Unravelling the mystery of endemic versus translocated populations of the endangered Australian lungfish (Neoceratodus forsteri)

The Australian lungfish is a primitive and endangered representative of the subclass Dipnoi. The distribution of this species is limited to south-east Queensland, with some populations considered endemic and others possibly descending from translocations in the late nineteenth century shortly after European discovery. Attempts to resolve the historical distribution of this species have met with conflicting results based on descriptive genetic studies. Understanding if all populations are endemic or some are the result of, or influenced by, translocation events, has implications for conservation management. In this work, we analysed the genetic variation at three types of markers (mtDNA genomes, 11 STRs and 5196 nuclear SNPs) using the approximate Bayesian computation (ABC) algorithm to compare several demographic models. We postulated different contributions of Mary River and Burnett River gene pools into the Brisbane River and North Pine River populations, related to documented translocation events. We ran the analysis for each marker type separately, and we also estimated the posterior probabilities of the models combining the markers. Nuclear SNPs have the highest power to correctly identify the true model among the simulated datasets (where the model was known), but different marker types typically provided similar answers. The most supported demographic model able to explain the real dataset implies that an endemic gene pool is still present in the Brisbane and North Pine Rivers and coexists with the gene pools derived from past documented translocation events. These results support the view that ABC modelling can be useful to reconstruct complex historical translocation events with contemporary implications, and will inform ongoing conservation efforts for the endangered and iconic Australian lungfish.

US Army basic combat training alters the relationship between body mass index and per cent body fat

INTRODUCTION/BACKGROUND

As a proxy for adiposity, body mass index (BMI) provides a practical public health metric to counter obesity-related disease trends. On an individual basis, BMI cannot distinguish fat and lean components of body composition. Further, the relationship between BMI and body composition may be altered in response to physical training. We investigated this dynamic relationship by examining the effect of US Army basic combat training (BCT) on the association between BMI and per cent body fat (%BF).

METHODS

BMI and %BF were measured at the beginning (week 1) and end (week 9) of BCT in female (n=504) and male (n=965) trainees. Height and weight were obtained for BMI, and body composition was obtained by dual X-ray absorptiometry. Sensitivity and specificity of BMI-based classification were determined at two BMI thresholds (25 kg/m2 and 27.5 kg/m2).

RESULTS

A progressive age-related increase in fat-free mass index (FFMI) was observed, with an inflection point at age 21 years. In soldiers aged 21+, BMI of 25.0 kg/m2 predicted 33% and 29% BF in women and 23% and 20% BF in men and BMI of 27.5 kg/m2 predicted 35% and 31% BF in women and 26% and 22% BF in men, at the start and end of BCT, respectively. Sensitivity and specificity of BMI-based classification of %BF were poor. Soldiers below BMI of 20 kg/m2 had normal instead of markedly reduced %BF, reflecting especially low FFMI.

CONCLUSIONS

BCT alters the BMI-%BF relationship, with lower %BF at a given BMI by the end of BCT compared with the beginning, highlighting the unreliability of BMI to try to estimate body composition. The specific BMI threshold of 25.0 kg/m2, defined as 'overweight', is an out-of-date metric for health and performance outcomes. To the extent that %BF reflects physical readiness, these data provide evidence of a fit and capable military force at BMI greater than 25.0 kg/m2.

Genetic structure of Australian glass shrimp, Paratya australiensis, in relation to altitude

Paratya australiensis Kemp (Decapoda: Atyidae) is a widely distributed freshwater shrimp in eastern Australia. The species has been considered as an important stream organism for studying genetics, dispersal, biology, behaviour and evolution in atyids and is a major food source for stream dwelling fishes. Paratya australiensis is a cryptic species complex consisting of nine highly divergent mitochondrial DNA lineages. Previous studies in southeast Queensland showed that “lineage 4” favours upstream sites at higher altitudes, with cooler water temperatures. This study aims to identify putative selection and population structure between high elevation and low elevation populations of this lineage at relatively small spatial scales. Sample localities were selected from three streams: Booloumba Creek, Broken Bridge Creek and Obi Obi Creek in the Conondale Range, southeast Queensland. Six sample localities, consisting of 142 individuals in total were sequenced using double digest Restriction Site Associated DNA-sequencing (ddRAD-seq) technique. Among the 142 individuals, 131 individuals shared 213 loci. Outlier analysis on 213 loci showed that 27 loci were putatively under selection between high elevation and low elevation populations. Outlier analysis on individual streams was also done to test for parallel patterns of adaptation, but there was no evidence of a parallel pattern. Population structure was observed using both the 27 outliers and 186 neutral loci and revealed similar population structure in both cases. Therefore, we cannot differentiate between selection and drift here. The highest genetic differentiation was observed between high elevation and low elevation populations of Booloumba Creek, with small levels of differentiation in the other two streams.

