Resolving taphonomic and preparation biases in silicified faunas through paired acid residues and X-ray microscopy.

Paired petrography and acid maceration has shown that preferential silicification of shelly faunas can bias recovery based on taxon and body size. Here, silicified fossils from the Upper Ordovician Edinburg Formation, Strasburg Junction, Virginia, USA, were analyzed using X-ray tomographic microscopy (µCT) in conjunction with recovered residues from acid maceration of the same materials to further examine sources of potential bias. Results reveal that very small (<~1 mm) fossils are poorly resolved in µCT when scanning at lower resolutions (~30 µm), underestimating abundance of taxa including ostracods and bryozoans. Acid maceration, meanwhile, fails to recover poorly silicified fossils prone to disarticulation and/or fragmentation during digestion. Tests for patterns of breakage, however, indicate no significant size or taxonomic bias during extraction. Comparisons of individual fossils from 3-D fossil renders and maceration residues reveal patterns of fragmentation that are taxon-specific and allow the differentiation of biostratinomic and preparational breakage. Multivariate ordinations and cluster analyses of µCT and residue data in general produce concordant results but indicate that the variation in taxonomic composition of our samples is compromised by the resolvability of small size classes in µCT imaging, limiting the utility of this method for addressing paleoecological questions in these specific samples. We suggest that comparability of results will depend strongly on the sample size, taphonomic history, textural, and compositional characteristics of the samples in question, as well as µCT scan parameters. Additionally, applying these methods to different deposits will test the general applicability of the conclusions drawn on the relative strengths and weaknesses of the methods.

Earthworms (Clitellata, Megadrili) of the world: an updated checklist of valid species and families, with notes on their distribution.

In the current paper we present an updated checklist of all the megadrile earthworms (Crassiclitellata: Annelida) in the world, and notes on the distribution of families worldwide. Biogeographic responses to geological phenomena including plate tectonics, as well as to past and present climate and habitat distributions, are the main factors determining the present distribution of earthworm families. A total of ca. 5,738 species/subspecies (5,406 species and 332 unique subspecies; i.e., not counting the nomino-typical subspecies) belonging to 23 families (including one non-crassiclitellate family: Moniligastridae) are currently recognized worldwide, of which three families (Tritogeniidae and Kazimierzidae from Southern Africa and Arecoidae, a new family from Brazil described herein), 35 genera and close to 1200 new taxa (including subspecies) were described in the 21st century. Nonetheless, the large number of still undescribed species will likely increase this value to well over 8,000 species. Ten families are monospecific and/or monogeneric and have a mostly restricted distribution. On the other hand, more than 87 widespread cosmopolitan species have been catalogued, some of them with important invasive potential, belonging mainly to families Lumbricidae, Acanthodrilidae, Benhamiidae, Megascolecidae, Rhinodrilidae and Ocnerodrilidae. Taxonomic housekeeping was performed for the preoccupied Rhinodrilidae genus Tairona Righi - herein substituted by Taironina nom. nov., and Guarani camaqua Rodríguez & Lima was reinstated and removed from synonymy with Criodrilus lacuum Hoffmeister, 1845, resulting in a wider definition of the Almidae family. Furthermore, Amynthas maximalis nom. nov. is proposed herein as a substitution name for the preoccupied name Amynthas maximus Qiu & Dong, 2019, and Arecoidae is proposed herein as a new monotypic family for the aquamegadrile species Areco reco Righi, Ayres & Bittencourt, 1978.

Localization and chemical speciation of europium(III) in Brassica napus plants.

