices and games by grade; logistic regression to evaluate relationships between player-related risk factors and risk of injury. RESULTS: A total of 259 RIs, 178 in practice and 81 in games, were recorded during the two seasons. Practice injury rates increased with grade level, while game injury rates were similar among fourth through fifth grade and sixth grade players and about twice as high among seventh and eighth grade players. The majority of RIs during the two seasons was minor (64%); the remainder was moderate (18%) and major (13%). Injured fourth through fifth grade players were significantly lighter in weight and had a lower BMI; otherwise, injured and non-injured players within each grade did not differ in age, body size and estimated biological maturity status. Logistic regressions within grade revealed no significant associations between injury and age, height, BMI, and maturity status. CONCLUSION: Game injury rates are higher than practice injury rates, and the incidence of injury tends to increase with grade level. Age, height, BMI and maturity status were not related to the risk of injury in youth football players.

Growth status and estimated growth rate of youth football players: a community-based study.

OBJECTIVE: To characterize the growth status of participants in community-sponsored youth football programs and to estimate rates of growth in height and weight. DESIGN: Mixed-longitudinal over 2 seasons. SETTING: Two communities in central Michigan. PARTICIPANTS: Members of 33 youth football teams in 2 central Michigan communities in the 2000 and 2001 seasons (Mid-Michigan PONY Football League). METHODS: Height and weight of all participants were measured prior to each season, 327 in 2000 and 326 in 2001 (n = 653). The body mass index (kg/m) was calculated. Heights and weights did not differ from season to season and between the communities; the data were pooled and treated cross-sectionally. Increments of growth in height and weight were estimated for 166 boys with 2 measurements approximately 1 year apart to provide an estimate of growth rate. MAIN OUTCOME MEASURE: Growth status (size-attained) of youth football players relative to reference data (CDC) for American boys and estimated growth rate relative to reference values from 2 longitudinal studies of American boys. RESULTS: Median heights of youth football players approximate the 75th percentiles, while median weights approximate the 75th percentiles through 11 years and then drift toward the 90th percentiles of the reference. Median body mass indexes of youth football players fluctuate about the 85th percentiles of the reference. Estimated growth rates in height approximate the reference and may suggest earlier maturation, while estimated growth rates in weight exceed the reference. CONCLUSION: Youth football players are taller and especially heavier than reference values for American boys. Estimated rates of growth in height approximate medians for American boys and suggest earlier maturation. Estimated rates of growth in weight exceed those of the reference and may place many youth football players at risk for overweight/obesity, which in turn may be a risk factor for injury.

Rapid divergence of microsatellite abundance among species of Drosophila.

Among major taxonomic groups, microsatellites exhibit considerable variation in composition and allele length, but they also show considerable conservation within many major groups. This variation may be explained by slow microsatellite evolution so that all species within a group have similar patterns of variation, or by taxon-specific mutational or selective constraints. Unfortunately, comparing microsatellites across species and studies can be problematic because of biases that may exist among different isolation and analysis protocols. We present microsatellite data from five Drosophila species in the Drosophila subgenus: D. arizonae, D. mojavensis, and D. pachea (three cactophilic species), and D. neotestacea and D. recens (two mycophagous species), all isolated at the same time using identical protocols. For each species, we compared the relative abundance of motifs, the distribution of repeat size, and the average number of repeats. Dimers were the most abundant microsatellites for each species. However, we found considerable variation in the relative abundance of motif size classes among species, even between sister taxa. Frequency differences among motifs within size classes for the three cactophilic species, but not the two mycophagous species, are consistent with other studied Drosophila. Frequency distributions of repeat number, as well as mean size, show significant differences among motif size classes but not across species. Sizes of microsatellites in these five species are consistent with D. virilis, another species in the subgenus Drosophila, but they have consistently higher means than in D. melanogaster, in the subgenus Sophophora. These results confirm that many aspects of microsatellite variation evolve quickly but also are subject to taxon-specific constraints. In addition, the nature of microsatellite evolution is dependent on temporal and taxonomic scales, and some variation is conserved across broad taxonomic levels despite relatively high rates of mutation for these loci.