Technical note: Examining the use of ethylenediaminetetraacetic acid for humic extraction of ancient bone

We examined the efficacy of ethylenediaminetetraacetic acid (EDTA) for removing humic contaminants from collagen extracted from ancient bone. Humic contaminants must be removed to obtain reliable stable isotope values from ancient bone collagen, given that humic acids have consistently lower δ¹³C values than collagen. The purpose of our research was to examine if EDTA treatment could effectively remove humic contaminants from bone collagen and thus serve as an alternative to the commonly implemented sodium hydroxide (NaOH) treatment, which may be associated with large collagen losses in poorly preserved samples. We compared the isotopic and elemental composition of ancient samples treated with EDTA alone, samples demineralized in hydrochloric acid (HCl) and rinsed in EDTA, samples treated with HCl alone, and samples demineralized in HCl and rinsed with NaOH. The samples used in the analyses were selected because they presented evidence of substantial humic contamination. We found that NaOH was the most effective agent for reducing humic contaminants as evidenced by the samples treated with this agent having higher δ¹³C values and lower C:N ratios relative to other treatments. The results from samples treated with EDTA suggest that this chemical cannot effectively remove humic contaminants given that these samples had significantly higher C:N ratios and lower δ¹³C and δ¹⁵N values relative to the HCl/NaOH treatment. Our results demonstrate that when performing stable isotope analysis of ancient bone collagen suspected to be contaminated with humic acids, NaOH is the most effective chemical agent to remove humic contaminants, while EDTA cannot perform this task.     

Preparation of Enantiomerically Pure (S)‐(−)‐1‐(1′‐naphthyl)‐ethanol by the Fungus Alternaria alternata

(S)‐(?)‐1‐(1′‐napthyl)‐ethanol (S‐NE) is an important intermediate for the preparation of mevinic acid analogs, which is used for the treatment of hyperlipidemia. The objectives of the study were to isolate a microorganism that could effectively reduce 1‐acetonaphthone (1‐ACN) to S‐NE, to determine the influence that the physicochemical parameters would have on the reduction by the isolated microorganism, and to attempt large‐scale studies with the microorganism. Over the years fungi have been considered a promising biocatalyst and it has been presumed that many fungal species have not been isolated and therefore the current study focused on possible isolation of these microorganisms. A total of 72 fungal isolates were screened for their ability to reduce 1‐ACN to its corresponding alcohol. The isolate, EBK‐62, identified as Alternaria alternata, was found to be the most successful at reducing the ketone to the corresponding alcohol in the submerged culture. The reaction conditions were systematically optimized for the reducing agent A. alternata EBK‐62, which showed high stereospecificity and good conversion for the reduction. The preparative scale study was carried out in a 2 L bioreactor and a total of 4.9 g of S‐NE in optically pure form (>99% enantiomeric excess) was produced in 48 h. Chirality 28:669–673, 2016. © 2016 Wiley Periodicals, Inc.     

Epidemiology of Dermatophytes in Belgium: A 5 Years’ Survey

Dermatophytes are among the most common fungal agents causing superficial skin infections worldwide. Epidemiology of these infections is evolving and variable in every country. This report presents the Belgian epidemiological data regarding the distribution of dermatophytes species isolated by the two national reference centers for mycosis during a period of 5 years (2012–2016). Trichophyton rubrum was the most frequently isolated species, considering all sampling sites (60.3% on average between 2012 and 2016). More precisely, this dermatophyte was the major agent of Tinea unguium and Tinea corporis during this period, followed by species of the Trichophyton mentagrophytes complex. Moreover, Microsporum audouinii was the main etiological agent of Tinea capitis (TC) with a frequency of 52.5% on average between 2012 and 2016. Other African dermatophytes species such as Trichophyton soudanense and Trichophyton violaceum were also agents of TC with a respective prevalence of 11.6% and 11.5% on average. This study highlights a different dermatophyte distribution in Belgium in comparison with other European countries.

