More than skin and bones: Comparing extraction methods and alternative sources of DNA from avian museum specimens

Next‐generation sequencing has greatly expanded the utility and value of museum collections by revealing specimens as genomic resources. As the field of museum genomics grows, so does the need for extraction methods that maximize DNA yields. For avian museum specimens, the established method of extracting DNA from toe pads works well for most specimens. However, for some specimens, especially those of birds that are very small or very large, toe pads can be a poor source of DNA. In this study, we apply two DNA extraction methods (phenol–chloroform and silica column) to three different sources of DNA (toe pad, skin punch and bone) from 10 historical avian museum specimens. We show that a modified phenol–chloroform protocol yielded significantly more DNA than a silica column protocol (e.g., Qiagen DNeasy Blood & Tissue Kit) across all tissue types. However, extractions using the silica column protocol contained longer fragments on average than those using the phenol–chloroform protocol, probably as a result of loss of small fragments through the silica column. While toe pads yielded more DNA than skin punches and bone fragments, skin punches proved to be a reliable alternative source of DNA and might be especially appealing when toe pad extractions are impractical. Overall, we found that historical bird museum specimens contain substantial amounts of DNA for genomic studies under most extraction scenarios, but that a phenol–chloroform protocol consistently provides the high quantities of DNA required for most current genomic protocols.     

Species diversity and phylogeography of Cornus kousa (Asian dogwood) captured by genomic and genic microsatellites

Cornus kousa (Asian dogwood), an East Asia native tree, is the most economically important species of the dogwood genus, owing to its desirable horticultural traits and ability to hybridize with North America‐native dogwoods. To assess the species genetic diversity and to better inform the ongoing and future breeding efforts, we assembled an herbarium and arboretum collection of 131 noncultivated C. kousa specimens. Genotyping and capillary electrophoresis analyses of our C. kousa collection with the newly developed genic and published nuclear genomic microsatellites permitted assessment of genetic diversity and evolutionary history of the species. Regardless of the microsatellite type used, the study yielded generally similar insights into the C. kousa diversity with subtle differences deriving from and underlining the marker used. The accrued evidence pointed to the species distinct genetic pools related to the plant country of origin. This can be helpful in the development of the commercial cultivars for this important ornamental crop with increased pyramided utility traits. Analyses of the C. kousa evolutionary history using the accrued genotyping datasets pointed to an unsampled ancestor population, possibly now extinct, as per the phylogeography of the region. To our knowledge, there are few studies utilizing the same gDNA collection to compare performance of genomic and genic microsatellites. This is the first detailed report on C. kousa species diversity and evolutionary history inference.     

The use of fine-wire EMG to investigate shoulder muscle recruitment patterns during cello bowing: The results of a pilot study

The physical mechanics of music making is important both in the prevention of injuries and in guiding how music is performed and taught. Electromyography has potential as a resource in understanding the loads involved in instrumental playing; however, only a small number of projects have been undertaken, and little is understood on the muscle activity used during bowing on string instruments. This study aimed to measure the muscle activity at the bowing shoulder of a cellist during cello playing and to establish if fine-wire EMG is useful in understanding muscle recruitment in string players without interfering with normal playing ability. This project used a combination of fine-wire and surface EMG to evaluate the muscular load placed on the right shoulder of a professional cellist whilst playing a set of various bowing exercises. The results indicated that different bowing techniques produced statistically different muscle activity levels, with the supraspinatus muscle in particular maintaining higher mean contraction (20% MVC) during all bowing patterns tested. Fine-wire EMG was useful in measuring shoulder muscle load and did not interfere with normal playing technique of the subject. Overall, the study presents a working protocol from which future studies may be able conduct further research.     

Association of CAT polymorphisms with catalase activity and exposure to environmental oxidative stimuli

We tested the hypotheses that catalase activity is modified by CAT single nucleotide polymorphisms (SNPs) (-262;-844), and by their interactions with oxidant exposures (coal dusts, smoking), lymphotoxin alpha (LTA, NcoI) and tumor necrosis factor (TNF, -308) in 196 miners. Erythrocyte catalase, superoxide dismutase, and glutathione peroxidase activities were measured. The CAT -262 SNP was related to lower catalase activity (104, 87 and 72 k/g hemoglobin for CC, CT and TT, respectively, p < 0.0001). Regardless of CAT SNPs, the LTA NcoI but not the TNF-308 SNP was associated with catalase activity (p = 0.04 and p = 0.8). CAT -262 T carriers were less frequent in highly exposed miners (OR = 0.39 [0.20–0.78], p = 0.007). In CAT -262 T carriers only, catalase activity decreased with high dust exposure (p = 0.01). Haplotype analyses (combined CAT SNPs) confirm these results. Results show that CAT -262 and LTA NcoI SNPs, and interaction with coal dust exposure, influenced catalase activity.     