Genome-Wide SNPs Identify Limits to Connectivity in the Extreme Freshwater Disperser, Spangled Perch Leiopotherapon unicolor (Terapontidae)

The utility of restriction-site associated DNA sequencing (RADseq) to resolve fine-scale population structure was tested on an abundant and vagile fish species in a tropical river. Australia's most widespread freshwater fish, the "extreme disperser" Leiopotherapon unicolor was sampled from 6 locations in an unregulated system, the Daly River in Australia's Northern Territory. Despite an expectation of high connectivity based on life history knowledge of this species derived from arid zone habitats, L. unicolor was not a panmictic population in the tropical lower Daly. Using ~14000 polymorphic RADseq loci, we found a pattern of upstream versus downstream population subdivision and evidence for differentiation among tributary populations. The magnitude of population structure was low with narrow confidence intervals (global FST = 0.014; 95% CI = 0.012-0.016). Confidence intervals around pairwise FST estimates were all nonzero and consistent with the results of clustering analyses. This population structure was not explained by spatially heterogeneous selection acting on a subset of loci, or by sampling groups of closely related individuals (average within-site relatedness ≈ 0). One implication of the low but significant structure observed in the tropics is the possibility that L. unicolor may exhibit contrasting patterns of migratory biology in tropical versus arid zone habitats. We conclude that the RADseq revolution holds promise for delineating subtle patterns of population subdivision in species characterized by high within-population variation and low among-population differentiation.

Trabecular microstructure is influenced by race and sex in Black and White young adults

Lower fracture rates in Black men and women compared to their White counterparts are incompletely understood. High-resolution imaging specific to trabecular bone may provide insight. Black participants have enhanced trabecular morphology. These differences may contribute to the lower fracture risk in Black versus White individuals.

INTRODUCTION

Lower fracture rates in Black men and women compared to their White counterparts may be explained by favorable bone microstructure in Black individuals. Individual trabecular segmentation (ITS) analysis, which characterizes the alignment and plate- and rod-like nature of trabecular bone using high-resolution peripheral quantitative computed tomography (HR-pQCT), may provide insight into trabecular differences by race/ethnic origin.

PURPOSE

We determined differences in trabecular bone microarchitecture, connectivity, and alignment according to race/ethnic origin and sex in young adults.

METHODS

We analyzed HR-pQCT scans of 184 adult (24.2 ± 3.4 years) women (n = 51 Black, n = 50 White) and men (n = 34 Black, n = 49 White). We used ANCOVA to compare bone outcomes, and adjusted for age, height, and weight.

RESULTS

Overall, the effect of race on bone outcomes did not differ by sex, and the effect of sex on bone outcomes did not differ by race. After adjusting for covariates, Black participants and men of both races had greater trabecular plate volume fraction, plate thickness, plate number density, plate surface area, and greater axial alignment of trabeculae, leading to higher trabecular bone stiffness compared to White participants and women, respectively (p < 0.05 for all).

CONCLUSION

These findings demonstrate that more favorable bone microarchitecture in Black individuals compared to White individuals and in men compared to women is not unique to the cortical bone compartment. Enhanced plate-like morphology and greater trabecular axial alignment, established in young adulthood, may contribute to the improved bone strength and lower fracture risk in Black versus White individuals and in men compared to women.

Systematics of the palisade trapdoor spiders (Euoplos) of south-eastern Queensland (Araneae : Mygalomorphae : Idiopidae): four new species distinguished by their burrow entrance architecture

Within the spiny trapdoor spider genus Euoplos Rainbow exists a group of species from south-eastern Queensland that create unusual ‘palisade’ burrow entrances. Despite their intriguing burrows, the group was only recently circumscribed, and all species within it were undescribed. In this study, by undertaking a molecular phylogenetic analysis of two mitochondrial markers and seven nuclear markers, we confirm that the palisade trapdoor spiders, here formally named the ‘turrificus-group’, are monophyletic. We further recognise four species based on morphological, molecular and behavioural characters: E. crenatus, sp. nov., E. goomboorian, sp. nov., E. thynnearum, sp. nov. and E. turrificus, sp. nov. Morphological taxonomic data for each species are presented alongside information on their distribution, habitat preferences and burrow architecture. A key to species within the turrificus-group is also provided. The unusual burrow entrances of these spiders, which project out from the surrounding substrate, are found to exhibit structural autapomorphies, which allow species-level identification. Consequently, we include features of burrow architecture in our key and species diagnoses. This provides a non-intrusive method for distinguishing species in the field. Finally, we conclude that all species within the turrificus-group are likely to represent short-range endemic taxa. http://zoobank.org/urn:lsid:zoobank.org:pub:F2E042DC-DA14-4751-A48B-A367ABC272D9

Size, shape, and identity of surface crystals and their relationship to sensory perception of grittiness in soft smear-ripened cheeses