     

Lunar influences in the diet habits and selectivity of larval clingfish Gobiesox marmoratus

The influence of the lunar cycle on the feeding habits, feeding success and selectivity was tested in situ on larval stages of the clingfish Gobiesox marmoratus (Gobiesocidae). Gobiesox marmoratus larvae and their prey were collected in the water column during the lunar cycle in austral spring 2015 and 2016, in shallow waters (<30 m depth) of El Quisco, central Chile. Feeding incidence was high (80–100%) throughout the moon cycle. The diet was composed of 32 prey items, being gastropod larvae and invertebrate eggs the most important. Prey composition varied among lunar phases with the lowest prey richness during new moon. During 2016, G. marmoratus larvae ingested the lowest number, but the largest prey during new moon. In spring 2015, there were no significant changes in the abundance of each prey taxon in the water column among moon phases, but in spring 2016 there were significant differences in the abundance of cypris and copepod nauplii, particularly between full and new moon. Feeding selectivity index showed that gastropod larvae were positively selected throughout the lunar cycle during spring 2015. In spring 2016, invertebrate eggs were selectively ingested in full moon and third quarter, but at a new moon G. marmoratus larvae selected gastropod larvae. Mean temperature of the water column and its vertical gradient and nocturnal cloud cover influences the feeding success of larval G. marmoratus. Lunar illumination favoured only an increase of richness of prey items. Therefore, nocturnal cloud cover precludes a greater influence of lunar illumination in the larval trophic ecology of this crypto-benthic fish.     

“Lossless” compression of high resolution mass spectra of small molecules

Fourier transform ion cyclotron resonance (FTICR) provides the highest resolving power of any commercially available mass spectrometer. This advantage is most significant for species of low mass-to-charge ratio (m/z), such as metabolites. Unfortunately, FTICR spectra contain a very large number of data points, most of which are noise. This is most pronounced at the low m/z end of spectra, where data point density is the highest but peak density low. We therefore developed a filter that offers lossless compression of FTICR mass spectra from singly charged metabolites. The filter relies on the high resolving power and mass measurement precision of FTICR and removes only those m/z channels that cannot contain signal from singly charged organic species. The resulting pseudospectra still contain the same signal as the original spectra but less uninformative background. The filter does not affect the outcome of standard downstream chemometric analysis methods, such as principal component analysis, but use of the filter significantly reduces memory requirements and CPU time for such analyses. We demonstrate the utility of the filter for urinary metabolite profiling using direct infusion electrospray ionization and a 15 tesla FTICR mass spectrometer.     

Long-term zooplankton composition data reveal impacts of invasions on community composition in the Waikato lakes,New Zealand

Data collected on zooplankton community composition over longer time periods (>?10 years) are rare. We examined among-lake spatial and temporal trends of zooplankton communities from a monitoring programme undertaken in the Waikato region, New Zealand. A total of 39 lakes were sampled over a period of 12 years, between 2007 and 2019, with varying degrees of temporal effort. We focussed particularly on eight lakes, considered here as ‘long-term lakes’, where samples were collected with greater regularity (including 5 with 12 years of data). Among lakes, suspended sediment concentrations and indicators of lake trophic state were inferred to be important in determining the zooplankton distributions; as this region is dominated by shallow lakes, the relative importance of suspended sediments was high. Among the long-term lakes, the greatest dissimilarities in zooplankton community composition among years were in Lake Waahi, where the Australian Boeckella symmetrica was first detected in 2012. That is, the greatest temporal changes to zooplankton composition during the study period were due to the invasion by non-indigenous species, rather than changes in trophic state or other environmental variables; non-native species commonly dominated the individual counts of species through much of 2014 and 2015, with most samples since 2016 being again dominated by native species. Following this lake, the largest and shallowest lakes in the dataset—Whangape and Waikare—exhibited the greatest variability in community composition among years.

