Childcare centre soil microbiomes are influenced by substrate type and surrounding vegetation condition

Urban development has profoundly reduced human exposure to biodiverse environments, which is linked to a rise in human disease. The 'biodiversity hypothesis' proposes that contact with diverse microbial communities (microbiota) benefits human health, as exposure to microbial diversity promotes immune training and regulates immune function. Soils and sandpits in urban childcare centres may provide exposure to diverse microbiota that support immunoregulation at a critical developmental stage in a child's life. However, the influence of outdoor substrate (i.e., sand vs. soil) and surrounding vegetation on these environmental microbiota in urban childcare centres remains poorly understood. Here, we used 16S rRNA amplicon sequencing to examine the variation in bacterial communities in sandpits and soils across 22 childcare centres in Adelaide, Australia, plus the impact of plant species richness and habitat condition on these bacterial communities. We show that sandpits had distinct bacterial communities and lower alpha diversity than soils. In addition, we found that plant species richness in the centres' yards and habitat condition surrounding the centres influenced the bacterial communities in soils but not sandpits. These results demonstrate that the diversity and composition of childcare centre sandpit and soil bacterial communities are shaped by substrate type, and that the soils are also shaped by the vegetation within and surrounding the centres. Accordingly, there is potential to modulate the exposure of children to health-associated bacterial communities by managing substrates and vegetation in and around childcare centres.

Biodiversity and human health: A scoping review and examples of underrepresented linkages

Mounting evidence supports the connections between exposure to environmental typologies(such as green and blue spaces)and human health. However, the mechanistic links that connect biodiversity (the variety of life) and human health, and the extent of supporting evidence remain less clear. Here, we undertook a scoping review to map the links between biodiversity and human health and summarise the levels of associated evidence using an established weight of evidence framework. Distinct from other reviews, we provide additional context regarding the environment-microbiome-health axis, evaluate the environmental buffering pathway (e.g., biodiversity impacts on air pollution), and provide examples of three under- or minimally-represented linkages. The examples are (1) biodiversity and Indigenous Peoples' health, (2) biodiversity and urban social equity, and (3) biodiversity and COVID-19. We observed a moderate level of evidence to support the environmental microbiota-human health pathway and a moderate-high level of evidence to support broader nature pathways (e.g., greenspace) to various health outcomes, from stress reduction to enhanced wellbeing and improved social cohesion. However, studies of broader nature pathways did not typically include specific biodiversity metrics, indicating clear research gaps. Further research is required to understand the connections and causative pathways between biodiversity (e.g., using metrics such as taxonomy, diversity/richness, structure, and function) and health outcomes. There are well-established frameworks to assess the effects of broad classifications of nature on human health. These can assist future research in linking biodiversity metrics to human health outcomes. Our examples of underrepresented linkages highlight the roles of biodiversity and its loss on urban lived experiences, infectious diseases, and Indigenous Peoples' sovereignty and livelihoods. More research and awareness of these socioecological interconnections are needed.

Probiotic Cities: microbiome-integrated design for healthy urban ecosystems

Combining microbiome science and biointegrated design offers opportunities to help address the intertwined challenges of urban ecosystem degradation and human disease. Biointegrated materials have the potential to combat superbugs and remediate pollution while inoculating landscape materials with microbiota can promote human immunoregulation and biodiverse green infrastructure, contributing to 'probiotic cities'.

Policy implications of the microbiota-gut-brain axis

The microbiota-gut-brain axis facilitates communication between the gut microbiota and the brain. It has implications for health and environmental policy. Microbiota are linked to neurological and metabolic disorders, and our exposure to health-promoting microbiota depends on environmental quality. Microbiota-gut-brain axis interventions could inform policy initiatives to address systemic health issues.

Light-dark cycles may influence in situ soil bacterial networks and diurnally-sensitive taxa

Soil bacterial taxa have important functional roles in ecosystems (e.g. nutrient cycling, soil formation, plant health). Many factors influence their assembly and regulation, with land cover types (e.g. open woodlands, grasslands), land use types (e.g. nature reserves, urban green space) and plant-soil feedbacks being well-studied factors. However, changes in soil bacterial communities in situ over light-dark cycles have received little attention, despite many plants and some bacteria having endogenous circadian rhythms that could influence soil bacterial communities. We sampled surface soils in situ across 24-h light-dark cycles (at 00:00, 06:00, 12:00, 18:00) at two land cover types (remnant vegetation vs. cleared, grassy areas) and applied 16S rRNA amplicon sequencing to investigate changes in bacterial communities. We show that land cover type strongly affected soil bacterial diversity, with soils under native vegetation expressing 15.4%-16.4% lower alpha diversity but 4.9%-10.6% greater heterogeneity than soils under cleared vegetation. In addition, we report time-dependent and site-specific changes in bacterial network complexity and between 598-922 ASVs showing significant changes in relative abundance across times. Native site node degree (bacterial interactions) at the phylum level was 16.0% higher in the early morning than in the afternoon/evening. Our results demonstrate for the first time that light-dark cycles have subtle yet important effects on soil bacterial communities in situ and that land cover influences these dynamics. We provide a new view of soil microbial ecology and suggest that future studies should consider the time of day when sampling soil bacteria.

Opportunities and challenges for microbiomics in ecosystem restoration

Microbiomics is the science of characterizing microbial community structure, function, and dynamics. It has great potential to advance our understanding of plant-soil-microbe processes and interaction networks which can be applied to improve ecosystem restoration. However, microbiomics may be perceived as complex and the technology is not accessible to all. The opportunities of microbiomics in restoration ecology are considerable, but so are the practical challenges. Applying microbiomics in restoration must move beyond compositional assessments to incorporate tools to study the complexity of ecosystem recovery. Advances in metaomic tools provide unprecedented possibilities to aid restoration interventions. Moreover, complementary non-omic applications, such as microbial inoculants and biopriming, have the potential to improve restoration objectives by enhancing the establishment and health of vegetation communities.

The aerobiome-health axis: a paradigm shift in bioaerosol thinking

Historically, a primary aim of bioaerosol research has been to understand and prevent 'unhealthy' human exposures to pathogens and allergens. However, there has been a recent paradigm shift in thinking about bioaerosols. Exposure to a diverse aerobiome - the microbiome of the air - is now considered necessary to be healthy.