Soft smear-ripened cheeses undergo extensive surface crystallization and radial demineralization of calcium, magnesium, and phosphorus, which likely contributes to radial softening during ripening. Furthermore, anecdotal evidence suggests that grittiness is a common characteristic of smear-ripened cheeses. The primary aims of the present study were to evaluate the intensity of perceived grittiness while assessing other key sensory attributes in US artisanal and European protected designation of origin smear-ripened cheeses, and to relate perceived grittiness to the size, shape, and identity of crystals present in the cheese surface smears. Fully ripened wheels of 24 different varieties of smear-ripened cheeses, 16 produced in the United States and 8 in the European Union, were obtained from retail sources. A trained sensory panel (n = 12) was employed to evaluate intensity of grittiness. Crystals present in the cheese smears were identified by powder X-ray diffractometry and polarized light microscopy, and further evaluated in polarized light microscopy micrographs by image analysis for size and shape characteristics. Mean sensory scores for the 24 cheeses ranged from no perceived grittiness to easily identifiable grittiness. Surface crystals included ikaite, struvite, calcite, and brushite, and mean crystal length and area ranged among cheeses from 27 to 1,096 μm, and 533 to 213,969 μm², respectively. Panel threshold for grittiness occurred at a mean crystal length of about 66 μm and mean crystal area of about 2,913 μm². Cheeses with mean values at or below these thresholds displayed negligible perceived grittiness. In contrast, for cheeses with mean values above these thresholds, the mean sensory scores for grittiness were highly correlated with mean crystal length and crystal area (r = 0.93 and 0.96, respectively). Results suggest that surface crystals in soft smear-ripened cheeses influence sensory perception of texture in complex ways that likely include radial softening and grittiness development. A better understanding of factors that govern surface crystal formation may lead to improved control over crystallization and more consistent cheese texture.

Monitoring age-related trends in genomic diversity of Australian lungfish

An important challenge for conservation science is to detect declines in intraspecific diversity so that management action can be guided towards populations or species at risk. The lifespan of Australian lungfish (Neoceratodus forsteri) exceeds 80 years, and human impacts on breeding habitat over the last half century may have impeded recruitment, leaving populations dominated by old postreproductive individuals, potentially resulting in a small and declining breeding population. Here, we conduct a "single-sample" evaluation of genetic erosion within contemporary populations of the Australian lungfish. Genetic erosion is a temporal decline in intraspecific diversity due to factors such as reduced population size and inbreeding. We examined whether young individuals showed signs of reduced genetic diversity and/or inbreeding using a novel bomb radiocarbon dating method to age lungfish nonlethally, based on 14 C ratios of scales. A total of 15,201 single nucleotide polymorphic (SNP) loci were genotyped in 92 individuals ranging in age from 2 to 77 years old. Standardized individual heterozygosity and individual inbreeding coefficients varied widely within and between riverine populations, but neither was associated with age, so perceived problems with recruitment have not translated into genetic erosion that could be considered a proximate threat to lungfish populations. Conservation concern has surrounded Australian lungfish for over a century. However, our results suggest that long-lived threatened species can maintain stable levels of intraspecific variability when sufficient reproductive opportunities exist over the course of a long lifespan.

Characterization and identification of surface crystals on smear-ripened cheese by polarized light microscopy

Surface crystallization and radial demineralization of Ca, P, and Mg occur in smear-ripened cheese. Furthermore, crystals of ikaite, struvite, calcite, and brushite have been identified in cheese smears by powder X-ray diffractometry (PXRD), and ikaite and struvite exist in smears as single crystals. Polarized light microscopy (PLM) is a simple, inexpensive, and well-established method in geology to detect and identify single crystals. However, use of PLM to identify cheese crystals has not been reported previously. The specific objectives of this research were (1) to identify crystals in cheese smears using selected PLM criteria; (2) to compare identification by PLM against PXRD; and (3) to develop and evaluate a novel treatment for smear material to improve crystal analyses by both PLM and PXRD. Duplicate wheels of 4 cheeses produced by different manufacturers were obtained from retail sources. Scrapings of surface smears were prepared and analyzed by PLM and PXRD by previously described methods. Crystals were categorized by PLM based on angle of extinction (AE), birefringence behavior under crossed polarizers and quartz filters, and size and shape (circularity) by image analysis. Crystals observed by PLM fell almost exclusively into 2 readily differentiated groups based on birefringence behavior and estimated angle of extinction. Group 1 (n = 18) were highly birefringent with AE = 88-92°, whereas group 2 (n = 28) had no birefringence with AE = 13-26°. Group 2 crystals were significantly larger and more circular than group 1 crystals. Group 1 and 2 were identified as struvite and ikaite, respectively, based on known birefringence and AE characteristics. Struvite was identified in all 4 cheeses by PLM but in only 3 cheeses by PXRD. Ikaite was identified in 3 cheeses by PLM but in only 2 cheeses by PXRD. These discrepancies occurred because the smear scrapings from 1 cheese contained excessive amorphous matter that caused extreme background noise, potentially obscuring diffractogram peaks that may have been present. To minimize noise, smear scrapings were dispersed in aqueous NaOH (pH 10) before analyses, which resulted in consistent results by PXRD and PLM. The method also rendered high-quality images by PLM. Data suggest that PLM may offer a simple and inexpensive means to identify struvite, ikaite, and possibly other single crystals in cheese smears.