     

Tooth development and histology patterns in lamniform sharks (Elasmobranchii,Lamniformes) revisited

The dentition of lamniforme sharks exhibits several characters that have been used extensively to resolve the phylogenetic relationships of extant taxa, yet some uncertainties remain. Also, the development of different teeth of a tooth file within the jaws of most extant lamniforms has not been documented to date. High‐resolution micro‐computed tomography is used here to re‐evaluate the importance of two dental characters within the order Lamniformes, which were considered not to be phylogenetically informative, the histotype and the number of teeth per tooth file. Additionally, the development and mineralization patterns of the teeth of the two osteodont lamniforms Lamna nasus and Alopias superciliosus were compared. We discuss the importance of these dental characters for phylogenetic interpretations to assess the quality of these characters in resolving lamniform relationships. The dental characters suggest that (1) Lamniformes are the only modern‐level sharks exhibiting the osteodont histotype, (2) the osteodont histotype in lamniform sharks is a derived state in modern‐level sharks (Elasmobranchii), (3) the osteodont type, conversely is convergently achieved when the clade Chondrichthyes is considered and thus might comprise a functional rather than a phylogenetic signal, and (4) there is an increase in the number of teeth per file throughout lamniform phylogeny. Structural development of the teeth of L. nasus and A. superciliosus is congruent with a previous investigation of the lamniform shark Carcharodon carcharias. J. Morphol. 277:1584–1598, 2016. © 2016 Wiley Periodicals, Inc.     

Effects of high temperature on body size and weight of Ophraella communa

Ophraella communa LeSage (Coleoptera: Chrysomelidae) is an effective biological control agent of the invasive common ragweed, Ambrosia artemisiifolia L. Body size, one of the most important life-history characters for many insects, affects O. communa mating choice. Temperature is one of the most important factors on body size, especially high temperatures. Adult body lengths were significantly inhibited after eggs, larvae and pupae of O. communa experienced high temperature stresses. With exception of subsequent female body after exposure of larvae to high temperatures, the body weights of females and males were not affected by temperatures. Since adult insect fecundities are often in proportion to their body sizes, we concluded that high temperatures may influence the population expansion of O. communa in the field.     

Isolation and selection of virulent isolates of Beauveria bassiana for biological control of Ommatissus lybicus in Kerman province

Date palm (Phoenix dactylifera) is the most important economic crop in Kerman province. The palm date leafhopper (Ommatissus lybicus) is one of the most important and key pests that causes high level damage to date crop. Date is an organic fruit in this area, and biological control has been introduced as the best long-term strategy in this region. To investigate appropriate biological control agents in Kerman province during 2005–2007, 178 isolates were collected from naturally infected O. lybicus for the first time recorded in the world, and Beauveria bassiana was introduced as a suitable biological control agent for control of this pest.     

Bole epiphytic bryophytes on <Emphasis Type="Italic">Lithocarpus xylocarpus</Emphasis> (Kurz) Markgr. in the Ailao Mountains,SW China

Epiphytic bryophytes growing on Lithocarpus xylocarpus (Kurz) Markgr. trunks of different diameter classes in primary (132 plots) and secondary (84 plots) Lithocarpus forests in the Ailao Mountains, SW China, were surveyed and analyzed to determine species composition and richness, and to identify environmental variables that may affect it. Among the 65 species (belonging to 32 genera, 19 families) found, 28 occurred in both forests, with Syrrhopodon gardneri (Hook.) Schwaegr. predominanting. Species richness and total coverage in primary forest were significantly higher than in secondary forest. We suggest that a period of perhaps much more than 110 years is necessary for the recovery of epiphytic bryoflora in montane forest of SW China. Fan, turf, and smooth mat are the most important life forms, with high occurrences in both forests. The life form composition of epiphytic bryophytes is determined mainly by microhabitat and host age. Tree age, the presence of primary forest, bark pH, and plot exposure are the environmental variables that have significantly influenced the composition of epiphytic bryophytes. Tree age explained most variations in epiphytic bryoflora. Bark pH is another important parameter that significantly influenced the epiphytic bryophyte community, but seemed indirectly correlated with tree age. Primary forest is a favorable habitat for epiphytes, due mainly to its diversified canopy structure and the presence of large diameter hosts. Moisture-laden southwest trade winds and forest structure could differentiate microclimate and impel a distinct composition of epiphytes in windward and leeward exposures.     