For the reliable safety assessment of repositories of highly radioactive waste, further development of the modelling of radionuclide migration and transfer in the environment is necessary, which requires a deeper process understanding at the molecular level. Eu(III) is a non-radioactive analogue for trivalent actinides, which contribute heavily to radiotoxicity in a repository. For in-depth study of the interaction of plants with trivalent f elements, we investigated the uptake, speciation, and localization of Eu(III) in Brassica napus plants at two concentrations, 30 and 200 µM, as a function of the incubation time up to 72 h. Eu(III) was used as luminescence probe for combined microscopy and chemical speciation analyses of it in Brassica napus plants. The localization of bioassociated Eu(III) in plant parts was explored by spatially resolved chemical microscopy. Three Eu(III) species were identified in the root tissue. Moreover, different luminescence spectroscopic techniques were applied for an improved Eu(III) species determination in solution. In addition, transmission electron microscopy combined with energy-dispersive X-ray spectroscopy was used to localize Eu(III) in the plant tissue, showing Eu-containing aggregates. By using this multi-method setup, a profound knowledge on the behavior of Eu(III) within plants and changes in its speciation could be obtained, showing that different Eu(III) species occur simultaneously within the root tissue and in solution.

A comprehensive study on the interaction of Eu(III) and U(VI) with plant cells (Daucus carota) in suspension.

Daucus carota suspension cells showed a high affinity towards Eu(III) and U(VI) based on a single-step bioassociation process with an equilibrium after 48-72 h. Cells responded with an increased metabolic activity towards heavy metal stress. Luminescence spectroscopy pointed to multiple species for both f-block elements in the culture media, providing initial hints of their interaction with cells and released metabolites. Using nuclear magnetic resonance spectroscopy, we could prove that malate, as an released metabolite in the culture medium, was found to complex with U. Luminescence spectroscopy also showed that Eu(III)-EDTA species are interacting with the cells. Furthermore, Eu(III) and U(VI) coordination is dominated by phosphate groups provided by the cells. We found that Ca ion channels of D. carota cells were involved in the uptake of U(VI), which led to a bioprecipitation of U(VI) in the vacuole of the cells, most probably as uranyl(VI) phosphates along with an intracellular sorption of U(VI) on biomembranes by lipid structures. Eu(III) could be found locally concentrated in the cell wall and in the cytoplasm with a co-localization with phosphorous and oxygen.

Endocytosis is a significant contributor to uranium(VI) uptake in tobacco (Nicotiana tabacum) BY-2 cells in phosphate-deficient culture.

Endocytosis of metals in plants is a growing field of study involving metal uptake from the rhizosphere. Uranium, which is naturally and artificially released into the rhizosphere, is known to be taken up by certain species of plant, such as Nicotiana tabacum, and we hypothesize that endocytosis contributes to the uptake of uranium in tobacco. The endocytic uptake of uranium was investigated in tobacco BY-2 cells using an optimized setup of culture in phosphate-deficient medium. A combination of methods in biochemistry, microscopy and spectroscopy, supplemented by proteomics, were used to study the interaction of uranium and the plant cell. We found that under environmentally relevant uranium concentrations, endocytosis remained active and contributed to 14% of the total uranium bioassociation. Proteomics analyses revealed that uranium induced a change in expression of the clathrin heavy chain variant, signifying a shift in the type of endocytosis taking place. However, the rate of endocytosis remained largely unaltered. Electron microscopy and energy-dispersive X-ray spectroscopy showed an adsorption of uranium to cell surfaces and deposition in vacuoles. Our results demonstrate that endocytosis constitutes a considerable proportion of uranium uptake in BY-2 cells, and that endocytosed uranium is likely targeted to the vacuole for sequestration, providing a physiologically safer route for the plant than uranium transported through the cytosol.

Phanerozoic parasitism and marine metazoan diversity: dilution versus amplification.

Growing evidence suggests that biodiversity mediates parasite prevalence. We have compiled the first global database on occurrences and prevalence of marine parasitism throughout the Phanerozoic and assess the relationship with biodiversity to test if there is support for amplification or dilution of parasitism at the macroevolutionary scale. Median prevalence values by era are 5% for the Paleozoic, 4% for the Mesozoic, and a significant increase to 10% for the Cenozoic. We calculated period-level shareholder quorum sub-sampled (SQS) estimates of mean sampled diversity, three-timer (3T) origination rates, and 3T extinction rates for the most abundant host clades in the Paleobiology Database to compare to both occurrences of parasitism and the more informative parasite prevalence values. Generalized linear models (GLMs) of parasite occurrences and SQS diversity measures support both the amplification (all taxa pooled, crinoids and blastoids, and molluscs) and dilution hypotheses (arthropods, cnidarians, and bivalves). GLMs of prevalence and SQS diversity measures support the amplification hypothesis (all taxa pooled and molluscs). Though likely scale-dependent, parasitism has increased through the Phanerozoic and clear patterns primarily support the amplification of parasitism with biodiversity in the history of life. This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.