Patterns of genetic structuring at the northern limits of the Australian smelt (Retropinna semoni) cryptic species complex

Freshwater fishes often exhibit high genetic population structure due to the prevalence of dispersal barriers (e.g., waterfalls) whereas population structure in diadromous fishes tends to be weaker and driven by natal homing behaviour and/or isolation by distance. The Australian smelt (Retropinnidae: Retropinna semoni) is a native fish with a broad distribution spanning inland and coastal drainages of south-eastern Australia. Previous studies have demonstrated variability in population genetic structure and movement behaviour (potamodromy, facultative diadromy, estuarine residence) across the southern part of its geographic range. Some of this variability may be explained by the existence of multiple cryptic species. Here, we examined genetic structure of populations towards the northern extent of the species’ distribution, using ten microsatellite loci and sequences of the mitochondrial cyt b gene. We tested the hypothesis that genetic connectivity among rivers should be low due to a lack of dispersal via the marine environment, but high within rivers due to dispersal. We investigated populations corresponding with two putative cryptic species, SEQ-North (SEQ-N), and SEQ-South (SEQ-S) lineages occurring in south east Queensland drainages. These two groups formed monophyletic clades in the mtDNA gene tree and among river phylogeographic structure was also evident within each clade. In agreement with our hypothesis, highly significant overall F_ST values suggested that both groups exhibit very low dispersal among rivers (SEQ-S F_ST = 0.13; SEQ-N F_ST= 0.27). Microsatellite data indicated that connectivity among sites within rivers was also limited, suggesting dispersal may not homogenise populations at the within-river scale. Northern groups in the Australian smelt cryptic species complex exhibit comparatively higher among-river population structure and smaller geographic ranges than southern groups. These properties make northern Australian smelt populations potentially susceptible to future conservation threats, and we define eight genetically distinct management units along south east Queensland to guide future conservation management. The present findings at least can assist managers to plan for effective conservation and management of different fish species along coastal drainages of south east Queensland, Australia.

Spiny trapdoor spiders (Euoplos) of eastern Australia: Broadly sympatric clades are differentiated by burrow architecture and male morphology

Spiders of the infraorder Mygalomorphae are fast becoming model organisms for the study of biogeography and speciation. However, these spiders can be difficult to study in the absence of fundamental life history information. In particular, their cryptic nature hinders comprehensive sampling, and linking males with conspecific females can be challenging. Recently discovered differences in burrow entrance architecture and male morphology indicated that these challenges may have impeded our understanding of the trapdoor spider genus Euoplos in Australia's eastern mesic zone. We investigated the evolutionary significance of these discoveries using a multi-locus phylogenetic approach. Our results revealed the existence of a second, previously undocumented, lineage of Euoplos in the eastern mesic zone. This new lineage occurs in sympatry with a lineage previously known from the region, and the two are consistently divergent in their burrow entrance architecture and male morphology, revealing the suitability of these characters for use in phylogenetic studies. Divergent burrow entrance architecture and observed differences in microhabitat preferences are suggested to facilitate sympatry and syntopy between the lineages. Finally, by investigating male morphology and plotting it onto the phylogeny, we revealed that the majority of Euoplos species remain undescribed, and that males of an unnamed species from the newly discovered lineage had historically been linked, erroneously, to a described species from the opposite lineage. This paper clarifies the evolutionary relationships underlying life history diversity in the Euoplos of eastern Australia, and provides a foundation for urgently needed taxonomic revision of this genus.

A novel genus and cryptic species harboured within the monotypic freshwater crayfish genus Tenuibranchiurus Riek, 1951 (Decapoda: Parastacidae)

Identifying species groups is an important yet difficult task, with there being no single accepted definition as to what constitutes a species, nor a set of criteria by which they should be delineated. Employing the General Lineage Concept somewhat circumvents these issues, as this concept allows multiple concordant lines of evidence to be used as support for species delimitation, where a species is defined as any independently evolving lineage. Genetically diverse groups have previously been identified within the monotypic parastacid genus Tenuibranchiurus Riek, 1951, but no further investigation of this diversity has previously been undertaken. Analysis of two mitochondrial DNA gene regions has previously identified two highly divergent groups within this taxon, representing populations from Queensland (Qld) and New South Wales (NSW), respectively. Additional testing within this study of both mitochondrial and nuclear DNA through species discovery analyses identified genetically diverse groups within these regions, which were further supported by lineage validation methods. The degree of genetic differentiation between Qld and NSW populations supports the recognition of two genera; with Qld retaining the original genus name Tenuibranchiurus, and NSW designated as Gen. nov. until a formal description is completed. Concordance between the species discovery and lineage validation methods supports the presence of six species within Tenuibranchiurus and two within Gen. nov. The recognition of additional species removes the monotypy of the genus, and the methods used can improve species identification within groups of organisms with taxonomic problems and cryptic diversity.

Temporal Changes Rather than Long-Term Repeated Burning Predominately Control the Shift in the Abundance of Soil Denitrifying Community in an Australian Sclerophyll Forest

To understand the temporal dynamics of soil bacterial denitrifying community in response to long-term prescribed burning and its resilience and recovery following a fire, a wet sclerophyll forest study site under two treatments (2 yearly burning (2YB) and no burning (NB)) and with 40-year-old burning history was used. Similar temporal patterns in the abundance of total (16S rRNA) and denitrifying (narG, nirK, nirS, nosZ) bacteria between two burning treatments revealed strong temporal influences. The magnitude of burning impacts on the abundance of 16S rRNA and denitrification genes was smaller compared with the impact of sampling time, but significant burning and temporal impacts were recorded for all (P < 0.001)-except for the nirS gene. Impacts of prescribed fire on the abundance of soil denitrifying community could be observed immediately after fire, and this impact diminished over a 24-month period prior to the next prescribed burning event. In conclusion, temporal changes govern the fluctuations of the abundance of soil denitrifying genes over the sampling period and the denitrifying community can recover after fire, suggesting that this community is resilient to the effects of prescribed burning. A combination of biotic and abiotic factors may account for the different temporal dynamics of denitrification gene abundance.