Urban centre green metrics in Great Britain: A geospatial and socioecological study

Green infrastructure plays a vital role in urban ecosystems. This includes sustaining biodiversity and human health. Despite a large number of studies investigating greenspace disparities in suburban areas, no known studies have compared the green attributes (e.g., trees, greenness, and greenspaces) of urban centres. Consequently, there may be uncharacterised socioecological disparities between the cores of urban areas (e.g., city centres). This is important because people spend considerable time in urban centres due to employment, retail and leisure opportunities. Therefore, the availability of--and disparities in--green infrastructure in urban centres can affect many lives and potentially underscore a socio-ecological justice issue. To facilitate comparisons between urban centres in Great Britain, we analysed open data of urban centre boundaries with a central business district and population of ≥100,000 (n = 68). Given the various elements that contribute to 'greenness', we combine a range of different measurements (trees, greenness, and accessible greenspaces) into a single indicator. We applied the normalised difference vegetation index (NDVI) to estimate the mean greenness of urban centres and the wider urban area (using a 1 km buffer) and determined the proportion of publicly accessible greenspace within each urban centre with Ordnance Survey Open Greenspace data. Finally, we applied a land cover classification algorithm using i-Tree Canopy to estimate tree coverage. This is the first study to define and rank urban centres based on multiple green attributes. The results suggest important differences in the proportion of green attributes between urban centres. For instance, Exeter scored the highest with a mean NDVI of 0.15, a tree coverage of 11.67%, and an OS Greenspace coverage of 0.05%, and Glasgow the lowest with a mean NDVI of 0.02, a tree cover of 1.95% and an OS Greenspace coverage of 0.00%. We also demonstrated that population size negatively associated with greenness and tree coverage, but not greenspaces, and that green attributes negatively associated with deprivation. This is important because it suggests that health-promoting and biodiversity-supporting resources diminish as population and deprivation increase. Disparities in green infrastructure across the country, along with the population and deprivation-associated trends, are important in terms of socioecological and equity justice. This study provides a baseline and stimulus to help local authorities and urban planners create and monitor equitable greening interventions in urban/city centres.

Ecosystem restoration is integral to humanity's recovery from COVID-19

COVID-19 has devastated global communities and economies. The pandemic has exposed socioeconomic disparities and weaknesses in health systems worldwide. Long-term health effects and economic recovery are major concerns. Ecosystem restoration-ie, the repair of ecosystems that have been degraded-relates directly to tackling the health and socioeconomic burdens of COVID-19, because stable and resilient ecosystems are fundamental determinants of health and socioeconomic stability. Here, we use COVID-19 as a case study, showing how ecosystem restoration can reduce the risk of infection and adverse sequelae and have an integral role in humanity's recovery from COVID-19. The next decade will be crucial for humanity's recovery from COVID-19 and for ecosystem repair. Indeed, in the absence of effective, large-scale restoration, 95% of the Earth's land could be degraded by 2050. The UN Decade on Ecosystem Restoration (2021-30) declaration reflects the growing urgency and scale at which we should repair ecosystems. Importantly, ecosystem restoration could also help to combat the health and socioeconomic issues that are associated with COVID-19, yet it is poorly integrated into current responses to the disease. Ecosystem restoration can be a core public health intervention and assist in COVID-19 recovery if it is closely integrated with socioeconomic, health, and environmental policies.

Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice

Humans are inextricably linked to each other and our natural world, and microorganisms lie at the nexus of those interactions. Microorganisms form genetically flexible, taxonomically diverse, and biochemically rich communities, i.e., microbiomes that are integral to the health and development of macroorganisms, societies, and ecosystems. Yet engagement with beneficial microbiomes is dictated by access to public resources, such as nutritious food, clean water and air, safe shelter, social interactions, and effective medicine. In this way, microbiomes have sociopolitical contexts that must be considered. The Microbes and Social Equity (MSE) Working Group connects microbiology with social equity research, education, policy, and practice to understand the interplay of microorganisms, individuals, societies, and ecosystems. Here, we outline opportunities for integrating microbiology and social equity work through broadening education and training; diversifying research topics, methods, and perspectives; and advocating for evidence-based public policy that supports sustainable, equitable, and microbial wealth for all.

Germaphobia! Does Our Relationship With and Knowledge of Biodiversity Affect Our Attitudes Toward Microbes?

Germaphobia – a pathological aversion to microorganisms – could be contributing to an explosion in human immune-related disorders via mass sterilization of surfaces and reduced exposure to biodiversity. Loss of biodiversity and people’s weaker connection to nature, along with poor microbial literacy may be augmenting the negative consequences of germaphobia on ecosystem health. In this study, we created an online questionnaire to acquire data on attitudes toward, and knowledge of microbes. We collected data on nature connectedness and interactions with nature and explored the relationships between these variables. Although the study had an international reach (n = 1,184), the majority of responses came from England, United Kingdom (n = 993). We found a significant association between attitudes toward microbes and both duration and frequency of visits to natural environments. A higher frequency of visits to nature per week, and a longer duration spent in nature per visit, was significantly associated with positive attitudes toward microbes. We found no association between nature connectedness and attitudes toward microbes. We found a significant relationship between knowledge of “lesser known” microbial groups (e.g., identifying that fungi, algae, protozoa, and archaea are microbes) and positive attitudes toward microbes. However, we also found that people who identified viruses as being microbes expressed less positive views of microbes overall–this could potentially be attributed to a “COVID-19 effect.” Our results suggest that basic microbial literacy and nature engagement may be important in reducing/preventing germaphobia-associated attitudes. The results also suggest that a virus-centric phenomenon (e.g., COVID-19) could increase broader germaphobia-associated attitudes. As the rise of immune-related disorders and mental health conditions have been linked to germaphobia, reduced biodiversity, and non-targeted sterilization, our findings point to a feasible strategy to potentially help ameliorate these negative consequences. Further research is needed, but greater emphasis on microbial literacy and promoting time spent in nature could potentially be useful in promoting resilience in human health and more positive/constructive attitudes toward the foundations of our ecosystems—the microorganisms.