Parasitism and host behavior in the context of a changing environment: The Holocene record of the commercially important bivalve Chamelea gallina, northern Italy.

Rapid warming and sea-level rise are predicted to be major driving forces in shaping coastal ecosystems and their services in the next century. Though forecasts of the multiple and complex effects of temperature and sea-level rise on ecological interactions suggest negative impacts on parasite diversity, the effect of long term climate change on parasite dynamics is complex and unresolved. Digenean trematodes are complex life cycle parasites that can induce characteristic traces on their bivalve hosts and hold potential to infer parasite host-dynamics through time and space. Previous work has demonstrated a consistent association between sea level rise and increasing prevalence of trematode traces, but a number of fundamental questions remain unanswered about this paleoecological proxy. Here we examine the relationships of host size, shape, and functional morphology with parasite prevalence and abundance, how parasites are distributed across hosts, and how all of these relationships vary through time, using the bivalve Chamelea gallina from a Holocene shallow marine succession in the Po coastal plain. Trematode prevalence increased and decreased in association with the transition from a wave-influenced estuarine system to a wave-dominated deltaic setting. Prevalence and abundance of trematode pits are associated with large host body size, reflecting ontogenetic accumulation of parasites, but temporal trends in median host size do not explain prevalence trends. Ongoing work will test the roles of temperature, salinity, and nutrient availability on trematode parasitism. Parasitized bivalves in one sample were shallower burrowers than their non-parasitized counterparts, suggesting that hosts of trematodes can be more susceptible to their predators, though the effect is ephemeral. Like in living parasite-host systems, trematode-induced malformations are strongly aggregated among hosts, wherein most host individuals harbor very few parasites while a few hosts have many. We interpret trace aggregation to support the assumption that traces are a reliable proxy for trematode parasitism in the fossil record.

Bioassociation of U(VI) and Eu(III) by Plant (Brassica napus) Suspension Cell Cultures-A Spectroscopic Investigation.

In this study, we investigated the interaction of U(VI) and Eu(III) with Brassica napus suspension plant cells as a model system. Concentration-dependent (0-200 µM) bioassociation experiments showed that more than 75% of U(VI) and Eu(III) were immobilized by the cells. In addition to this phenomenon, time-dependent studies for 1 to 72 h of exposure showed a multistage bioassociation process for cells that were exposed to 200 µM U(VI), where, after initial immobilization of U(VI) within 1 h of exposure, it was released back into the culture medium starting within 24 h. A remobilization to this extent has not been previously observed. The MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay was used to correlate the bioassociation behavior of Eu and U with the cell vitality. Speciation studies by spectroscopy and in silico methods highlighted various U and Eu species over the course of exposure. We were able to observe a new U species, which emerged simultaneously with the remobilization of U back into the solution, which we assume to be a U(VI) phosphate species. Thus, the interaction of U(VI) and Eu(III) with released plant metabolites could be concluded.

Experimentally modelling cocoa bean fermentation reveals key factors and their influences.

Cocoa bean fermentation still remains a rather empirical process. The research presented here employed an artificial system of fermentation, using controlled incubations, in order to achieve greater control over the external influences that cocoa beans are exposed to, with the aim of experimentally modelling changes to bean components (responses). Experimental design was used, in a first-ever attempt, to study the effects of five factors and their interactions on the profiles of pH, peptides, and flavanols in the bean during the incubations. Temperature, incubation time and the concentration of acetic acid were the main factors influencing the three responses. Moreover, there was a significant amount of factor interaction, revealing the process to be more complex than initially thought, especially with respect to the role of ethanol. Using the model, one was also able to accurately predict the response of the bean to the exposure to specific factors.