Complete mitogenomes for two lineages of the Australian smelt, Retropinna semoni (Osmeriformes: Retropinnidae)

Complete mitochondrial genome sequences were determined for two lineages (“CEQ” and “SEQ”) of the Australian smelt, Retropinna semoni. Both mitogenomes contain the typical vertebrate arrangement of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and control region. A conventional start codon for ND2 was not present in either lineage; instead CTG (Leucine) was present at this position. These sequences will be a useful resource for evolutionary studies of a significant species complex in the Australian freshwater fish fauna.

Diversity and phylogeny of south-east Queensland Bathynellacea

The crustacean order Bathynellacea is amongst the most diverse and widespread groups of subterranean aquatic fauna (stygofauna) in Australia. Interest in the diversity and biogeography of Australian Bathynellacea has grown markedly in recent years. However, relatively little information relating to this group has emerged from Queensland. The aim of this study was to investigate bathynellacean diversity and phylogeny in south-east Queensland. Relationships between the south-east Queensland fauna and their continental relatives were evaluated through the analysis of combined mitochondrial and nuclear DNA sequence data. Bathynellaceans were collected from alluvial groundwater systems in three catchments in south-east Queensland. This study revealed a diverse bathynellacean fauna with complex evolutionary relationships to related fauna elsewhere in Queensland, and on the wider Australian continent. The multifamily assemblage revealed here is likely to represent several new species, and at least one new genus within the Parabathynellidae. These taxa likely have relatively restricted geographic distributions. Interestingly, the south-east Queensland Bathynellacea appeared to be distantly related to their north-east Queensland counterparts. Although it was not possible to determine the generic identities of their closest relatives, the south-east Queensland Parabathynellidae appear to be most closely affiliated with southern and eastern Australian lineages. Together with previous survey data, the findings here suggest that there is likely to be considerable bathynellacean diversity in alluvial groundwater systems across the wider Queensland region. Further assessment of stygofauna distributions in south-east Queensland is necessary to understand the biological implications of significant groundwater use and development in the region.

Complete mitochondrial genome of the endangered Mary River turtle (Elusor macrurus) and low mtDNA variation across the species' range

Elusor macrurus is an endangered short-necked turtle restricted to the Mary River catchment in south-eastern Queensland. Shotgun sequencing of genomic DNA was used to generate a complete mitochondrial genome sequence for E. macrurus using the Illumina MiSeq platform. The mitogenome is 16 499 base pairs (bp) long with 37 genes arranged in the typical vertebrate order and a relatively short 918-bp control region, which does not feature extensive tandem repeats as observed in some turtles. Primers were designed to amplify a 1270-bp region that includes 81% of the typically hypervariable control region. Two haplotypes were detected in a sample of 22 wild-caught individuals from eight sites across its natural range. The Mary River turtle is a species with low mtDNA nucleotide variability relative to other Chelidae. The combination of a very restricted distribution and dramatic reduction in population size due to exploitation for the pet trade are the conditions likely to have led to very low mtDNA variability in this endangered species.

Human effects on ecological connectivity in aquatic ecosystems: Integrating scientific approaches to support management and mitigation

Understanding the drivers and implications of anthropogenic disturbance of ecological connectivity is a key concern for the conservation of biodiversity and ecosystem processes. Here, we review human activities that affect the movements and dispersal of aquatic organisms, including damming of rivers, river regulation, habitat loss and alteration, human-assisted dispersal of organisms and climate change. Using a series of case studies, we show that the insight needed to understand the nature and implications of connectivity, and to underpin conservation and management, is best achieved via data synthesis from multiple analytical approaches. We identify four key knowledge requirements for progressing our understanding of the effects of anthropogenic impacts on ecological connectivity: autecology; population structure; movement characteristics; and environmental tolerance/phenotypic plasticity. Structuring empirical research around these four broad data requirements, and using this information to parameterise appropriate models and develop management approaches, will allow for mitigation of the effects of anthropogenic disturbance on ecological connectivity in aquatic ecosystems.

Vertical Distribution of Soil Denitrifying Communities in a Wet Sclerophyll Forest under Long-Term Repeated Burning

Soil biogeochemical cycles are largely mediated by microorganisms, while fire significantly modifies biogeochemical cycles mainly via altering microbial community and substrate availability. Majority of studies on fire effects have focused on the surface soil; therefore, our understanding of the vertical distribution of microbial communities and the impacts of fire on nitrogen (N) dynamics in the soil profile is limited. Here, we examined the changes of soil denitrification capacity (DNC) and denitrifying communities with depth under different burning regimes, and their interaction with environmental gradients along the soil profile. Results showed that soil depth had a more pronounced impact than the burning treatment on the bacterial community size. The abundance of 16S rRNA and denitrification genes (narG, nirK, and nirS) declined exponentially with soil depth. Surprisingly, the nosZ-harboring denitrifiers were enriched in the deeper soil layers, which was likely to indicate that the nosZ-harboring denitrifiers could better adapt to the stress conditions (i.e., oxygen deficiency, nutrient limitation, etc.) than other denitrifiers. Soil nutrients, including dissolved organic carbon (DOC), total soluble N (TSN), ammonium (NH(4)(+)), and nitrate (NO(3)(-)), declined significantly with soil depth, which probably contributed to the vertical distribution of denitrifying communities. Soil DNC decreased significantly with soil depth, which was negligible in the depths below 20 cm. These findings have provided new insights into niche separation of the N-cycling functional guilds along the soil profile, under a varied fire disturbance regime.