Grassland area determines beetle assemblage dissimilarity from surrounding floodplain forest

Patch size is known to affect biodiversity in fragmented landscapes, but is usually examined in systems where the surrounding matrix habitat is unfavourable. We examined beetle diversity in a floodplain ecosystem that is characterised by naturally occurring grassland patches within a dominant matrix of contrasting yet habitable forest. We asked whether differences in the beetle assemblage between grassland and forest vegetation depended on the area of the grassland patch, which is a function of its flooding frequency and duration: smaller grasslands tend to be higher on the floodplain and are flooded less often and for shorter periods than larger grasslands. We found a negative relationship between grassland area and beetle abundance and species richness, and a positive relationship between grassland area and compositional dissimilarity from the surrounding forest. As expected, we found an overall difference in composition between forest and grassland assemblages, with five beetle species more common in the grasslands. Our study indicates that floodplain grasslands not only support beetle assemblages that are distinct from the surrounding forest, but that assemblages from the larger grasslands are compositionally more distinct than those from smaller grasslands. A likely cause of this pattern is the reduced edge effects and greater environmental contrast between forest and large grasslands that may be exposed to greater variation in local climate. Ongoing changes to flood regimes and potential encroachment of forest plants may decrease grassland area in the future, which may reduce spatial heterogeneity in the insect community in this unique floodplain ecosystem.     

Human genetic databanks in Australia: indications of inconsistency and confusion

This paper reports on a survey of human biotechnology organizations in Australia. The study provides insights into the nature, use and practices involved with human genetic databanking in the country. The survey was conducted at a time when databanks were becoming increasingly important to an expanding genomics industry, and while the nature and extent of industry regulation was being debated. The data revealed a surprising level of confusion and inconsistency in the interpretation of terminology and in ethical practice, even among those organizations subject to the relevant government ethics guidelines. It is argued that despite the extensive level of public consultation, recommendations for reform and actual reform in the intervening years, human genetic databanking remains an under-regulated sector of the human biotechnology industry in Australia, and at least as far as the private sector is concerned, will remain so in the foreseeable future.     

Cortisol Patterns Are Associated with T Cell Activation in HIV

Objective

The level of T cell activation in untreated HIV disease is strongly and independently associated with risk of immunologic and clinical progression. The factors that influence the level of activation, however, are not fully defined. Since endogenous glucocorticoids are important in regulating inflammation, we sought to determine whether less optimal diurnal cortisol patterns are associated with greater T cell activation.

Methods

We studied 128 HIV-infected adults who were not on treatment and had a CD4⁺ T cell count above 250 cells/µl. We assessed T cell activation by CD38 expression using flow cytometry, and diurnal cortisol was assessed with salivary measurements.

Results

Lower waking cortisol levels correlated with greater T cell immune activation, measured by CD38 mean fluorescent intensity, on CD4⁺ T cells (r = −0.26, p = 0.006). Participants with lower waking cortisol also showed a trend toward greater activation on CD8⁺ T cells (r = −0.17, p = 0.08). A greater diurnal decline in cortisol, usually considered a healthy pattern, correlated with less CD4⁺ (r = 0.24, p = 0.018) and CD8⁺ (r = 0.24, p = 0.017) activation.

Conclusions

These data suggest that the hypothalamic-pituitary-adrenal (HPA) axis contributes to the regulation of T cell activation in HIV. This may represent an important pathway through which psychological states and the HPA axis influence progression of HIV.     

Model-Based Assessment of Estuary Ecosystem Health Using the Latent Health Factor Index,with Application to the Richibucto Estuary

The ability to quantitatively assess ecological health is of great interest to those tasked with monitoring and conserving ecosystems. For decades, biomonitoring research and policies have relied on multimetric health indices of various forms. Although indices are numbers, many are constructed based on qualitative procedures, thus limiting the quantitative rigor of the practical interpretations of such indices. The statistical modeling approach to construct the latent health factor index (LHFI) was recently developed. With ecological data that otherwise are used to construct conventional multimetric indices, the LHFI framework expresses such data in a rigorous quantitative model, integrating qualitative features of ecosystem health and preconceived ecological relationships among such features. This hierarchical modeling approach allows unified statistical inference of health for observed sites (along with prediction of health for partially observed sites, if desired) and of the relevance of ecological drivers, all accompanied by formal uncertainty statements from a single, integrated analysis. Thus far, the LHFI approach has been demonstrated and validated in a freshwater context. We adapt this approach to modeling estuarine health, and illustrate it on the previously unassessed system in Richibucto in New Brunswick, Canada, where active oyster farming is a potential stressor through its effects on sediment properties. Field data correspond to health metrics that constitute the popular AZTI marine biotic index and the infaunal trophic index, as well as abiotic predictors preconceived to influence biota. Our paper is the first to construct a scientifically sensible model that rigorously identifies the collective explanatory capacity of salinity, distance downstream, channel depth, and silt–clay content–all regarded a priori as qualitatively important abiotic drivers–towards site health in the Richibucto ecosystem. This suggests the potential effectiveness of the LHFI approach for assessing not only freshwater systems but aquatic ecosystems in general.     

The Histone Variant His2Av is Required for Adult Stem Cell Maintenance in the Drosophila Testis

Many tissues are sustained by adult stem cells, which replace lost cells by differentiation and maintain their own population through self-renewal. The mechanisms through which adult stem cells maintain their identity are thus important for tissue homeostasis and repair throughout life. Here, we show that a histone variant, His2Av, is required cell autonomously for maintenance of germline and cyst stem cells in the Drosophila testis. The ATP-dependent chromatin-remodeling factor Domino is also required in this tissue for adult stem cell maintenance possibly by regulating the incorporation of His2Av into chromatin. Interestingly, although expression of His2Av was ubiquitous, its function was dispensable for germline and cyst cell differentiation, suggesting a specific role for this non-canonical histone in maintaining the stem cell state in these lineages.