Melanin is an essential component for the integrity of the cell wall of Aspergillus fumigatus conidia

Background  

Aspergillus fumigatus is the most common agent of invasive aspergillosis, a feared complication in severely immunocompromised patients. Despite the recent commercialisation of new antifungal drugs, the prognosis for this infection remains uncertain. Thus, there is a real need to discover new targets for therapy. Particular attention has been paid to the biochemical composition and organisation of the fungal cell wall, because it mediates the host-fungus interplay. Conidia, which are responsible for infections, have melanin as one of the cell wall components. Melanin has been established as an important virulence factor, protecting the fungus against the host's immune defences. We suggested that it might also have an indirect role in virulence, because it is required for correct assembly of the cell wall layers of the conidia.     

Influence of precipitating agents on thermodynamic parameters of protein crystallization solutions

X‐ray crystallography is the most powerful method for determining three‐dimensional structures of proteins to (near‐)atomic resolution, but protein crystallization is a poorly explained and often intractable phenomenon. Differential Scanning Calorimetry was used to measure the thermodynamic parameters (ΔG, ΔH, ΔS) of temperature‐driven unfolding of two globular proteins, lysozyme, and ribonuclease A, in various salt solutions. The mixtures were categorized into those that were conducive to crystallization of the protein and those that were not. It was found that even fairly low salt concentrations had very large effects on thermodynamic parameters. High concentrations of salts conducive to crystallization stabilized the native folded forms of proteins, whereas high concentrations of salts that did not crystallize them tended to destabilize them. Considering the ΔH and TΔS contributions to the ΔG of unfolding separately, high concentrations of crystallizing salts were found to enthalpically stabilize and entropically destabilize the protein, and vice‐versa for the noncrystallizing salts. These observations suggest an explanation, in terms of protein stability and entropy of hydration, of why some salts are good crystallization agents for a given protein and others are not. This in turn provides theoretical insight into the process of protein crystallization, suggesting ways of predicting and controlling it. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 642–652, 2016.     

Microhabitat nest‐site selection by ducks in the boreal forest

The boreal forest is one of the North America’s most important breeding areas for ducks, but information about the nesting ecology of ducks in the region is limited. We collected microhabitat data related to vegetation structure and composition at 157 duck nests and paired random locations in Alberta’s boreal forest region from 2016 to 2018. We identified fine‐scale vegetation features selected by ducks for all nests, between nesting guilds, and among five species using conditional logistic regression. Ducks in the boreal forest selected nest sites with greater overhead and graminoid cover, but less forb cover than random sites. Characteristics of the nest sites of upland‐ and overwater‐nesting guilds differed, with species nesting in upland habitat selecting nests that provided greater shrub cover and less lateral concealment and species nesting over water selecting nests with less shrub cover. We examined the characteristics of nest sites of American Wigeon (Mareca americana), Blue‐winged Teal (Spatula discors), Green‐winged Teal (Anas crecca), Mallards (Anas platyrhynchos), and Ring‐necked Ducks (Aythya collaris), and found differences among species that may facilitate species coexistence at a regional scale. Our results suggest that females of species nesting in upland habitat selected nest sites that optimized concealment from aerial predators while also allowing detection of and escape from terrestrial predators. Consequently, alteration in the composition and heterogeneity of vegetation and predator communities caused by climate change and industrial development in the boreal forest of Canada may affect the nest‐site selection strategies of boreal ducks.     

Monitoring occurrence,extinction, and colonization probabilities for gibbon populations