The Effects of Anthropogenic Sound and Artificial Light Exposure on Microbiomes: Ecological and Public Health Implications

Globally, anthropogenic sound and artificial light pollution have increased to alarming levels. Evidence suggests that these can disrupt critical processes that impact ecosystems and human health. However, limited focus has been given to the potential effects of sound and artificial light pollution on microbiomes. Microbial communities are the foundations of our ecosystems. They are essential for human health and provide myriad ecosystem services. Therefore, disruption to microbiomes by anthropogenic sound and artificial light could have important ecological and human health implications. In this mini-review, we provide a critical appraisal of available scientific literature on the effects of anthropogenic sound and light exposure on microorganisms and discuss the potential ecological and human health implications. Our mini-review shows that a limited number of studies have been carried out to investigate the effects of anthropogenic sound and light pollution on microbiomes. However, based on these studies, it is evident that anthropogenic sound and light pollution have the potential to significantly influence ecosystems and human health via microbial interactions. Many of the studies suffered from modest sample sizes, suboptimal experiments designs, and some of the bioinformatics approaches used are now outdated. These factors should be improved in future studies. This is an emerging and severely underexplored area of research that could have important implications for global ecosystems and public health. Finally, we also propose the photo-sonic restoration hypothesis: does restoring natural levels of light and sound help to restore microbiomes and ecosystem stability?

The impact of cross-kingdom molecular forensics on genetic privacy

Recent advances in metagenomic technology and computational prediction may inadvertently weaken an individual's reasonable expectation of privacy. Through cross-kingdom genetic and metagenomic forensics, we can already predict at least a dozen human phenotypes with varying degrees of accuracy. There is also growing potential to detect a "molecular echo" of an individual's microbiome from cells deposited on public surfaces. At present, host genetic data from somatic or germ cells provide more reliable information than microbiome samples. However, the emerging ability to infer personal details from different microscopic biological materials left behind on surfaces requires in-depth ethical and legal scrutiny. There is potential to identify and track individuals, along with new, surreptitious means of genetic discrimination. This commentary underscores the need to update legal and policy frameworks for genetic privacy with additional considerations for the information that could be acquired from microbiome-derived data. The article also aims to stimulate ubiquitous discourse to ensure the protection of genetic rights and liberties in the post-genomic era. Video abstract.

Exposure to airborne bacteria depends upon vertical stratification and vegetation complexity

Exposure to biodiverse aerobiomes supports human health, but it is unclear which ecological factors influence exposure. Few studies have investigated near-surface green space aerobiome dynamics, and no studies have reported aerobiome vertical stratification in different urban green spaces. We used columnar sampling and next generation sequencing of the bacterial 16S rRNA gene, combined with geospatial and network analyses to investigate urban green space aerobiome spatio-compositional dynamics. We show a strong effect of habitat on bacterial diversity and network complexity. We observed aerobiome vertical stratification and network complexity that was contingent on habitat type. Tree density, closer proximity, and canopy coverage associated with greater aerobiome alpha diversity. Grassland aerobiomes exhibited greater proportions of putative pathogens compared to scrub, and also stratified vertically. We provide novel insights into the urban ecosystem with potential importance for public health, whereby the possibility of differential aerobiome exposures appears to depend on habitat type and height in the airspace. This has important implications for managing urban landscapes for the regulation of aerobiome exposure.

Forensic Applications of Microbiomics: A Review

The rise of microbiomics and metagenomics has been driven by advances in genomic sequencing technology, improved microbial sampling methods, and fast-evolving approaches in bioinformatics. Humans are a host to diverse microbial communities in and on their bodies, which continuously interact with and alter the surrounding environments. Since information relating to these interactions can be extracted by analyzing human and environmental microbial profiles, they have the potential to be relevant to forensics. In this review, we analyzed over 100 papers describing forensic microbiome applications with emphasis on geolocation, personal identification, trace evidence, manner and cause of death, and inference of the postmortem interval (PMI). We found that although the field is in its infancy, utilizing microbiome and metagenome signatures has the potential to enhance the forensic toolkit. However, many of the studies suffer from limited sample sizes and model accuracies, and unrealistic environmental settings, leaving the full potential of microbiomics to forensics unexplored. It is unlikely that the information that can currently be elucidated from microbiomics can be used by law enforcement. Nonetheless, the research to overcome these challenges is ongoing, and it is foreseeable that microbiome-based evidence could contribute to forensic investigations in the future.

The Holobiont Blindspot: Relating Host-Microbiome Interactions to Cognitive Biases and the Concept of the "Umwelt"

Cognitive biases can lead to misinterpretations of human and non-human biology and behavior. The concept of the Umwelt describes phylogenetic contrasts in the sensory realms of different species and has important implications for evolutionary studies of cognition (including biases) and social behavior. It has recently been suggested that the microbiome (the diverse network of microorganisms in a given environment, including those within a host organism such as humans) has an influential role in host behavior and health. In this paper, we discuss the host’s microbiome in relation to cognitive biases and the concept of the Umwelt. Failing to consider the role of host–microbiome (collectively termed a “holobiont”) interactions in a given behavior, may underpin a potentially important cognitive bias – which we refer to as the Holobiont Blindspot. We also suggest that microbially mediated behavioral responses could augment our understanding of the Umwelt. For example, the potential role of the microbiome in perception and action could be an important component of the system that gives rise to the Umwelt. We also discuss whether microbial symbionts could be considered in System 1 thinking – that is, decisions driven by perception, intuition and associative memory. Recognizing Holobiont Blindspots and considering the microbiome as a key factor in the Umwelt and System 1 thinking has the potential to advance studies of cognition. Furthermore, investigating Holobiont Blindspots could have important implications for our understanding of social behaviors and mental health. Indeed, the way we think about how we think may need to be revisited.

Vertical Stratification in Urban Green Space Aerobiomes

BACKGROUND

Exposure to a diverse environmental microbiome is thought to play an important role in "educating" the immune system and facilitating competitive exclusion of pathogens to maintain human health. Vegetation and soil are key sources of airborne microbiota--the aerobiome. A limited number of studies have attempted to characterize the dynamics of near surface green space aerobiomes, and no studies to date have investigated these dynamics from a vertical perspective. Vertical stratification in the aerobiome could have important implications for public health and for the design, engineering, and management of urban green spaces.

OBJECTIVES

The primary objectives of this study were to: a) assess whether significant vertical stratification in bacterial species richness and evenness (alpha diversity) of the aerobiome occurred in a parkland habitat in Adelaide, South Australia; b) assess whether significant compositional differences (beta diversity) between sampling heights occurred; and c) to preliminarily assess whether there were significant altitudinal differences in potentially pathogenic and beneficial bacterial taxa.

