Fungal Spore Richness and Abundance of Allergenic Taxa: Comparing a Portable Impactor and Passive Trap Indoors and Outdoors in an Urban Setting

Fungal spores are common airborne allergens, and fungal richness has been implicated in allergic disease. Amplicon sequencing of environmental DNA from air samples is a promising method to estimate fungal spore richness with semi-quantification of hundreds of taxa and can be combined with quantitative PCR to derive abundance estimates. However, it remains unclear how the choice of air sampling method influences these estimates. This study compared active sampling with a portable impactor and passive sampling with a passive trap over different durations to estimate fungal spore richness and the abundance of allergenic taxa. Air sampling was conducted indoors and outdoors at 12 residences, including repeated measurements with a portable impactor and passive traps with 1-day and 7-day durations. ITS2 amplicon sequence data were transformed to spore equivalents estimated by quantitative PCR, repeated active samples were combined, and abundance-based rarefaction was performed to standardize sample coverage for estimation of genus-level richness and spore abundance. Rarefied fungal richness was similar between methods indoors but higher for passive traps with a 7-day duration outdoors. Rarefied abundance of allergenic genera was similar between methods but some genera had lower abundance for passive traps with a 1-day duration, which differed indoors and outdoors indicating stochasticity in the collection of spores on collocated samplers. This study found that similar estimates of fungal spore richness and abundance of allergenic taxa can be obtained using a portable impactor or a passive trap within one day and that increased passive sample duration provides limited additional information.

Insights into an analytical simulation of a natural convection flow controlled by Arrhenius kinetics in a micro-channel

The focus of this paper is the investigation of an Arrhenius-driven chemical reaction in an upstanding micro-channel over an imposed transverse magnetic field with fully developed constant free convection flow. Subject to suitable boundary conditions, the temperature and velocity equations are resolved in non-dimensional form employing the homotopy perturbation method (HPM). the fundamental flow behaviors of temperature, velocity, and volumetric flow are explored as a consequence of regulating characteristics such as fluid-wall interaction parameter, rarefaction parameter, chemical reaction parameters, wall-ambient temperature difference ratio, and Hartman number. The findings are carefully investigated and graphically represented in several mesh grid graphs. It was established that increasing the values of the rarefaction parameters and chemical reaction results in an upsurge in the fluid velocity and volume flow rate, respectively, whereas increasing the Hartman number results in observable flow retardation. Additionally, when the chemical reactant parameter is ignored, the numerical comparison is in excellent agreement with the previously published results.

Mesostigmata diversity by manure type: a reference study and new datasets from southwestern Iran

Manure-inhabiting Mesostigmata mites are important biological control agents of pest flies. However, the biodiversity of this mite community is mainly known from Europe and America, and especially from cattle manure. This study examined the diversity and abundance of Mesostigmata mites associated with various types of manure in an (intensive) agricultural region of the Middle East, i.e., the city Ahvaz and its suburbs, in southwest Iran. Mite samples were extracted from manure of cattle, buffalo, sheep, horse, poultry and quail in 30 livestock and poultry farms. In total, 40 species belonging to 24 genera and 16 families were identified. The most diverse families were Laelapidae with eight species, Macrochelidae with seven and Parasitidae with six. Macrocheles muscaedomesticae and Uroobovella marginata were the most widespread species, recorded in 28 and 27 out of 30 collection sites, respectively. Two species, M. sumbaensis and U. marginata, were found in all studied manures. Simpson's diversity index recorded the highest diversity in buffalo and sheep manure. Real and theoretical species richness (rarefaction curves) were congruent in number of individuals. The presence of seven species of Macrochelidae in the manure confirms that these are important predators of the house fly for the region of Ahvaz and its suburbs. Members of the Parasitidae were highly prevalent, with one species known as a specialized predator of house fly eggs. This work aims to encourage further studies on the diversity of Mesostigmata in these agricultural settings, and further continue assessing the feasibility of these mites as effective biocontrol agents of filth flies in different types of manure and from different corners of the world.