All gibbon species (Family: Hylobatidae) are considered threatened with extinction and recognized on the International Union for Conservation of Nature Red List of Threatened Species. Because gibbons are one of the most threatened families of primates, monitoring their status is now critically important. Long-term monitoring programs applying occupancy approaches, in addition to assessing occurrence probability, improves understanding of other population parameters such as site extinction or colonization probabilities, which elucidate temporal and spatial changes and are therefore important for guiding conservation efforts. In this study, we used multiple season occupancy models to monitor occurrence, extinction, and colonization probabilities for northern yellow-cheeked crested gibbon Nomascus annamensis in three adjacent protected areas in the Central Annamites mountain range, Vietnam. We collected data at 30 listening posts in 2012, 2014, and 2016 using the auditory point count method. Occurrence probabilities were highest in 2012 (0.74, confidence interval [CI]: 0.56–0.87) but slightly lower in 2014 (0.66, CI: 0.51–0.79) and 2016 (0.67, CI: 0.49–0.81). Extinction probabilities during the 2012–2014 and 2014–2016 intervals were 0.26 (0.14–0.44) and 0.25 (0.12–0.44), respectively. Colonization probabilities during 2012–2014 were 0.44 (0.19–0.73) and between 2014 and 2016 was 0.51 (0.26–0.75). Although local site extinctions have occurred, high recolonization probability helped to replenish the unoccupied sites and kept the occurrence probability stable. Long-term monitoring programs which use occurrence probability alone might not fully reveal the true dynamics of gibbon populations. We strongly recommend including multiple season occupancy models to monitor occurrence, extinction, and colonization probabilities in long-term gibbon monitoring programs.     

Discerning the dietary habits of the smooth butterfly ray Gymnura lessae using two distinct methods,otolith identification and metagenetics

Two different methods, metagenetics and free-otolith identification, were used to identify prey in the stomach contents of 531 Gymnura lessae captured by trawling in Mobile Bay, Alabama 2016–2018. Both methods were found to produce analogous results and were therefore combined into a single complete dataset. All prey were teleosts; the families Sciaenidae and Engraulidae were the most important prey (prey specie index of relative importance 89.3% I_PSRI). Multivariate analyses indicated that the diet of G. lessae varied with sex and seasonality. Specifically, variability was probably due to morphologically larger females consuming larger teleost prey species compared with males, whereas seasonal variability was probably due to changes in the available prey community composition. The findings indicate that both metagenetics and free otolith identification, used independently or complementarily, offer robust means of characterising dietary habits for teleost-specialised species such as G. lessae, which may play an important role in the structure and maintenance of coastal food webs such as those in Mobile Bay.     

Development and assessment of Diversity Arrays Technology for high-throughput DNA analyses in <Emphasis Type="Italic">Musa</Emphasis>

Diversity Arrays Technology (DArT) is a DNA hybridisation-based molecular marker technique that can detect simultaneously variation at numerous genomic loci without sequence information. This efficiency makes it a potential tool for a quick and powerful assessment of the structure of germplasm collections. This article demonstrates the usefulness of DArT markers for genetic diversity analyses of Musa spp. genotypes. We developed four complexity reduction methods to generate DArT genomic representations and we tested their performance using 48 reference Musa genotypes. For these four complexity reduction methods, DArT markers displayed high polymorphism information content. We selected the two methods which generated the most polymorphic genomic representations (PstI/BstNI 16.8%, PstI/TaqI 16.1%) to analyze a panel of 168 Musa genotypes from two of the most important field collections of Musa in the world: Cirad (Neufchateau, Guadeloupe), and IITA (Ibadan, Nigeria). Since most edible cultivars are derived from two wild species, Musa acuminata (A genome) and Musa balbisiana (B genome), the study is restricted mostly to accessions of these two species and those derived from them. The genomic origin of the markers can help resolving the pedigree of valuable genotypes of unknown origin. A total of 836 markers were identified and used for genotyping. Ten percent of them were specific to the A genome and enabled targeting this genome portion in relatedness analysis among diverse ploidy constitutions. DArT markers revealed genetic relationships among Musa genotype consistent with those provided by the other markers technologies, but at a significantly higher resolution and speed and reduced cost.     