METHODS

We combined an innovative columnar sampling method at soil level, 0.0, 0.5, 1.0, and 2.0 m , using passive petri dish sampling to collect airborne bacteria. We used a geographic information system (GIS) to select study sites, and we used high-throughput sequencing of the bacterial 16S rRNA gene to assess whether significant vertical stratification of the aerobiome occurred.

RESULTS

Our results provide evidence of vertical stratification in both alpha and beta (compositional) diversity of airborne bacterial communities, with diversity decreasing roughly with height. We also found significant vertical stratification in potentially pathogenic and beneficial bacterial taxa.

DISCUSSION

Although additional research is needed, our preliminary findings point to potentially different exposure attributes that may be contingent on human height and activity type. Our results lay the foundations for further research into the vertical characteristics of urban green space aerobiomes and their implications for public health and urban planning. https://doi.org/10.1289/EHP7807.

The Lovebug Effect: Is the human biophilic drive influenced by interactions between the host, the environment, and the microbiome?

Psychological frameworks are often used to investigate the mechanisms involved with our affinity towards, and connection with nature--such as the Biophilia Hypothesis and Nature Connectedness. Recent revelations from microbiome science suggest that animal behaviour can be strongly influenced by the host's microbiome--for example, via the bidirectional communication properties of the gut-brain axis. Here, we build on this theory to hypothesise that a microbially-influenced mechanism could also contribute to the human biophilic drive - the tendency for humans to affiliate and connect with nature. Humans may be at an evolutionary advantage through health-regulating exchange of environmental microbiota, which in turn could influence our nature affinity. We present a conceptual model for microbially-influenced nature affinity, calling it the Lovebug Effect. We present an overview of the potential mechanistic pathways involved in the Lovebug Effect, and consider its dependence on the hologenome concept of evolution, direct behavioural manipulation, and host-microbiota associated phenotypes independent of these concepts. We also discuss its implications for human health and ecological resilience. Finally, we highlight several possible approaches to scrutinise the hypothesis. The Lovebug Effect could have important implications for our understanding of exposure to natural environments for health and wellbeing, and could contribute to an ecologically resilient future.

Flavor-specific enhancement of electronic cigarette liquid consumption and preference in mice

BACKGROUND

The use of electronic cigarettes has increased over the past decade. To determine how the abuse liability of electronic cigarette liquids (e-liquids) differs from nicotine alone, and to determine the impact of flavor, we compared nicotine-containing fruit- and tobacco-flavored e-liquids, and their nicotine-free versions, to nicotine alone in mouse models of oral consumption, reward and aversion.

METHODS

Adult male C57BL/6 J mice voluntarily consumed oral nicotine, equivalent nicotine concentrations of fruit- and tobacco-flavored e-liquid, and equivalent dilutions of the nicotine-free versions in 2-bottle choice tests. Conditioned place preference and place aversion were assessed with peripherally administered e-liquids or nicotine. Serum nicotine and cotinine levels were measured after subcutaneous injections of e-liquid or nicotine.

RESULTS

Mice showed higher consumption and preference for the fruit-flavored e-liquid compared with nicotine alone. This increase was not due to the flavor itself as consumption of the nicotine-free fruit-flavored e-liquid was not elevated until the highest concentration tested. The increased consumption and preference were not observed with the tobacco-flavored e-liquid. The conditioned place preference, place aversion and nicotine pharmacokinetics of the fruit-flavored e-liquid were not significantly different from nicotine alone.

CONCLUSIONS

Our data suggest that fruit, but not tobacco flavor, increased the oral consumption of e-liquid compared with nicotine alone. Moreover, this enhancement was not due to increased consumption of the flavor itself, altered rewarding or aversive properties after peripheral administration, or altered pharmacokinetics. This flavor-specific enhancement suggests that some flavors may lead to higher nicotine intake and increased use of e-liquids compared with nicotine alone.

Let Nature Be Thy Medicine: A Socioecological Exploration of Green Prescribing in the UK

Prescribing nature-based health interventions (green prescribing)-such as therapeutic horticulture or conservation activities-is an emerging transdisciplinary strategy focussed on reducing noncommunicable diseases. However, little is known about the practice of, and socioecological constraints/opportunities associated with, green prescribing in the UK. Furthermore, the distribution of green prescribing has yet to be comprehensively mapped. In this study, we conducted a socioecological exploration of green prescribing. We deployed online questionnaires to collect data from general practitioners (GPs) and nature-based organisations (NBOs) around the UK and conducted spatial analyses. Our results indicate that GPs and NBOs perceive and express some common and distinct constraints to green prescribing. This highlights the need to promote cross-disciplinary communication pathways. Greenspace presence and abundance within close proximity (100 and 250 m) to GP surgeries (but not greenness-as a proxy for vegetation cover) and NBO presence within 5 km were associated with higher levels of green prescribing provision. Lower levels of deprivation were associated with higher frequency of NBOs. This suggests that the availability of greenspaces and NBOs could be important for green prescribing provision, but there could be greater opportunities in less deprived areas. Important foci for future research should be to establish transdisciplinary collaborative pathways, efficient infrastructure management and a common vocabulary in green prescribing-with the overall aim of reducing inequalities and enhancing planetary health.

Microbiome-Inspired Green Infrastructure: A Toolkit for Multidisciplinary Landscape Design

Incorporating recent advances in environmental microbiome research and policy is a major challenge for urban design. We set out a framework for managing construction projects so that multidisciplinary teams of researchers and practitioners can explicitly consider environmental microbiota in design and construction contexts, thereby increasing ecosystem functionality and public health.

