Inter- and intra-observer variation in phytolith morphometry.

BACKGROUND: Archaeobotanists and palaeoecologists extensively use geometric morphometrics to identify plant opal phytoliths. Particularly when applied to assemblages of phytoliths from concentrations retrieved from closed contexts, morphometric data from archaeological phytoliths compared with similar data from reference material may allow taxonomic attribution. Observer variation is one aspect of phytolith morphometry that has received little attention but may be an important source of error, and hence cause of potential misidentification of plant remains. SCOPE: To investigate inter- and intra-observer variation in phytolith morphometry, eight researchers (observers) from different laboratories measured 50 samples each from three phytolith morphotypes, Bilobate, Bulliform flabellate and Elongate dendritic, three times, under the auspices of the International Committee for Phytolith Morphometrics (ICPM). METHODS: Data for 17 size and shape variables were collected for each phytolith by manually digitising a phytolith outline (mask) from a photograph, followed by measurement of the mask with open-source morphometric software. KEY RESULTS: Inter-observer variation ranged from 0 to 23% difference from the mean of all observers. Intra-observer variation ranged from 0 to 9% difference from the mean of individual observers per week. Inter- and intra-observer variation was generally higher among inexperienced researchers. CONCLUSIONS: Scaling errors were a major cause of variation and occurred more with less experienced researchers, which is likely related to familiarity with data collection. The results indicate that inter- and intra-observer variation can be substantially reduced by providing clear instructions for and training with the equipment, photo capturing, software, data collection and data cleaning. In this paper, the ICPM provides recommendations to minimise variation.Advances in automatic data collection may eventually reduce inter- and intra-observer variation, but until this is common practice, the ICPM recommends that phytolith morphometric analyses adhere to standardised guidelines to assure that measured phytolith variables are accurate, consistent and comparable between different researchers and laboratories.

Phylogenetic, ecological and intraindividual variability patterns in grass phytolith shape.

BACKGROUND AND AIMS: Grass silica short cell (GSSC) phytoliths appear to be the most reliable source of fossil evidence for tracking the evolutionary history and paleoecology of grasses. In recent years, modern techniques that quantitatively assess phytolith shape variation have widened opportunities for the classification of grass fossil phytoliths. However, phylogenetic, ecological and intraindividual variability patterns in phytolith shape remain largely unexplored. METHODS: The full range of intraindividual phytolith shape variation [3650 two-dimensional (2-D) outlines] from 73 extant grass species, 48 genera, 18 tribes and eight subfamilies (particularly Pooideae) was analysed using geometric morphometric analysis based on semi-landmarks spanning phytolith outlines. KEY RESULTS: The 2-D phytolith shape is mainly driven by deep-time diversification of grass subfamilies. There is distinct phytolith shape variation in early-diverging lineages of Pooideae (Meliceae, Stipeae). The amount of intraindividual variation in phytolith shape varies among species, resulting in a remarkable pattern across grass phylogeny. CONCLUSIONS: The phylogenetic pattern in phytolith shape was successfully revealed by applying geometric morphometrics to 2-D phytolith shape outlines, strengthening the potential of phytoliths to track the evolutionary history and paleoecology of grasses. Geometric morphometrics of 2-D phytolith shape is an excellent tool for analysis requiring large numbers of phytolith outlines, making it useful for quantitative palaeoecological reconstruction.

Inter- and intraspecific variation in grass phytolith shape and size: a geometric morphometrics perspective.

BACKGROUND AND AIMS: The relative contributions of inter- and intraspecific variation to phytolith shape and size have only been investigated in a limited number of studies. However, a detailed understanding of phytolith variation patterns among populations or even within a single plant specimen is of key importance for the correct taxonomic identification of grass taxa in fossil samples and for the reconstruction of vegetation and environmental conditions in the past. In this study, we used geometric morphometric analysis for the quantification of different sources of phytolith shape and size variation. METHODS: We used landmark-based geometric morphometric methods for the analysis of phytolith shapes in two extant grass species (Brachypodium pinnatum and B. sylvaticum). For each species, 1200 phytoliths were analysed from 12 leaves originating from six plants growing in three populations. Phytolith shape and size data were subjected to multivariate Procrustes analysis of variance (ANOVA), multivariate regression, principal component analysis and linear discriminant analysis. KEY RESULTS: Interspecific variation largely outweighed intraspecific variation with respect to phytolith shape. Individual phytolith shapes were classified with 83 % accuracy into their respective species. Conversely, variation in phytolith shapes within species but among populations, possibly related to environmental heterogeneity, was comparatively low. CONCLUSIONS: Our results imply that phytolith shape relatively closely corresponds to the taxonomic identity of closely related grass species. Moreover, our methodological approach, applied here in phytolith analysis for the first time, enabled the quantification and separation of variation that is not related to species discrimination. Our findings strengthen the role of grass phytoliths in the reconstruction of past vegetation dynamics.