Forcing fermentation: Profiling proteins, peptides and polyphenols in lab-scale cocoa bean fermentation.

This study encompassed the lab-scale fermentation of cocoa beans in 300-g heaps under controlled laboratory conditions, in order to replicate the microbial dynamics and metabolomic changes that usually occur in large-scale spontaneous fermentations. Growth profiles of yeast and acetic acid bacteria (AAB) with the native assortment of microbes as well as with the use of a starter culture were very similar to those observed in literature. Greater production of acetic acid by AAB not only led to more acidic-tasting liquor but also contributed to bitterness, due to polyphenol preservation. It also brought about a drastic drop in pH leading to greater proteolytic activity. Peptides generated through proteolysis also showed incredible similarity to those reported in literature, in particular, those speculated to be involved in cocoa-specific flavour. A closer look at the naturally occurring peptide repertoires of our fermentation trials, generated by the breakdown of cocoa storage protein, pointed to a potential peptide responsible for cocoa-specific aroma.

Multiparametric magnetic resonance imaging: Overview of the technique, clinical applications in prostate biopsy and future directions.

Multiparametric magnetic resonance imaging (mpMRI) has managed to change the paradigms on prostate cancer detection and risk classification. The most clear-cut indication of mpMRI in guidelines is the patients with a history of negative biopsy/increasing prostate-specific antigen (PSA), and presence of additional findings supporting its use in non biopsied patients and active surveillance. mpMRI complements standard clinical exam, PSA measurements, and systematic biopsy, and will miss some tumors that lack enough size or change in tissue density. Use of mpMRI is likely to increase, and further developments in the technique will be important for safe adoption of focal therapy concepts. Here we present a brief summary about mpMRI and its use in detection, risk classification and follow-up of prostate cancer.

Surges in trematode prevalence linked to centennial-scale flooding events in the Adriatic.

The forecasts of increasing global temperature and sea level rise have led to concern about the response of parasites to anthropogenic climate change. Whereas ecological studies of parasite response to environmental shifts are necessarily limited to short time scales, the fossil record can potentially provide a quantitative archive of long-term ecological responses to past climate transitions. Here, we document multi-centennial scale changes in prevalence of trematodes infesting the bivalve host Abra segmentum through multiple sea-level fluctuations preserved in brackish Holocene deposits of the Po Plain, Italy. Prevalence values were significantly elevated (p < 0.01) in samples associated with flooding surfaces, yet the temporal trends of parasite prevalence and host shell length, cannot be explained by Waltherian facies change, host availability, salinity, diversity, turnover, or community structure. The observed surges in parasite prevalence during past flooding events indicate that the ongoing global warming and sea-level rise will lead to significant intensification of trematode parasitism, suppressed fecundity of common benthic organisms, and negative impacts on marine ecosystems, ecosystem services, and, eventually, to human well-being.

Increase in predator-prey size ratios throughout the Phanerozoic history of marine ecosystems.

The escalation hypothesis posits that predation by increasingly powerful and metabolically active carnivores has been a major driver of metazoan evolution. We test a key tenet of this hypothesis by analyzing predatory drill holes in fossil marine shells, which provide a ~500-million-year record of individual predator-prey interactions. We show that drill-hole size is a robust predictor of body size among modern drilling predators and that drill-hole size (and thus inferred predator size and power) rose substantially from the Ordovician to the Quaternary period, whereas the size of drilled prey remained stable. Together, these trends indicate a directional increase in predator-prey size ratios. We hypothesize that increasing predator-prey size ratios reflect increases in prey abundance, prey nutrient content, and predation among predators.

Decoupling biogeochemical records, extinction, and environmental change during the Cambrian SPICE event.