Differential gene expression and gene-set enrichment analysis in Caco-2 monolayers during a 30-day timeline with Dexamethasone exposure

Glucocorticoid hormones affect gene expression via activation of glucocorticoid receptor NR3C1, causing modulation of inflammation and autoimmune activation. The glucocorticoid Dexamethasone is an important pharmaceutical for the treatment of colitis and other inflammatory bowel diseases. While suppressive effects of glucocorticoids on activated immune cells is significant, their effects upon epithelial cells are less well studied. Previous research shows that the effects of Dexamethasone treatment on polarized Caco-2 cell layer permeability is delayed for >10 treatment days (as measured by transepithelial electrical resistance). In vivo intestinal epithelial cells turn over every 3–5 days; we therefore hypothesized that culture age may produce marked effects on gene expression, potentially acting as a confounding variable. To investigate this issue, we cultured polarized Caco-2 monolayers during a 30-day timecourse with ~15 days of continuous Dexamethasone exposure. We collected samples during the timecourse and tested differential expression using a 250-plex gene expression panel and Nanostring nCounter® system. Our custom panel was selectively enriched for KEGG annotations for tight-junction, actin cytoskeleton regulation, and colorectal cancer-associated genes, allowing for focused gene ontology-based pathway enrichment analyses. To test for confounding effects of time and Dexamethasone variables, we used the Nanostring nSolver differential expression data model which includes a mixturenegative binomial modelwith optimization. We identified a time-associated “EMT-like” signature with differential expression seen in important actomyosin cytoskeleton, tight junction, integrin, and cell cycle pathway genes. Dexamethasone treatment resulted in a subtle yet significant counter-signal showing suppression of actomyosin genes and differential expression of various growth factor receptors.

A Fermi-degenerate three-dimensional optical lattice clock

Strontium optical lattice clocks have the potential to simultaneously interrogate millions of atoms with a high spectroscopic quality factor of 4 × 10¹⁷ Previously, atomic interactions have forced a compromise between clock stability, which benefits from a large number of atoms, and accuracy, which suffers from density-dependent frequency shifts. Here we demonstrate a scalable solution that takes advantage of the high, correlated density of a degenerate Fermi gas in a three-dimensional (3D) optical lattice to guard against on-site interaction shifts. We show that contact interactions are resolved so that their contribution to clock shifts is orders of magnitude lower than in previous experiments. A synchronous clock comparison between two regions of the 3D lattice yields a measurement precision of 5 × 10^-19 in 1 hour of averaging time.

Ultrastable Silicon Cavity in a Continuously Operating Closed-Cycle Cryostat at 4 K

We report on a laser locked to a silicon cavity operating continuously at 4 K with 1×10^{-16} instability and a median linewidth of 17 mHz at 1542 nm. This is a tenfold improvement in short-term instability, and a 10^{4} improvement in linewidth, over previous sub-10-K systems. Operating at low temperatures reduces the thermal noise floor and, thus, is advantageous toward reaching an instability of 10^{-18}, a long-sought goal of the optical clock community. The performance of this system demonstrates the technical readiness for the development of the next generation of ultrastable lasers that operate with an ultranarrow linewidth and long-term stability without user intervention.

1.5 μm Lasers with Sub-10 mHz Linewidth

We report on two ultrastable lasers each stabilized to independent silicon Fabry-Pérot cavities operated at 124 K. The fractional frequency instability of each laser is completely determined by the fundamental thermal Brownian noise of the mirror coatings with a flicker noise floor of 4×10^{-17} for integration times between 0.8 s and a few tens of seconds. We rigorously treat the notorious divergences encountered with the associated flicker frequency noise and derive methods to relate this noise to observable and practically relevant linewidths and coherence times. The individual laser linewidth obtained from the phase noise spectrum or the direct beat note between the two lasers can be as small as 5 mHz at 194 THz. From the measured phase evolution between the two laser fields we derive usable phase coherence times for different applications of 11 to 55 s.

Factors Affecting the Release of Haemoglobin and Enzymes from Human Erythrocytes

The efflux of lactate dehydrogenase and haemoglobin from human erythrocytes during prolonged incubation at 37° was significantly reduced by ATP, ADP, AMP, UTP, creatine phosphate, or phosphoenolpyruvate and to a lesser extent by fructose, glucose 6-phosphate or fructose 6-phosphate, but not by glucose. Iodoacetate, however, markedly increased the loss of haemoglobin and slightly increased that of lactate dehydrogenase.

Phospholipase C greatly accelerated the relase of haemoglobin, lactate dehydrogenase, pyruvate kinase, hexokinase, glucose 6-phosphate dehydrogenase, and 6-phosphogluconate dehydrogenase from human erythrocytes, but this effect was also reduced in the presence of ATP or ADP. The loss of lactate dehydrogenase, malate dehydrogenase, and pyruvate kinase from the cells treated with phospholipase C increased as their ATP content fell. In a series of experiments in which the action of phospholipase C was stopped by the subsequent addition of trypsin, ATP and ADP (1 mmol/l) significantly reduced the efflux of haemoglobin, but AMP had no such effect.

The results are consistent with the conclusion from our previous work that enzyme leakage is related to diminution in the energy content of the cells. The protective action of AMP on cells not treated with phospholipase C, however, differs from earlier findings with rat lymphocytes and it is suggested that in red cells it might be converted into ATP or that it has a direct effect on the permeability of the cell membrane.

Exocyst complex protein expression in the human placenta

INTRODUCTION

Protein production and secretion are essential to syncytiotrophoblast function and are associated with cytotrophoblast cell fusion and differentiation. Syncytiotrophoblast hormone secretion is a crucial determinant of maternal-fetal health, and can be misregulated in pathological pregnancies. Although, polarized secretion is a key component of placental function, the mechanisms underlying this process are poorly understood.

OBJECTIVE

While the octameric exocyst complex is classically regarded as a master regulator of secretion in various mammalian systems, its expression in the placenta remained unexplored. We hypothesized that the syncytiotrophoblast would express all exocyst complex components and effector proteins requisite for vesicle-mediated secretion more abundantly than cytotrophoblasts in tissue specimens.

METHODS

A two-tiered immunobiological approach was utilized to characterize exocyst and ancillary proteins in normal, term human placentas. Exocyst protein expression and localization was documented in tissue homogenates via immunoblotting and immunofluorescence labeling of placental sections.

RESULTS

The eight exocyst proteins, EXOC1, 2, 3, 4, 5, 6, 7, and 8, were found in the human placenta. In addition, RAB11, an important exocyst complex modulator, was also expressed. Exocyst and Rab protein expression appeared to be regulated during trophoblast differentiation, as the syncytiotrophoblast expressed these proteins with little, if any, expression in cytotrophoblast cells. Additionally, exocyst proteins were localized at or near the syncytiotrophoblast apical membrane, the major site of placental secretion.

DISCUSSION/CONCLUSION

Our findings highlight exocyst protein expression as novel indicators of trophoblast differentiation. The exocyst's regulated localization within the syncytiotrophoblast in conjunction with its well known functions suggests a possible role in placental polarized secretion.