Spatial scaling of plant and bird diversity from 50 to 10,000 ha in a lowland tropical rainforest

While there are numerous studies of diversity patterns both within local communities and at regional scales, the intermediate scale of tens to thousands of km² is often neglected. Here we present detailed local data on plant communities (using 20 × 20 m plots) and bird communities (using point counts) for a 50 ha ForestGEO plot in lowland rainforest at Wanang, Papua New Guinea. We compare these local diversity patterns with those documented in the surrounding 10,000 ha of lowland rainforest. Woody plant species richness was lower within 50 ha (88% of 10,000 ha richness), even when both were surveyed with identical sampling effort. In contrast, bird communities exhibited identical species accumulation patterns at both spatial scales. Similarity in species composition (Chao-Jaccard) remained constant while similarity in dominance structure (Bray–Curtis) decreased with increased distance between samples across the range from < 1 to 13.8 km for both plant and bird communities. The similarity decay was more rapid in plants, but in both cases was slow. The results indicate low to zero beta-diversity at the spatial scale represented here, particularly for birds but also for woody plants. A 50 ha plot provided a highly accurate representation of broader-scale diversity and community composition within 10,000 ha for birds, and a relatively good representation for woody plants. This suggests potential for wider generalization of data from ForestGEO plots which are almost always locally unreplicated, at least for those in lowland tropical forest.

New microsatellite markers for Ellipse, Venustaconcha ellipsiformis (Bivalvia: Unionidae), with notes on optimal sample size and cross-species amplification

Venustaconcha ellipsiformis (Unionidae) is a freshwater mussel species inhabiting small to medium streams of the Midwestern United States; however, its occurrence is rather sporadic and populations are often isolated. Due to anthropogenic habitat degradation and water pollution, this species is designated as some sort of conservation status in many states. To prioritize conservation strategies, highly variable genetic markers are necessary to assess population genetic structure and potential genetic erosion of V. ellipsiformis. Using whole genome sequence data, we developed and characterized microsatellite markers for V. ellipsiformis. Among 23 tetranucleotide loci tested, 14 loci were consistently amplified and showed polymorphism. Analyses performed on three populations in the upper Mississippi River basin showed that the number of alleles per locus ranged from 2 to 11 and the observed heterozygosity varied from 0.15 to 0.75. Based on genotypic and allelic rarefaction curves, these loci had adequate statistical power to genetically discriminate between individuals and the sample size was large enough to capture most alleles available in the populations at most loci. Finally, cross-species screening of the loci successfully amplified and showed polymorphism in six species in the tribe Lampsilini. The microsatellite loci developed in this study provide a valuable addition to extant genetic markers for freshwater mussels and can be useful to provide high-level resolution of population genetic parameters for V. ellipsiformis. Such information will be of great value for resource managers developing and prioritizing conservation strategies for imperiled mussel species.

Towards optimal selection of stimuli polarity method for effective evoking auditory brainstem responses

Towards eliminating stimulus artifacts, alternating polarity stimuli have been widely adopted in eliciting the auditory brainstem response. However, considering the difference in the physiologic basis of the positive and negative polarity stimuli on the auditory system, it is unclear whether alternating polarity stimuli would adversely affect the auditory brainstem response characteristics. This research proposes a new polarity method for stimulus artifacts elimination, Sum polarity, that separately utilized the rarefaction and condensation stimuli and then summed the two evoked responses. We compared the waveform morphology and latencies of the auditory brainstem responses evoked by familiar stimuli (including click, tone-burst, and chirp) with different polarity methods in normal-hearing subjects to investigate the new method's effectiveness. The experimental results showed that alternating polarity of the click and chirp had little effect on the auditory brainstem response. In contrast, alternating polarity affected the waveform morphology and latencies of the auditory brainstem responses to the low-frequency tone-burst, with the effect decreasing as the stimulus frequency increased. These results demonstrated the performance of any polarity method is related to the characteristics of the stimulus signal itself, and no polarity method is optimal for all types of stimuli. Based on the analysis of experimental results, a fixed polarity and alternating polarity were recommended for the click and chirp auditory brainstem responses, respectively. Furthermore, considering the apparent latency differences between the responses to opposite polarity stimuli, the Sum polarity was suggested for the tone-burst auditory brainstem responses. Moreover, this work verified the feasibility of the Sum polarity, which offers another choice for eliminating stimulus artifacts in an evoked potential acquisition.