Several positive carbon isotope excursions in Lower Paleozoic rocks, including the prominent Upper Cambrian Steptoean Positive Carbon Isotope Excursion (SPICE), are thought to reflect intermittent perturbations in the hydrosphere-biosphere system. Models explaining these secular changes are abundant, but the synchronicity and regional variation of the isotope signals are not well understood. Examination of cores across a paleodepth gradient in the Upper Cambrian central Missouri intrashelf basin (United States) reveals a time-transgressive, facies-dependent nature of the SPICE. Although the SPICE event may be a global signal, the manner in which it is recorded in rocks should and does vary as a function of facies and carbonate platform geometry. We call for a paradigm shift to better constrain facies, stratigraphic, and biostratigraphic architecture and to apply these observations to the variability in magnitude, stratigraphic extent, and timing of the SPICE signal, as well as other biogeochemical perturbations, to elucidate the complex processes driving the ocean-carbonate system.

Aseptic artificial fermentation of cocoa beans can be fashioned to replicate the peptide profile of commercial cocoa bean fermentations.

The fermentation of cocoa beans is essential for the generation of flavour precursors that are required later on to form the flavour components of chocolate. From the many different precursors that are generated, oligopeptides and free amino acids comprise a significant proportion as some of them form Maillard reaction products during the roasting process. Therefore, the diversity of peptides is an important contributing factor to the quality of a fermentation which is in turn controlled by proteolytic activity within the cocoa bean, and is driven by changes in the presence of fermentation by-products as a result of microbial activity outside the bean. Being able to control proteolytic activity within the bean using only the presence of fermentation by-products would prove a valuable tool in the study of these proteases and the processing of cocoa storage proteins. Thus, this tool would help elucidate key mechanisms that generate the components responsible for flavour. In this study, we describe an artificial fermentation system, free from microbial activity, which is able to replicate proteolytic degradation of protein as well as to generate similar peptide fragments as seen during a commercial fermentation. It was also found that acidification is a main contributor to protein degradation.

Trace Fossil Evidence of Trematode-Bivalve Parasite-Host Interactions in Deep Time.

Parasitism is one of the most pervasive phenomena amongst modern eukaryotic life and yet, relative to other biotic interactions, almost nothing is known about its history in deep time. Digenean trematodes (Platyhelminthes) are complex life cycle parasites, which have practically no body fossil record, but induce the growth of characteristic malformations in the shells of their bivalve hosts. These malformations are readily preserved in the fossil record, but, until recently, have largely been overlooked by students of the fossil record. In this review, we present the various malformations induced by trematodes in bivalves, evaluate their distribution through deep time in the phylogenetic and ecological contexts of their bivalve hosts and explore how various taphonomic processes have likely biased our understanding of trematodes in deep time. Trematodes are known to negatively affect their bivalve hosts in a number of ways including castration, modifying growth rates, causing immobilization and, in some cases, altering host behaviour making the host more susceptible to their own predators. Digeneans are expected to be significant agents of natural selection. To that end, we discuss how bivalves may have adapted to their parasites via heterochrony and suggest a practical methodology for testing such hypotheses in deep time.

Assessment of cytotoxicity exerted by leaf extracts from plants of the genus Rhododendron towards epidermal keratinocytes and intestine epithelial cells.