Crystal fingerprinting: elucidating the crystals of Cheddar, Parmigiano-Reggiano, Gouda, and soft washed-rind cheeses using powder x-ray diffractometry

Crystals in cheese may be considered defects or positive features, depending on the variety and mode of production (industrial, artisanal). Powder x-ray diffractometry (PXRD) offers a simple means to identify and resolve complex combinations of crystals that contribute to cheese characteristics. The objective of the present research was to demonstrate the application of PXRD to study crystals from a range of different cheese types, specifically Cheddar, Parmigiano-Reggiano, Gouda, and soft washed-rind (smear ripened) cheeses. In studies of Parmigiano-Reggiano and long-aged Gouda, PXRD has confirmed that hard (crunchy) crystals that form abundantly within these cheeses consist of tyrosine. Furthermore, PXRD has tentatively identified the presence of an unusual form of crystalline leucine in large (up to 6 mm in diameter) spherical entities, or “pearls”, that occur abundantly in 2-year-old Parmigiano Reggiano and long-aged Gouda cheeses, and on the surface of rindless hard Italian-type cheese. Ongoing investigations into the nature of these “pearls” are providing new insight into the roles that crystals play in the visual appearance and texture of long-aged cheeses. Crystals also sometimes develop profusely in the eyes of long-aged Gouda, which have been shown by PXRD to consist of tyrosine and the aforementioned presumptive form of crystalline leucine. Finally, crystals have been shown by PXRD to form in the smears of soft washed-rind cheeses. These crystals may be associated in some cheeses with gritty mouth feel and with zonal body softening that occurs during ripening. Heightened interest in artisanal cheeses highlights the need to better understand crystals and their contributions to cheese characteristics.

Phylogeography and limited distribution of the endangered freshwater crayfish, Euastacus urospinosus

Conservation plans can benefit from understanding patterns of genetic structure because many endangered species are spatially fragmented. In particular, headwater species in high elevations are expected to exhibit a high level of population structure, as dispersal through lowland streams may be limited. Euastacus urospinosus is an endangered freshwater crayfish that, until recently, was thought to have a distribution of just 200 km2. In the current study, we identified a total of 26 locations for this species across a 1225 km2 region spanning the Brisbane and Mary River catchments of south-east Queensland, Australia. We then used mitochondrial DNA sequence data to investigate the population structure and the phylogeographic divergence between four uplands. We found significant population differentiation for this species, which conforms to the headwater model of genetic structure. Further, we found that fragmentation between these uplands is most likely historical, as the first divergence between lineages dated back 2.1 million years. Overall, we found no reason to remove the conservation rating of ‘endangered’ for this species. Conservation plans should seek to preserve the genetic integrity of these uplands by considering them to be genetically distinct and isolated populations.

CXCL1 is a negative regulator of mast cell chemotaxis to airway smooth muscle cell products in vitro

BACKGROUND

Activated mast cells (MC) numbers on airway smooth muscle (ASM) are increased in eosinophilic asthma. In vitro, asthmatic cytokine-stimulated ASM cell-conditioned medium (CM) induces more MC chemotaxis than CM from nonasthmatic ASM cells. Intriguingly the nonasthmatic ASM CM inhibits MC chemotaxis to the asthmatic ASM CM. However, the inhibitory factor(s) in the nonasthmatic ASM CM is still to be identified.

OBJECTIVE

To identify the factor(s) released by nonasthmatic ASM cells that inhibits MC chemotaxis.

METHODS

Confluent, serum-starved ASM cells from donors with and without asthma were stimulated with IL-1β and T-helper (Th)1 (TNFα and IFNγ) or Th2 (IL-4, IL-13) cytokines, or left unstimulated. CM samples were collected after 24 h, and a potential inhibitory factor identified using cytokine protein arrays. Its production was assessed using ELISA and RT-PCR and inhibitory role investigated in MC chemotaxis and Ca(2+) mobilization assays.

RESULTS

Only CXCL1 was produced in greater amounts by nonasthmatic than asthmatic ASM cells following Th1 and Th2 cytokine stimulation. CXCL1 mRNA expression was also increased. Exogenous rh-CXCL1 significantly inhibited MC intracellular Ca(2+) mobilization and chemotaxis to either CXCL10, CXCL8 or CM collected from asthmatic ASM cells following Th1 or Th2 cytokine stimulation. Neutralizing CXCL1 in nonasthmatic ASM CM or blocking its receptor significantly promoted MC chemotaxis.

CONCLUSIONS

CXCL1 was a major factor regulating MC chemotaxis in vitro. Its differential release by ASM cells may explain the differences observed in MC localization to the ASM of people with and without asthma.

CLINICAL RELEVANCE

CXCL1 inhibition of MC recruitment to the ASM may lead to new targets to limit asthma pathophysiology.