TEMS: results of a specialist centre

INTRODUCTION

Transanal endoscopic microsurgery (TEMS) is becoming more widespread due to the increasing body of evidence to support its role. Previous published data has reported recurrence rates in excess of 10% for benign polyps after TEMS.

METHODS

Bradford Royal Infirmary is a tertiary referral centre for TEMS and early rectal cancer in the UK. Data for all TEMS operations were entered into a prospective database over a 7-year period. Demographic data, complications and recurrence rates were recorded. Both benign adenomas and malignant lesions were included.

RESULTS

A total of 164 patients (65% male), with a mean age of 68 years were included; 114 (70%) of the lesions resected were benign adenomas, and 50 (30%) were malignant lesions. Median polyp size was 4 (range 0.6-14.5) cm. Mean length of operation was 55 (range 10-120) min. There were no recurrences in any patients with a benign adenoma resected; two patients with malignant lesions developed recurrences. Three intra-operative complications were recorded, two rectal perforations (repaired primarily, one requiring defunctioning stoma), and a further patient suffered a blood loss of >300 ml requiring transfusion. Six patients developed strictures requiring dilation either endoscopically or under anaesthetic in the post-operative period.

CONCLUSIONS

We have demonstrated that TEMS procedures performed in a specialist centre provide low rates of both recurrence and complication. Within a specialist centre, TEMS surgery should be offered to all patients for rectal lesions, both benign and malignant, that are amenable to TEMS.

IFPA Meeting 2012 Workshop Report I: comparative placentation and animal models, advanced techniques in placental histopathology, human pluripotent stem cells as a model for trophoblast differentiation

Workshops are an important part of the IFPA annual meeting as they allow for discussion of specialized topics. At IFPA meeting 2012 there were twelve themed workshops, three of which are summarized in this report. These workshops related to various aspects of placental biology but collectively covered areas of models and technical issues involved in placenta research: 1) comparative placentation and animal models; 2) advanced techniques in placental histopathology; 3) human pluripotent stem cells as a model for trophoblast differentiation.

A placental sub-proteome: the apical plasma membrane of the syncytiotrophoblast

As a highly vascularized tissue, the placenta mediates gas and solute exchange between maternal and fetal circulations. In the human placenta, the interface with maternal blood is a unique epithelial structure known as the syncytiotrophoblast. Previously we developed a colloidal-silica based method to generate highly enriched preparations of the apical plasma membrane of the syncytiotrophoblast. Using similar preparations, a proteomics assessment of this important sub-proteome has identified 340 proteins as part of this apical membrane fraction. The expression of 38 of these proteins was previously unknown in the human placental syncytiotrophoblast. Together with previous studies, the current proteomic database expands our knowledge of the proteome of the syncytiotrophoblast apical plasma membrane from normal placentas to include more than 500 proteins. This database is a valuable resource for future comparisons to diseased placentas. Additionally, this data set provides a basis for further experimental studies of placenta and trophoblast function.

Where's the glass? Biomarkers, molecular clocks, and microRNAs suggest a 200-Myr missing Precambrian fossil record of siliceous sponge spicules

The earliest evidence for animal life comes from the fossil record of 24-isopropylcholestane, a sterane found in Cryogenian deposits, and whose precursors are found in modern demosponges, but not choanoflagellates, calcareans, hexactinellids, or eumetazoans. However, many modern demosponges are also characterized by the presence of siliceous spicules, and there are no convincing demosponge spicules in strata older than the Cambrian. This temporal disparity highlights a problem with our understanding of the Precambrian fossil record--either these supposed demosponge-specific biomarkers were derived from the sterols of some other organism and are simply retained in modern demosponges, or spicules do not primitively characterize crown-group demosponges. Resolving this issue requires resolving the phylogenetic placement of another group of sponges, the hexactinellids, which not only make a spicule thought to be homologous to the spicules of demosponges, but also make their first appearance near the Precambrian/Cambrian boundary. Using two independent analytical approaches and data sets--traditional molecular phylogenetic analyses and the presence or absence of specific microRNA genes--we show that demosponges are monophyletic, and that hexactinellids are their sister group (together forming the Silicea). Thus, spicules must have evolved before the last common ancestor of all living siliceans, suggesting the presence of a significant gap in the silicean spicule fossil record. Molecular divergence estimates date the origin of this last common ancestor well within the Cryogenian, consistent with the biomarker record, and strongly suggests that siliceous spicules were present during the Precambrian but were not preserved.

The expression of caveolin-1 and the distribution of caveolae in the murine placenta and yolk sac: parallels to the human placenta

The expression pattern of caveolin-1 and the distribution of caveolae in the murine placental labyrinth and visceral yolk sac have been determined. Immunoblot analysis demonstrates that both placenta and yolk sac express the protein caveolin-1. Immunofluorescence microscopy was used to determine which cell types in the placental labyrinth and yolk sac express caveolin-1. In yolk sac, detectable caveolin-1 was restricted to endothelial cells and smooth muscle cells of the vitelline vasculature and to mesothelial cells. Endoderm, the major cell type in the yolk sac, does not express caveolin-1 as assessed by this assay. In the labyrinth region of the placenta, endothelial cells express caveolin-1 but this protein was not detectable in any of the three trophoblast layers. These tissues were also examined by electron microscopy to determine which cell types contain the specialized plasma membrane microdomains known as caveolae. Morphologically detectable caveolae were present in endothelial and smooth muscle cells, as well as mesothelial cells of the yolk sac and in endothelial cells of the placental labyrinth. Neither endodermal cells of the yolk sac nor trophoblastic cells in the placental labyrinth contained caveolae-like structures. We conclude that caveolin-1 and caveolae have restricted distribution in the murine placenta and yolk sac and that this parallels the situation in human placenta.