Uncovering the role of Symbiodiniaceae assemblage composition and abundance in coral bleaching response by minimizing sampling and evolutionary biases

BACKGROUND

Biodiversity and productivity of coral-reef ecosystems depend upon reef-building corals and their associations with endosymbiotic Symbiodiniaceae, which offer diverse functional capabilities to their hosts. The number of unique symbiotic partners (richness) and relative abundances (evenness) have been hypothesized to affect host response to climate change induced thermal stress. Symbiodiniaceae assemblages with many unique phylotypes may provide greater physiological flexibility or form less stable symbioses; assemblages with low abundance phylotypes may allow corals to retain thermotolerant symbionts or represent associations with less-suitable symbionts.

RESULTS

Here we demonstrate that true richness of Symbiodiniaceae phylotype assemblages is generally not discoverable from direct enumeration of unique phylotypes in association records and that cross host-species comparisons are biased by sampling and evolutionary patterns among species. These biases can be minimized through rarefaction of richness (rarefied-richness) and evenness (Probability of Interspecific Encounter, PIE), and analyses that account for phylogenetic patterns. These standardized metrics were calculated for individual Symbiodiniaceae assemblages composed of 377 unique ITS2 phylotypes associated with 123 coral species. Rarefied-richness minimized correlations with sampling effort, while maintaining important underlying characteristics across host bathymetry and geography. Phylogenetic comparative methods reveal significant increases in coral bleaching and mortality associated with increasing Symbiodiniaceae assemblage richness and evenness at the level of host species.

CONCLUSIONS

These results indicate that the potential flexibility afforded by assemblages characterized by many phylotypes present at similar relative abundances does not result in decreased bleaching risk and point to the need to characterize the overall functional and genetic diversity of Symbiodiniaceae assemblages to quantify their effect on host fitness under climate change.

The role of exercise in the reversal of IGF-1 deficiencies in microvascular rarefaction and hypertension

Hypertension has been linked with peripheral and central reductions in vascular density, and with devastating effects on brain function. However, the underlying mechanisms in the relationship between blood pressure and cognitive impairment have yet to be fully elucidated. Here, we review compelling evidence from two lines of inquiry: one that links microvascular rarefaction with insulin-like growth factor 1 (IGF-1) deficiencies, and another which posits that vascular dysfunction precedes hypertension. Based on the findings from experimental and clinical studies, we propose that these lines of evidence converge, and suggest that age-related declines in IGF-1 concentrations precede microvascular rarefaction, initiate an increase in vascular resistance, and therefore are causally linked to onset of hypertension. Physical exercise provides a relevant model for supporting our premise, given the well-established effects of exercise in attenuating vascular dysfunction, hypertension, IGF-1 deficiency, and cognitive decline. We highlight here the role of exercise-induced increases in blood flow in improving vascular integrity and enhancing angiogenesis via the actions of IGF-1, resulting in reversal of rarefaction and hypertension, and enhancement of cerebral blood flow and cognition.

Metabolomic richness and fingerprints of deep-sea coral species and populations

INTRODUCTION

From shallow water to the deep sea, corals form the basis of diverse communities with significant ecological and economic value. These communities face many anthropogenic stressors including energy and mineral extraction activities, ocean acidification and rising sea temperatures. Corals and their symbionts produce a diverse assemblage of compounds that may help provide resilience to some of these stressors.

OBJECTIVES

We aim to characterize the metabolomic diversity of deep-sea corals in an ecological context by investigating patterns across space and phylogeny.

METHODS

We applied untargeted Liquid Chromatography-Mass Spectrometry to examine the metabolomic diversity of the deep-sea coral, Callogorgia delta, across three sites in the Northern Gulf of Mexico as well as three other deep-sea corals, Stichopathes sp., Leiopathes glaberrima, and Lophelia pertusa, and a shallow-water species, Acropora palmata.

RESULTS

Different coral species exhibited distinct metabolomic fingerprints and differences in metabolomic richness including core ions unique to each species. C. delta was generally least diverse while Lophelia pertusa was most diverse. C. delta from different sites had different metabolomic fingerprints and metabolomic richness at individual and population levels, although no sites exhibited unique core ions. Two core ions unique to C. delta were putatively identified as diterpenes and thus may possess a biologically important function.

CONCLUSION

Deep-sea coral species have distinct metabolomic fingerprints and exhibit high metabolomic diversity at multiple scales which may contribute to their capabilities to respond to both natural and anthropogenic stressors, including climate change.