The relation between geomorphology and forest community types of the Haut-Saint-Laurent,Quebec

The highly disturbed community types of the Haut-Saint-Laurent in southern Quebec were classified using an hierarchic approach with three levels: geomorphology, pedology and vegetation. Considered as distinct entities were, on the one hand, the herbaceous and shrub species that made up ecological groups as defined by Meilleur et al. (1992), and, on the other hand, individual tree species. Great importance was given to geomorphological variables because they are one of the most stable ecological factors of the region. We identified 47 community types from 452 sites sampled, based on a TWINSPAN analysis of the vegetation data. Binary Discriminant Analysis (BDA) showed the importance of disturbance on community composition, especially for sites included in the forest mosaic. Other important abiotic parameters included morphogenic features, topography and drainage. The BDA showed that 24 community types were found to be significantly associated with at least one morphogenic feature. The results indicate that the Beech-Hemlock association is a more stable state for mesic sites than the often cited Sugar Maple with Hickory. On glacial deposits, the presence of Thuja occidentalis is significantly associated with grazing practices. The other 23 community types are not significantly associated with any morphogenic features. On one hand, these types tend to be ubiquitous on different deposits with the same drainage class and reveal that their composition was altered through disturbances. On the other hand, some community types are more associated with microclimates as is the case of Sugar Maple with Striped Maple, or with their ecological amplitude limits as is the case of Sugar Maple with Ironwood and Aspen or Sugar Maple with Red Maple and Black Ash. A classification of the stands, given the high number of disturbed communities within the territory, appears difficult to use as a basis for ecological units.     

Plasmodium falciparum centromeres display a unique epigenetic makeup and cluster prior to and during schizogony

Centromeres are essential for the faithful transmission of chromosomes to the next generation, therefore being essential in all eukaryotic organisms. The centromeres of Plasmodium falciparum, the causative agent of the most severe form of malaria, have been broadly mapped on most chromosomes, but their epigenetic composition remained undefined. Here, we reveal that the centromeric histone variant PfCENH3 occupies a 4–4.5 kb region on each P. falciparum chromosome, which is devoid of pericentric heterochromatin but harbours another histone variant, PfH2A.Z. These CENH3 covered regions pinpoint the exact position of the centromere on all chromosomes and revealed that all centromeric regions have similar size and sequence composition. Immunofluorescence assay of PfCENH3 strongly suggests that P. falciparum centromerescluster to a single nuclear location prior to and during mitosis and cytokinesis but dissociate soon after invasion. In summary, we reveal a dynamic association of Plasmodium centromeres, which bear a unique epigenetic signature and conform to a strict structure. These findings suggest that DNA‐associated and epigenetic elements play an important role in centromere establishment in this important human pathogen.     

Overstorey Control of Understorey Species Composition in a Near-natural Temperate Broadleaved Forest in Denmark

Little is known about the importance of the forest overstorey relative to other factors in controlling the spatial variability in understorey species composition in near-natural temperate broadleaved forests. We addressed this question for the 19 ha ancient forest Suserup Skov (55°22′ N, 11°34′ E) in Denmark, one of the few old-growth temperate broadleaved forest remnants in north-western Europe, by inventorying understorey species composition and environmental conditions in 163 100 m² plots. We use unconstrained and constrained ordinations, variation partitioning, and Indicator Species Analysis to provide a quantitative assessment of the importance of the forest overstorey in controlling understorey species composition. Comparison of the gradients extracted by unconstrained and constrained ordinations showed that the main gradients in understorey species composition in our old-growth temperate broadleaved forest remnant are not caused by variability in the forest overstorey, but are related to topography and soil, edge effects, and unknown broad-scale factors. Nevertheless, overstorey-related variables uniquely accounted for 15% of the total explained variation in understorey species composition, with the pure overstorey-related (R_po), topography and soil (R_pt), edge and anthropogenic disturbance effects (R_pa), and spatial (R_ps) variation fractions being of equal magnitude. The forward variable selection showed that among the overstorey-related variables understorey light availability and to a lesser extent vertical forest structure were most important for understorey species composition. No unique influence of overstorey tree species identity could be documented. There were many indicator species for high understorey light levels and canopy gap centres, but none for medium or low light or closed canopy. Hence, no understorey species behaved as obligate shade plants. Our study shows that, the forest overstorey has a weak control of understorey species composition in near-natural broadleaved forest, in contrast to results from natural and managed forests comprising both conifer and broadleaved species. Nevertheless, >20% of the understorey species found were indicators of high light conditions or canopy openings. Hence, variability in canopy structure and understorey light availability is important for maintaining understorey species diversity.