Correlative fluorescence and electron microscopy in tissues: immunocytochemistry

Correlative microscopy is a collection of procedures that rely upon two or more imaging modalities to examine the same specimen. The imaging modalities employed should each provide unique information and the combined correlative data should be more information rich than that obtained by any of the imaging methods alone. Currently the most common form of correlative microscopy combines fluorescence and electron microscopy. While much of the correlative microscopy in the literature is derived from studies of model cell culture systems we have focused, primarily, on correlative microscopy in tissue samples. The use of tissue, particularly human tissue, may add constraints not encountered in cell culture systems. Ultrathin cryosections, typically used for immunoelectron microscopy, have served as the substrate for correlative fluorescence and electron microscopic immunolocalization in our studies. In this work, we have employed the bifunctional reporter FluoroNanogold. This labeling reagent contains both a fluorochrome and a gold-cluster compound and can be imaged by sequential fluorescence and electron microscopy. This approach permits the examination of exactly the same sub-cellular structures in both fluorescence and electron microscopy with a high level of spatial resolution.

Placental dysferlin expression is reduced in severe preeclampsia

Dysferlin (DYSF) and myoferlin (MYOF), members of the ferlin family of membrane proteins, are co-expressed in human placental syncytiotrophoblast (STB). Although the role of these ferlin proteins in the placenta has yet to be established, it has been suggested that DYSF and MYOF may contribute to the stability of the apical STB plasma membrane. The release of STB-derived cellular debris increases in the setting of preeclampsia (PE), suggesting relative destabilization of the hemochorial interface. To test whether PE was associated with alterations in placental expression of DYSF and/or MYOF, a cross-sectional study was performed using specimens of villous placenta collected form women with severe PE (n=10) and normotensive controls (n=10). DYSF and MYOF expression were examined using quantitative real-time RT-PCR, immunoblotting, and immunofluorescence labeling of tissue specimens. Placental DYSF expression was 57% lower at the mRNA level (p=0.03) and 38% lower at the protein level (p=0.026) in severe PE as compared to normotensive subjects. There were no differences in placental MYOF protein or mRNA expression between these groups. No appreciable changes in the distribution of DYSF or MYOF within placental villi was observed in PE relative to control specimens. We conclude that DYSF expression is reduced in severe PE relative to gestational age-matched controls. As DYSF has a role in membrane repair, these data suggest a role for DYSF in the stability of the apical STB plasma membrane and may account, at least in part, for the increased shedding of microparticles from this membrane in PE.

Placental proteomics: a shortcut to biological insight

Proteomics analysis of biological samples has the potential to identify novel protein expression patterns and/or changes in protein expression patterns in different developmental or disease states. An important component of successful proteomics research, at least in its present form, is to reduce the complexity of the sample if it is derived from cells or tissues. One method to simplify complex tissues is to focus on a specific, highly purified sub-proteome. Using this approach we have developed methods to prepare highly enriched fractions of the apical plasma membrane of the syncytiotrophoblast. Through proteomics analysis of this fraction we have identified over five hundred proteins several of which were previously not known to reside in the syncytiotrophoblast. Herein, we focus on two of these, dysferlin and myoferlin. These proteins, largely known from studies of skeletal muscle, may not have been found in the human placenta were it not for discovery-based proteomics analysis. This new knowledge, acquired through a discovery-driven approach, can now be applied for the generation of hypothesis-based experimentation. Thus discovery-based and hypothesis-based research are complimentary approaches that when coupled together can hasten scientific discoveries.

Proteomics of the human placenta: promises and realities

Proteomics is an area of study that sets as its ultimate goal the global analysis of all of the proteins expressed in a biological system of interest. However, technical limitations currently hamper proteome-wide analyses of complex systems. In a more practical sense, a desired outcome of proteomics research is the translation of large protein data sets into formats that provide meaningful information regarding clinical conditions (e.g., biomarkers to serve as diagnostic and/or prognostic indicators of disease). Herein, we discuss placental proteomics by describing existing studies, pointing out their strengths and weaknesses. In so doing, we strive to inform investigators interested in this area of research about the current gap between hyperbolic promises and realities. Additionally, we discuss the utility of proteomics in discovery-based research, particularly as regards the capacity to unearth novel insights into placental biology. Importantly, when considering under studied systems such as the human placenta and diseases associated with abnormalities in placental function, proteomics can serve as a robust 'shortcut' to obtaining information unlikely to be garnered using traditional approaches.

Mechanically evoked 5-hydroxytryptamine release is mediated by caveolin-associated cholesterol rich membrane domains

5-Hydroxytryptamine (5-HT) from enterochromaffin cells activates neural reflexes that govern intestinal motility and secretion. Mechanical stimulation of human enterochromaffin cell-derived BON cells activates a G alpha q-signalling pathway coupled to 5-HT release. Molecular mechanisms identifying elements of mechanosensory transduction are unknown. The aim of this study was to determine the role of caveolin and caveolin-associated cholesterol rich microdomains in mechanically stimulated 5-HT release from BON cells. Caveolin-1 transcripts and immunofluorescence were found in BON cells. In the static state, caveolins-1 and -2 co-precipitated with G alpha q in cholesterol rich cell fractions, but not with G alpha s, G alpha i/o and G beta. Mechanical stimulation transiently uncoupled G alpha q from caveolin-1 and increased 5-HT release. Disassembly of caveolin-associated membrane microdomains by filipin or by cholesterol depletion with methyl-beta-cyclodextrin decreased mechanically evoked 5-HT release. These results suggest that caveolin and caveolin-associated cholesterol rich membrane microdomains are key regulators in mechanically evoked 5-HT release from enterochromaffin cells.

Endothelial Expression of Fc Gamma Receptor IIb in the Full-term Human Placenta

In the third trimester, human placental endothelial cells express Fc gamma receptor IIb (FcgammaRIIb). This expression is unique because FcgammaRIIb is generally expressed on immune cells and is typically undetectable in adult endothelial cells. Recently, we found a novel FcgammaRIIb-defined, IgG-containing organelle in placental endothelial cells; this organelle may be a key structure for the transcytosis of IgG across the endothelial layer. In this study, we verify the expression of FcgammaRIIb in endothelial placenta cells and use reverse transcriptase-polymerase chain reaction (RT-PCR) and sequencing analyses to define the expressed FCGR2B mRNA transcript variant. We also investigated the distribution of FCGR2B mRNA and protein within the vascular tree of the full-term human placenta by RT-PCR and quantitative microscopy. The mRNA sequence of FCGR2B expressed specifically in placental endothelial cells is that of transcript variant 2. FcgammaRIIb expression and synthesis occur throughout the placental vascular tree but do not extend into the umbilical cord. This study provides additional information on FcgammaRIIb expression in the human placenta.