On species richness and rarefaction: size- and coverage-based techniques quantify different characteristics of richness change in biodiversity

Changes in biodiversity today shape the future patterns of biodiversity. This fact underlines the importance of understanding changes in biodiversity through time and space. The number of species, known as species richness, has long been studied as a key indicator that quantifies the state of biodiversity, and standardisation techniques, called rarefaction, have also been used to undertake a fair comparison of the richness observed at different times or locations. The present study asks whether utilising different rarefaction techniques attains comparable results when investigating changes in species richness. The study framework presents the statistical nature of two commonly adopted rarefaction techniques: size-based and coverage-based rarefaction. The key finding is that the rarefied richness results calculated by these two different rarefaction methods reflect different aspects of biodiversity change, the shift in community size and/or composition. This fact illuminates that richness analyses based on different rarefaction techniques can reach different conclusions that may be contradictory. The study also investigates the mechanism creating such divergence. As such, special care is required when evaluating biodiversity change using species richness as an indicator.

Diversity analysis of Plio-Pleistocene large mammal communities in the Omo-Turkana Basin, eastern Africa

Knowing how the diversity of large mammal communities changes across space and time provides an important ecological framework for studying hominin evolution. However, diversity studies that apply methods currently used by neoecologists are rare in paleoanthropology and are also challenging due to diversity's unusual statistical properties. Here, we apply up-to-date analytical methods for understanding how species- and genus-level large mammalian diversity in the Omo-Turkana Basin changed through time and across space at multiple spatiotemporal scales (within each formation:10^2-3 km² and 10^4-5 years; and within the basin as a whole: 10³ km² and 10⁵ years). We found that, on average, Koobi Fora's large mammal community was more diverse than Nachukui's, which in turn was more diverse than Shungura's. Diversity was stable through time within each of these formations (alpha diversity), as was diversity in the basin as a whole (gamma diversity). Compositional dissimilarity between these three formations (beta diversity) was relatively low through time, with a 0.6 average proportion of shared species, suggesting dispersal acted to homogenize the region. Though alpha and gamma diversity were fairly stable through time, we do observe several notable peaks: during the KBS Member in Koobi Fora (30% increase), the Lokalalei Member in Nachukui (120% increase), and at 1.7 Ma in the entire basin (100% increase). We conclude by (1) demonstrating that habitat heterogeneity was an important factor influencing alpha diversity within each of the three formations, and (2) hypothesizing that diversity stability may have been driven by equilibrial dynamics in which overall diversity was constrained by resource availability, implying biotic interactions were an important factor in structuring the communities that included hominins as members. Our findings demonstrate the need to quantify how large mammal diversity changes across time and space in order to further our understanding of hominin ecology and evolution.

Sex-Specific Characteristics of the Microcirculation

The requirements of metabolizing tissue are both continuous and variable; accordingly, the microvasculature serving that tissue must be similarly dynamic. Just as it is recognized that males and females of the same species have differing metabolic requirements, is it not likely that the microvasculature serving these tissues will differ by sex? This section focusing on the constituents of the microcirculation identifies what is known presently about the role sex plays in matching metabolic demand with microvascular function and areas requiring additional study. Many of the identified sex differences are subtle and easily ignored. In the aggregate, though, they can profoundly alter phenotype, especially under stressful conditions including pregnancy, exercise, and disease states ranging from diabetes to heart failure. Although the features presently identified to "have sex" range from differences in growth, morphology, protein expression, and intracellular signaling, males and females alike achieve homeostasis, likely by different means. Studies of microvascular sexual dimorphism are also identifying age as an independent but interacting factor requiring additional attention. Overall, attempting to ignore either sex and/or age is inappropriate and will prevent the design and implementation of appropriate interventions to present, ameliorate, or correct microvascular dysfunction.