Long-term exposure to very low doses of bisphenol S affects female reproduction.

Bisphenols belong to the endocrine disruptors, affecting reproduction even in extremely low doses. Bisphenol S (BPS) has become widely used as a substitute for the earlier-used bisphenol A; however, its harmlessness is questionable. The aim of this study was to evaluate the effect of BPS on folliculogenesis and oocyte quality after in vivo exposure to low doses of BPS. Four-week-old ICR females (n = 16 in each experimental group) were exposed to vehicle control (VC), BPS1 (0.001 ng BPS.g/bw/day), BPS2 (0.1 ng.g/bw/day), BPS3 (10 ng.g/bw/day) and BPS4 (100 ng.g/bw/day) for 4 weeks. Ovaries were subjected to stereology and nano liquid chromatography-mass spectrometry (LC/MS). Simultaneously, metaphase II oocytes were obtained after pregnant mare serum gonadotrophin and human chorionic gonadotrophin administration, followed by immunostaining. In particular, mating and two-cell embryo flushing were performed. We observed that BPS decreases the amount of ovarian follicles and BPS2 (0.1 ng.g/bw/day) affects the volume of antral follicles. Accordingly, ovarian proteome is affected after BPS2 treatment. While BPS2 dosing results mainly in cytoskeletal damage in matured oocytes, the effects of BPS3 and BPS4 seem to be due instead to epigenetic alterations in oocytes. Arguably, these changes lead to observed affection of in vivo fertilization rate after BPS3 and BPS4 treatment. BPS significantly affects female reproduction astoundingly in extremely low doses. These findings underline the necessity to assess the risk of ongoing BPS exposure for public health.

Involvement of K+ATP and Ca2+ channels in hydrogen sulfide-suppressed ageing of porcine oocytes.

BACKGROUND: Hydrogen sulfide has been shown to improve the quality of oocytes destined for in vitro fertilization. Although hydrogen sulfide is capable of modulating ion channel activity in somatic cells, the role of hydrogen sulfide in gametes and embryos remains unknown. Our observations confirmed the hypothesis that the KATP and L-type Ca2+ ion channels play roles in porcine oocyte ageing and revealed a plausible contribution of hydrogen sulfide to the modulation of ion channel activity. RESULTS: We confirmed the benefits of the activation and suppression of the KATP and L-type Ca2+ ion channels, respectively, for the preservation of oocyte quality. CONCLUSIONS: Our experiments identified hydrogen sulfide as promoting the desired ion channel activity, with the capacity to protect porcine oocytes against cell death. Further experiments are needed to determine the exact mechanism of hydrogen sulfide in gametes and embryos.

Endogenously produced hydrogen sulfide is involved in porcine oocyte maturation in vitro.

Hydrogen sulfide, one of three known gasotransmitters, is involved in physiological processes, including reproductive functions. Oocyte maturation and surrounding cumulus cell expansion play an essential role in female reproduction and subsequent embryonic development. Although the positive effects of exogenous hydrogen sulfide on maturing oocytes are well known, the role of endogenous hydrogen sulfide, which is physiologically released by enzymes, has not yet been described in oocytes. In this study, we observed the presence of Cystathionine ß-Synthase (CBS), Cystathionine γ-Lyase (CTH) and 3-Mercaptopyruvate Sulfurtransferase (3-MPST), hydrogen sulfide-releasing enzymes, in porcine oocytes. Endogenous hydrogen sulfide production was detected in immature and matured oocytes as well as its requirement for meiotic maturation. Individual hydrogen sulfide-releasing enzymes seem to be capable of substituting for each other in hydrogen sulfide production. However, meiosis suppression by inhibition of all hydrogen sulfide-releasing enzymes is not irreversible and this effect is a result of M-Phase/Maturation Promoting Factor (MPF) and Mitogen-Activated Protein Kinase (MAPK) activity inhibition. Futhermore, cumulus expansion expressed by hyaluronic acid (HA) production is affected by the inhibition of hydrogen sulfide production. Moreover, quality changes of the expanded cumuli are indicated. These results demonstrate hydrogen sulfide involvement in oocyte maturation as well as cumulus expansion. As such, hydrogen sulfide appears to be an important cell messenger during mammalian oocyte meiosis and adequate cumulus expansion.