Shared phylogeographic patterns between the ectocommensal flatworm Temnosewellia albata and its host, the endangered freshwater crayfish Euastacus robertsi

Comparative phylogeography of commensal species may show congruent patterns where the species involved share a common history. Temnosewellia is a genus of flatworms, members of which live in commensal relationships with host freshwater crustaceans. By constructing phylogenetic trees based on mitochondrial COI and 28S nuclear ribosomal gene sequences, this study investigated how evolutionary history has shaped patterns of intraspecific molecular variation in two such freshwater commensals. This study concentrates on the flatworm Temnosewellia albata and its critically endangered crayfish host Euastacus robertsi, which have a narrow climatically-restricted distribution on three mountaintops. The genetic data expands upon previous studies of Euastacus that suggested several vicariance events have led to the population subdivision of Euastacus robertsi. Further, our study compared historical phylogeographic patterning of these species. Our results showed that phylogeographic patterns shared among these commensals were largely congruent, featuring a shared history of limited dispersal between the mountaintops. Several hypotheses were proposed to explain the phylogeographic points of differences between the species. This study contributes significantly to understanding evolutionary relationships of commensal freshwater taxa.

A structural approach to understanding the interactions between colour, water-holding capacity and tenderness

The colour, water-holding capacity (WHC) and tenderness of meat are primary determinants of visual and sensory appeal. Although there are many factors which influence these quality traits, the end-results of their influence is often through key changes to the structure of muscle proteins and their spatial arrangement. Water acts as a plasticiser of muscle proteins and water is lost from the myofibrillar lattice structure as a result of protein denaturation and consequent reductions in the muscle fibre volume with increasing cooking temperature. Changes in the myofilament lattice arrangement also impact the light scattering properties and the perceived paleness of the meat. Causes of variation in the quality traits of raw meat do not generally correspond to variations in cooked meat and the differences observed between the raw muscle and cooked or further processed meat are discussed. The review will also identify the gaps in our knowledge and where further investigation would beneficial.

Genetic structuring of remnant forest patches in an endangered medicinal tree in North-western Ethiopia

Background

Habitat loss and fragmentation may have detrimental impacts on genetic diversity, population structure and overall viability of tropical trees. The response of tropical trees to fragmentation processes may, however, be species, cohort or region-specific. Here we test the hypothesis that forest fragmentation is associated with lower genetic variability and higher genetic differentiation in adult and seedling populations of Prunus africana in North-western Ethiopia. This is a floristically impoverished region where all but a few remnant forest patches have been destroyed, mostly by anthropogenic means.

Results

Genetic diversity (based on allelic richness) was significantly greater in large and less-isolated forest patches as well as in adults than seedlings. Nearly all pairwise F_ST comparisons showed evidence for significant population genetic differentiation. Mean F_ST values were significantly greater in seedlings than adults, even after correction for within population diversity, but varied little with patch size or isolation.

Conclusions

Analysis of long-lived adult trees suggests the formerly contiguous forest in North-western Ethiopia probably exhibited strong spatial patterns of genetic structure. This means that protecting a range of patches including small and isolated ones is needed to conserve the extant genetic resources of the valuable forests in this region. However, given the high livelihood dependence of the local community and the high impact of foreign investors on forest resources of this region, in situ conservation efforts alone may not be helpful. Therefore, these efforts should be supported with ex situ gene conservation actions.

Low interbasin connectivity in a facultatively diadromous fish: evidence from genetics and otolith chemistry

Southern smelts (Retropinna spp.) in coastal rivers of Australia are facultatively diadromous, with populations potentially containing individuals with diadromous or wholly freshwater life histories. The presence of diadromous individuals is expected to reduce genetic structuring between river basins due to larval dispersal via the sea. We use otolith chemistry to distinguish between diadromous and nondiadromous life histories and population genetics to examine interbasin connectivity resulting from diadromy. Otolith strontium isotope ((87) Sr:(86) Sr) transects identified three main life history patterns: amphidromy, freshwater residency and estuarine/marine residency. Despite the potential for interbasin connectivity via larval mixing in the marine environment, we found unprecedented levels of genetic structure for an amphidromous species. Strong hierarchical structure along putative taxonomic boundaries was detected, along with highly structured populations within groups using microsatellites (FST  = 0.046-0.181), and mtDNA (ΦST  = 0.498-0.816). The presence of strong genetic subdivision, despite the fact that many individuals reside in saline water during their early life history, appears incongruous. However, analysis of multielemental signatures in the otolith cores of diadromous fish revealed strong discrimination between river basins, suggesting that diadromous fish spend their early lives within chemically distinct estuaries rather than the more homogenous marine environment, thus avoiding dispersal and maintaining genetic structure.

The O-linked glycans of human von Willebrand factor modulate its interaction with ADAMTS-13

BACKGROUND

O-linked glycans (OLGs) are clustered on either side of the von Willebrand factor (VWF) A1 domain and modulate its interaction with platelets; however, their influence on the VWF interaction with ADAMTS-13 is unknown.

OBJECTIVES

To assess the role of the OLGs in VWF susceptibility to ADAMTS-13 proteolysis, which would help to explain their specific distribution.