BACKGROUND: Rhododendron leaf extracts were previously found to exert antimicrobial activities against a range of Gram-positive bacteria. In this study, we investigated which of the extracts with these antimicrobial properties would be best suited for further exploitation. Specifically, the project aims to identify biologically active compounds that affect bacterial but not mammalian cells when applied in medical treatments such as lotions for ectopic application onto skin, or as orally administered drugs. METHODS: Different concentrations of DMSO-dissolved remnants of crude methanol Rhododendron leaf extracts were incubated for 24 h with cultured epidermal keratinocytes (human HaCaT cell line) and epithelial cells of the intestinal mucosa (rat IEC6 cell line) and tested for their cytotoxic potential. In particular, the cytotoxic potencies of the compounds contained in antimicrobial Rhododendron leaf extracts were assessed by quantifying their effects on (i) plasma membrane integrity, (ii) cell viability and proliferation rates, (iii) cellular metabolism, (iv) cytoskeletal architecture, and (v) determining initiation of cell death pathways by morphological and biochemical means. RESULTS: Extracts of almost all Rhododendron species, when applied at 500 µg/mL, were potent in negatively affecting both keratinocytes and intestine epithelial cells, except material from R. hippophaeoides var. hippophaeoides. Extracts of R. minus and R. racemosum were non-toxic towards both mammalian cell types when used at 50 µg/mL, which was equivalent to their minimal inhibitory concentration against bacteria. At this concentration, leaf extracts from three other highly potent antimicrobial Rhododendron species proved non-cytotoxic against one or the other mammalian cell type: Extracts of R. ferrugineum were non-toxic towards IEC6 cells, and extracts of R. rubiginosum as well as R. concinnum did not affect HaCaT cells. In general, keratinocytes proved more resistant than intestine epithelial cells against the treatment with compounds contained in Rhododendron leaf extracts. CONCLUSIONS: We conclude that leaf extracts from highly potent antimicrobial R. minus and R. racemosum are safe to use at 50 µg/mL in 24-h incubations with HaCaT keratinocytes and IEC6 intestine epithelial cells in monolayer cultures. Extracts from R. rubiginosum as well as R. concinnum or R. ferrugineum are applicable to either keratinocytes or intestinal epithelial cells, respectively. Beyond the scope of the current study, further experiments are required to identify the specific compounds contained in those Rhododendron leaf extracts that exert antimicrobial activity while being non-cytotoxic when applied onto human skin or gastrointestinal tract mucosa. Thus, this study supports the notion that detailed phytochemical profiling and compound identification is needed for characterization of the leaf extracts from specific Rhododendron species in order to exploit their components as supplementary agents in antimicrobial phyto-medical treatments.

A complete Holocene record of trematode-bivalve infection and implications for the response of parasitism to climate change.

Increasing global temperature and sea-level rise have led to concern about expansions in the distribution and prevalence of complex-lifecycle parasites (CLPs). Indeed, numerous environmental variables can influence the infectivity and reproductive output of many pathogens. Digenean trematodes are CLPs with intermediate invertebrate and definitive vertebrate hosts. Global warming and sea level rise may affect these hosts to varying degrees, and the effect of increasing temperature on parasite prevalence has proven to be nonlinear and difficult to predict. Projecting the response of parasites to anthropogenic climate change is vital for human health, and a longer term perspective (10(4) y) offered by the subfossil record is necessary to complement the experimental and historical approaches of shorter temporal duration (10(-1) to 10(3) y). We demonstrate, using a high-resolution 9,600-y record of trematode parasite traces in bivalve hosts from the Holocene Pearl River Delta, that prevalence was significantly higher during the earliest stages of sea level rise, significantly lower during the maximum transgression, and statistically indistinguishable in the other stages of sea-level rise and delta progradation. This stratigraphic paleobiological pattern represents the only long-term high-resolution record of pathogen response to global change, is consistent with fossil and recent data from other marine basins, and is instructive regarding the future of disease. We predict an increase in trematode prevalence concurrent with anthropogenic warming and marine transgression, with negative implications for estuarine macrobenthos, marine fisheries, and human health.

Strong coupling of predation intensity and diversity in the Phanerozoic fossil record.

The importance of ecological interactions in driving the evolution of animals has been the focus of intense debate among paleontologists, evolutionary biologists, and macroecologists. To test whether the intensity of such interactions covaries with the secular evolutionary trend in global biodiversity, we compiled a species-level database of predation intensity, as measured by the frequency of common predation traces (drillings and repair scars ranging in age from Ediacaran to Holocene). The results indicate that the frequency of predation traces increased notably by the Ordovician, and not in the mid-Paleozoic as suggested by multiple previous studies. Importantly, these estimates of predation intensity and global diversity of marine metazoans correlate throughout the Phanerozoic fossil record regardless of corrections and methods applied. This concordance may represent (i) an ecological signal: long-term coupling of diversity and predation; (ii) a diversity-driven diffusion of predatory behaviors: an increased probability of more complex predatory strategies to appear at higher diversity levels; or (iii) a spurious concordance in signal capture: an artifact where rare species and less-frequent (e.g., trace-producing) predatory behaviors are both more detectable at times when sampling improves. The coupling of predation and diversity records suggests that macroevolutionary and macroecological patterns share common causative mechanisms that may reflect either historical processes or sampling artifacts.