Estimating and comparing microbial diversity in the presence of sequencing errors

Estimating and comparing microbial diversity are statistically challenging due to limited sampling and possible sequencing errors for low-frequency counts, producing spurious singletons. The inflated singleton count seriously affects statistical analysis and inferences about microbial diversity. Previous statistical approaches to tackle the sequencing errors generally require different parametric assumptions about the sampling model or about the functional form of frequency counts. Different parametric assumptions may lead to drastically different diversity estimates. We focus on nonparametric methods which are universally valid for all parametric assumptions and can be used to compare diversity across communities. We develop here a nonparametric estimator of the true singleton count to replace the spurious singleton count in all methods/approaches. Our estimator of the true singleton count is in terms of the frequency counts of doubletons, tripletons and quadrupletons, provided these three frequency counts are reliable. To quantify microbial alpha diversity for an individual community, we adopt the measure of Hill numbers (effective number of taxa) under a nonparametric framework. Hill numbers, parameterized by an order q that determines the measures' emphasis on rare or common species, include taxa richness (q = 0), Shannon diversity (q = 1, the exponential of Shannon entropy), and Simpson diversity (q = 2, the inverse of Simpson index). A diversity profile which depicts the Hill number as a function of order q conveys all information contained in a taxa abundance distribution. Based on the estimated singleton count and the original non-singleton frequency counts, two statistical approaches (non-asymptotic and asymptotic) are developed to compare microbial diversity for multiple communities. (1) A non-asymptotic approach refers to the comparison of estimated diversities of standardized samples with a common finite sample size or sample completeness. This approach aims to compare diversity estimates for equally-large or equally-complete samples; it is based on the seamless rarefaction and extrapolation sampling curves of Hill numbers, specifically for q = 0, 1 and 2. (2) An asymptotic approach refers to the comparison of the estimated asymptotic diversity profiles. That is, this approach compares the estimated profiles for complete samples or samples whose size tends to be sufficiently large. It is based on statistical estimation of the true Hill number of any order q ≥ 0. In the two approaches, replacing the spurious singleton count by our estimated count, we can greatly remove the positive biases associated with diversity estimates due to spurious singletons and also make fair comparisons across microbial communities, as illustrated in our simulation results and in applying our method to analyze sequencing data from viral metagenomes.

Visualizing Patterns of Marine Eukaryotic Diversity from Metabarcoding Data Using QIIME

PCR amplification followed by deep sequencing of homologous gene regions is increasingly used to characterize the diversity and taxonomic composition of marine eukaryotic communities. This approach may generate millions of sequences for hundreds of samples simultaneously. Therefore, tools that researchers can use to visualize complex patterns of diversity for these massive datasets are essential. Efforts by microbiologists to understand the Earth and human microbiomes using high-throughput sequencing of the 16S rRNA gene has led to the development of several user-friendly, open-source software packages that can be similarly used to analyze eukaryotic datasets. Quantitative Insights Into Microbial Ecology (QIIME) offers some of the most helpful data visualization tools. Here, we describe functionalities to import OTU tables generated with any molecular marker (e.g., 18S, COI, ITS) and associated metadata into QIIME. We then present a range of analytical tools implemented within QIIME that can be used to obtain insights about patterns of alpha and beta diversity for marine eukaryotes.

C-peptide preserves the renal microvascular architecture in the streptozotocin-induced diabetic rat

AIMS

C-peptide is renoprotective in type 1 diabetes, however, the mechanisms of its actions are not completely understood. We hypothesized that C-peptide attenuates diabetes-associated renal microvascular injury.

METHOD

After 4 or 8weeks of streptozotocin (STZ)-induced diabetes, rats received either vehicle or C-peptide in the presence of low or high doses of insulin. Urine albumin excretion (UAE) was measured prior to initiation of treatment (baseline) and 2 or 4weeks after treatment (sacrifice). Glomerular hypertrophy, glomerular filtration rate (GFR) and renal microvascular density, quantified ex vivo by 3D micro-CT reconstruction, were measured at sacrifice.

RESULTS

In rats receiving low doses of insulin, treatment with C-peptide reduced HbA1c levels by 24%. In these rats, the 107% increase in UAE rate from baseline to sacrifice in vehicle-treated rats was largely prevented with C-peptide. C-peptide also reduced diabetes-associated glomerular hyperfiltration by 30%, glomerular hypertrophy by 22% and increased the density of microvessels between 0 and 500μm in diameter by an average of 31% compared with vehicle-treated groups. Similar renoprotective effects of C-peptide were observed in rats treated with higher doses of daily insulin, despite no differences in HbA1c levels.

CONCLUSIONS

The study suggests that C-peptide is renoprotective by preserving the integrity of the renal microvasculature irrespective of glucose regulation.