Plant trait and vegetation data along a 1314 m elevation gradient with fire history in Puna grasslands, Perú.

Alpine grassland vegetation supports globally important biodiversity and ecosystems that are increasingly threatened by climate warming and other environmental changes. Trait-based approaches can support understanding of vegetation responses to global change drivers and consequences for ecosystem functioning. In six sites along a 1314 m elevational gradient in Puna grasslands in the Peruvian Andes, we collected datasets on vascular plant composition, plant functional traits, biomass, ecosystem fluxes, and climate data over three years. The data were collected in the wet and dry season and from plots with different fire histories. We selected traits associated with plant resource use, growth, and life history strategies (leaf area, leaf dry/wet mass, leaf thickness, specific leaf area, leaf dry matter content, leaf C, N, P content, C and N isotopes). The trait dataset contains 3,665 plant records from 145 taxa, 54,036 trait measurements (increasing the trait data coverage of the regional flora by 420%) covering 14 traits and 121 plant taxa (ca. 40% of which have no previous publicly available trait data) across 33 families.

The bisphenol S contamination level observed in human follicular fluid affects the development of porcine oocytes.

Bisphenol S (BPS), the main replacement for bisphenol A (BPA), is thought to be toxic, but limited information is available on the effects of Bisphenol S on ovarian follicles. In our study, we demonstrated the presence of Bisphenol S in the follicular fluid of women at a concentration of 22.4 nM. The effect of such concentrations of Bisphenol S on oocyte maturation and subsequent embryo development is still unknown. Therefore, we focused on the effect of Bisphenol S on in vitro oocyte maturation, fertilization, and embryo development. As a model, we used porcine oocytes, which show many physiological similarities to human oocytes. Oocytes were exposed to Bisphenol S concentrations similar to those detected in female patients in the ART clinic. We found a decreased ability of oocytes to successfully complete meiotic maturation. Mature oocytes showed an increased frequency of meiotic spindle abnormalities and chromosome misalignment. Alarming associations of oocyte Bisphenol S exposure with the occurrence of aneuploidy and changes in the distribution of mitochondria and mitochondrial proteins were demonstrated for the first time. However, the number and quality of blastocysts derived from oocytes that successfully completed meiotic maturation under the influence of Bisphenol S was not affected.

Acute low-dose bisphenol S exposure affects mouse oocyte quality.

Bisphenol S (BPS) is widely used to replace the known endocrine disruptor BPA in various products. We evaluated the effect of acute in vivo BPS exposure on oocyte quality, simulating the oral route of exposure via oral gavage. Eight-week-old ICR female mice (N = 15 per experimental group) were exposed to vehicle or BPS1-BPS4 (0.001, 0.1, 10, and 100 ng BPS x g bw-1 day-1, respectively) for seven days. Oocytes were isolated and matured in vitro. We observed that BPS exposure increased aberrant spindle formation in mature oocytes and induced DNA damage. Moreover, BPS3 significantly increased the chromatin repressive marks 5-methyl cytosine (5meC) and H3K27me2 in immature oocytes. In the BPS2 group, the increase in 5meC occurred during oocyte maturation. Transcriptome analysis revealed differential expression of early embryonic development transcripts in BPS2-exposed oocytes. These findings indicate that the biological effect of BPS is non-monotonic, affecting oocyte quality even at concentrations that are orders of magnitude below those measured in humans.

Epigenetic and non-epigenetic mode of SIRT1 action during oocyte meiosis progression.

BACKGROUND: SIRT1 histone deacetylase acts on many epigenetic and non-epigenetic targets. It is thought that SIRT1 is involved in oocyte maturation; therefore, the importance of the ooplasmic SIRT1 pool for the further fate of mature oocytes has been strongly suggested. We hypothesised that SIRT1 plays the role of a signalling molecule in mature oocytes through selected epigenetic and non-epigenetic regulation. RESULTS: We observed SIRT1 re-localisation in mature oocytes and its association with spindle microtubules. In mature oocytes, SIRT1 distribution shows a spindle-like pattern, and spindle-specific SIRT1 action decreases α-tubulin acetylation. Based on the observation of the histone code in immature and mature oocytes, we suggest that SIRT1 is mostly predestined for an epigenetic mode of action in the germinal vesicles (GVs) of immature oocytes. Accordingly, BML-278-driven trimethylation of lysine K9 in histone H3 in mature oocytes is considered to be a result of GV epigenetic transformation. CONCLUSIONS: Taken together, our observations point out the dual spatiotemporal SIRT1 action in oocytes, which can be readily switched from the epigenetic to non-epigenetic mode of action depending on the progress of meiosis.