METHODS

OLG sites were mutated individually and as clusters on either and both sides of the A1 domain, and expressed in HEK293T cells. First, their proteolysis by ADAMTS-13 was assayed in the presence of urea. Next, a parallel-flow chamber was used to analyze VWF-mediated platelet capture on collagen in the presence and absence of ADAMTS-13 under a shear stress of 1500 s(-1) . The decrease in platelet capture in the presence ADAMTS-13 was used as a measure of VWF proteolysis.

RESULTS

Initially, we found that, under denaturing conditions, the C-terminal S1486A and Cluster 2 and double cluster (DC) variants were less susceptible to ADAMTS-13 proteolysis than wild-type VWF. Next, we showed that addition of ADAMTS-13 diminished VWF-mediated platelet capture on collagen under flow; surprisingly, this was more pronounced with the S1486A, Cluster 2 and DC variants than with wild-type VWF, indicating that these are proteolyzed more rapidly under shear flow.

CONCLUSIONS

OLGs provide rigidity to peptide backbones, and our findings suggest that OLG in the A1-A2 linker region regulates VWF conformational changes under shear. Importantly, the impact of OLGs on ADAMTS-13 cleavage under shear stress is the opposite of that under denaturing conditions, highlighting the non-physiologic nature of in vitro cleavage assays.

Ecological drivers of biogeographic patterns of soil archaeal community

Knowledge about the biogeography of organisms has long been a focus in ecological research, including the mechanisms that generate and maintain diversity. In this study, we targeted a microbial group relatively underrepresented in the microbial biogeographic literature, the soil Archaea. We surveyed the archaeal abundance and community composition using real-time quantitative PCR and T-RFLP approaches for 105 soil samples from 2 habitat types to identify the archaeal distribution patterns and factors driving these patterns. Results showed that the soil archaeal community was affected by spatial and environmental variables, and 79% and 51% of the community variation was explained in the non-flooded soil (NS) and flooded soil (FS) habitat, respectively, showing its possible biogeographic distribution. The diversity patterns of soil Archaea across the landscape were influenced by a combination of stochastic and deterministic processes. The contribution from neutral processes was higher than that from deterministic processes associated with environmental variables. The variables pH, sample depth and longitude played key roles in determining the archaeal distribution in the NS habitat, while sampling depth, longitude and NH4 (+)-N were most important in the FS habitat. Overall, there might be similar ecological drivers in the soil archaeal community as in macroorganism communities.

Airway smooth muscle CXCR3 ligand production: regulation by JAK-STAT1 and intracellular Ca²⁺

In asthma, airway smooth muscle (ASM) chemokine (C-X-C motif) receptor 3 (CXCR3) ligand production may attract mast cells or T lymphocytes to the ASM, where they can modulate ASM functions. In ASM cells (ASMCs) from people with or without asthma, we aimed to investigate JAK-STAT1, JNK, and Ca²⁺ involvement in chemokine (C-X-C motif) ligand (CXCL)10 and CXCL11 production stimulated by interferon-γ, IL-1β, and TNF-α combined (cytomix). Confluent, growth-arrested ASMC were treated with inhibitors for pan-JAK (pyridone-6), JAK2 (AG-490), JNK (SP-600125), or the sarco(endo)plasmic reticulum Ca²⁺ATPase (SERCA) pump (thapsigargin), Ca²⁺ chelator (BAPTA-AM), or vehicle before and during cytomix stimulation for up to 24 h. Signaling protein activation as well as CXCL10/CXCL11 mRNA and protein production were examined using immunoblot analysis, real-time PCR, and ELISA, respectively. Cytomix-induced STAT1 activation was lower and CXCR3 ligand mRNA production was more sensitive to pyridone-6 and AG-490 in asthmatic than nonasthmatic ASMCs, but CXCL10/CXCL11 release was inhibited by the same proportion. Neither agent caused additional inhibition of release when used in combination with the JNK inhibitor SP-600125. Conversely, p65 NF-κB activation was higher in asthmatic than nonasthmatic ASMCs. BAPTA-AM abolished early CXCL10/CXCL11 mRNA production, whereas thapsigargin reduced it in asthmatic cells and inhibited CXCL10/CXCL11 release by both ASMC types. Despite these inhibitory effects, neither Ca²⁺ agent affected early activation of STAT1, JNK, or p65 NF-κB. In conclusion, intracellular Ca²⁺ regulated CXCL10/CXCL11 production but not early activation of the signaling molecules involved. In asthma, reduced ASM STAT1-JNK activation, increased NF-κB activation, and altered Ca²⁺ handling may contribute to rapid CXCR3 ligand production and enhanced inflammatory cell recruitment.

Development of a scalable image formation pipeline for multiscale gigapixel photography

We report on the image formation pipeline developed to efficiently form gigapixel-scale imagery generated by the AWARE-2 multiscale camera. The AWARE-2 camera consists of 98 "microcameras" imaging through a shared spherical objective, covering a 120° x 50° field of view with approximately 40 microradian instantaneous field of view (the angular extent of a pixel). The pipeline is scalable, capable of producing imagery ranging in scope from "live" one megapixel views to full resolution gigapixel images. Architectural choices that enable trivially parallelizable algorithms for rapid image formation and on-the-fly microcamera alignment compensation are discussed.