Association of PAT proteins with lipid storage droplets in term fetal membranes

As depots for neutral lipids, lipid storage droplets (LDs) accumulate with advancing gestation within the fetal membranes. Little is currently known about the proteins associated with the LDs of these cells. The PAT family [perilipin, adipose differentiation-related protein (ADRP), and tail-interacting protein of 47 kilodaltons (TIP47)] represents a unique group of proteins thought to contribute to LD formation and function. We examined the association of each of the PAT proteins with LDs of term fetal membranes. We found that large LDs of amnion epithelial cells were reactive for neutral lipid stains and simultaneously encoated with ADRP and TIP47, but not perilipin. Within the remaining cell types, LDs were frequently co-labeled with antibodies recognizing ADRP and TIP47; however, in cells harboring only small LDs, the majority of TIP47 labeling was cytoplasmic. Structures labeled with perilipin antibodies were present only in chorion laeve trophoblasts. Gene and protein expression analyses suggested this to be a small molecular weight perilipin isoform, such as that seen in steroidogenic cells. We conclude that LDs are heterogeneous among differing cell types of the fetal membranes. Subclassification of LDs based on associated proteins suggests that these organelles may serve specialized functions within individual cells.

Advanced techniques in placental biology -- workshop report

Major advances in placental biology have been realized as new technologies have been developed and existing methods have been refined in many areas of biological research. Classical anatomy and whole-organ physiology tools once used to analyze placental structure and function have been supplanted by more sophisticated techniques adapted from molecular biology, proteomics, and computational biology and bioinformatics. In addition, significant refinements in morphological study of the placenta and its constituent cell types have improved our ability to assess form and function in highly integrated manner. To offer an overview of modern technologies used by investigators to study the placenta, this workshop: Advanced techniques in placental biology, assembled experts who discussed fundamental principles and real time examples of four separate methodologies. Y. Sadovsky presented the principles of microRNA function as an endogenous mechanism of gene regulation. J. Robinson demonstrated the utility of correlative microscopy in which light-level and transmission electron microscopy are combined to provide cellular and subcellular views of placental cells. A. Croy provided a lecture on the use of microdissection techniques which are invaluable for isolating very small subsets of cell types for molecular analysis. Finally, G. Rice presented an overview methods on profiling of complex protein mixtures within tissue and/or fluid samples that, when refined, will offer databases that will underpin a systems approach to modern trophoblast biology.

Immunomodulation in type 1 diabetes by NBI-6024, an altered peptide ligand of the insulin B epitope

NBI-6024 is an altered peptide ligand (APL) corresponding to the 9-23 amino acid region of the insulin B chain (B(9-23)), an epitope recognized by inflammatory interferon-gamma-producing T helper (Th)1 lymphocytes in type 1 diabetic patients. Immunomodulatory effects of NBI-6024 administration in recent-onset diabetic patients in a phase I clinical trial (NBI-6024-0003) were measured in peripheral blood mononuclear cells using the enzyme-linked immunosorbent spot assay. Analysis of the mean magnitude of cytokine responses to B(9-23) and NBI-6024 for each cohort showed significant increases in interleukin-5 responses (a Th2 regulatory phenotype) in cohorts that received APL relative to those receiving placebo. A responder analysis showed that Th1 responses to B(9-23) and NBI-6024 were observed almost exclusively in the placebo-treated diabetic population but not in nondiabetic control subjects and that APL administration (five biweekly subcutaneous injections) significantly and dose-dependently reduced the percentage of patients with these Th1 responses. The results of this phase I clinical study strongly suggest that NBI-6024 treatment shifted the Th1 pathogenic responses in recent-onset type 1 diabetic patients to a protective Th2 regulatory phenotype. The significance of these findings on the clinical outcome of disease is currently under investigation in a phase II multidose study.

Thermodynamic model of quasiliquid formation on H2O ice: Comparison with experiment

We have developed a new thermodynamic theory of the quasiliquid layer, which has been shown to be effective in modeling the phenomenon in a number of molecular systems. Here we extend our analysis to H(2)O ice, which has obvious implications for environmental and atmospheric chemistry. In the model, the liquid layer exists in contact with an ice defined as a two-dimensional lattice of sites. The system free energy is defined by the bulk free energies of ice I(h) and liquid water and is minimized in the grand canonical ensemble. An additional configurational entropy term arises from the occupation of the lattice sites. Furthermore, the theory predicts that the layer thickness as a function of temperature depends only on the liquid activity. Two additional models are derived, where slightly different approximations are used to define the free energy. With these two models, we illustrate the connection between the quasiliquid phenomenon and multilayer adsorption and the possibility of a two-dimensional phase transition connecting a dilute low coverage phase of adsorbed H(2)O and the quasiliquid phase. The model predictions are in agreement with a subset of the total suite of experimental measurements of the liquid thickness on H(2)O ice as a function of temperature. The theory indicates that the quasiliquid layer is actually equivalent to normal liquid water, and we discuss the impact of such an identification. In particular, observations of the liquid layer to temperatures as low as 200 K indicate the possibility that the quasiliquid is, in fact, an example of deeply supercooled normal water. Finally, we briefly discuss the obvious extension of the pure liquid theory to a thermodynamic theory of interfacial solutions on ice in the environment.

In situ immunolabeling allows for detailed localization of prostaglandin synthesizing enzymes within amnion epithelium

Detailed information regarding the subcellular distribution of proteins within amnion epithelial cells is a goal of numerous placental biologists. In this report, we describe a versatile technique for in situ immunolabeling in amnion that is as technically permissible as traditional immunolabeling of cultured cells and, when coupled with confocal laser scanning microscopy, is similarly capable of providing detailed information regarding subcellular protein distribution. Using antibodies directed against sequential enzymes of the prostaglandin E biosynthesis cascade, we compared this novel method with immunofluorescent labeling using amnion cells in primary culture and cryosections of reflected fetal membrane rolls. By several criteria, we observed morphological variation between the cells cultured in vitro and the tissue specimens. Despite general consistencies in immunostaining patterns between the cryosectioned specimens and those labeled in situ, morphological preservation was superior using the latter technique. Relative to the cryosectioned specimens, in situ immunostaining was advantageous in that it permitted improved sampling efficiency, and allowed regional variations in labeling to be observed in a more global context within the tissue. Our results demonstrate that in situ immunolabeling provides a useful adjunct or alternative to immunolabeling using membrane roll preparations.