Disentangling complex fine‐scale ecological patterns by path modelling using GLMM and GIS

Question: How can statistical modelling tools (GLMM) and GIS be used as an aid in understanding complex ecological patterns? This general question was approached by using bryophyte demography data as an example. More specifically, we asked what is the contribution of terrain shape to explaining the performance and fate of plant individuals, controlling for all other known relationships? Location: Norway. Methods: Information on demography was obtained for 140 populations of the perennial clonal bryophyte Hylocomium splendens in Norway spruce forests during an 11‐year period (1992‐2002). Performance (size and branching pattern) was recorded for mature segments and fate was recorded for growing points. Positions of each of the more than 30 000 recorded bryophyte ramets were coupled with (micro‐) topographic characteristics (slope and convexity) derived from fine‐scale digital elevation models in a GIS framework. Carefully planned sequences of generalised linear mixed models (GLMM) were performed to test predictions from a conceptual path model. Results: We demonstrate strong dependence of size on branching, fate and on vertical position in the bryophyte carpet, and an effect of vertical position on branching pattern. Micro‐topography contributed to explaining plant performance by four different mechanisms: (1) a direct effect of slope on the segment's vertical position in the carpet; (2‐3) direct effects of both slope and convexity on fates of individuals via controls on risk of burial; and (4) an indirect effect of convexity on branching pattern via a direct effect on size. No indication of a direct effect of terrain on branching was found. Conclusions: Our study exemplifies the usefulness of GLMM for disentangling complex ecological relationships. Specifically, we recognise micro‐topography as a potentially important factor for plant demography in general and for performance and fate of individuals in particular.     

Environmental forcing as a main determinant of bloom dynamics of the Chrysochromulina algae

In this paper, we demonstrate that the seasonal dynamics in the abiotic factors, without including seasonal changes in the biological relationships, can appropriately account for the seasonal dynamics of Chrysochromulina spp. This is through the analysis of data on the population dynamics of Chrysochromulina spp. off southern Norway that is evaluated in relation to environmental factors and season by the analyses of 12 year monthly time-series. Chrysochromulina spp. abundance, nutrient concentrations, hydrographical properties, as well as current and wind data were analysed on a monthly scale by means of autoregressive moving average models, principal component analyses (PCA), and linear and nonlinear regression models. Seasonal development of the Chrysochromulina assemblage was well predicted from regression models forced with two PCA components representing seasonal variation in nutrient and chlorophyll a levels and ratios, inflow of North Seawater to the Skagerrak and northeasterly wind along the Norwegian coast. Assuming these to be general results, we might hypothesis that marine algal communities are governed by seasonally varying abiotic factors to a large extent.     

Microtubule-associated nuclear envelope proteins in interphase and mitosis

The LINC (linker of nucleoskeleton and cytoskeleton) complex forms a transcisternal bridge across the NE (nuclear envelope) that connects the cytoskeleton with the nuclear interior. This enables some proteins of the NE to communicate with the centrosome and the microtubule cytoskeleton. The position of the centrosome relative to the NE is of vital importance for many cell functions, such as cell migration and division, and centrosomal dislocation is a frequent phenotype in laminopathic disorders. Also in mitosis, a small group of transmembrane NE proteins associate with microtubules when they concentrate in a specific membrane domain associated with the mitotic spindle. The present review discusses structural and functional aspects of microtubule association with NE proteins and how this association may be maintained over the cell cycle.     

An institutional analysis of EPD programs and a global PCR registry

Purpose

A Product Category Rules (PCR) document specifies the quantification method and communication format of environmental impacts of a product category. To ensure neutrality and credibility of quantitative environmental information, the development of PCR documents is defined in ISO 14025. Hence, the rules are preconditions for comparative considerations and modular application of information entities and Environmental Product Declarations (EPD). However, with the growing number of EPD programs, the producers, purchasers, and consumers feel increasingly alienated in relation to the validity and legitimacy of the environmental information presented by EPDs. This results in a need for enhanced transparency of PCR development and EPD program compatibility. This article offers navigational assistance in this respect.

Methods

To identify harmonization potential, we compare PCR development regarding two aspects: quantitatively by mapping existing PCR and EPD documents, and qualitatively by comparing existing institutional structures with normative guidance. Information was gathered through an internet search and through direct correspondence with program operators.

Results and discussion

We identified 27 programs, 556 PCR documents, and 3614 EPD declarations (May 2013). There were significant differences in activity level between programs and sectors. Furthermore, the institutional structures differ widely from each other and from normative guidance on PCR development.

Conclusions

This first global PCR register guides practitioners in the search for PCR documents. The analysis of program institutional structures for PCR development and EPD verification indicates the involvement of different stakeholders on Type III environmental declarations. Regarding PCR compatibility and newly released guidance documents from the European Commission and the PCR Guidance Development Initiative, we recommend that operators (1) settle on a common (sector) categorization system, (2) implement a Stakeholder Identification Worksheet, (3) consider the mandatory involvement of consumer and environmental interests in the PCR review panel, (4) require PCR reviewers to declare potential conflicts of interest, and (5) consider installing mandatory third party verification of declarations for any external use.     

Outlier SNP markers reveal fine‐scale genetic structuring across European hake populations (Merluccius merluccius)

Shallow population structure is generally reported for most marine fish and explained as a consequence of high dispersal, connectivity and large population size. Targeted gene analyses and more recently genome‐wide studies have challenged such view, suggesting that adaptive divergence might occur even when neutral markers provide genetic homogeneity across populations. Here, 381 SNPs located in transcribed regions were used to assess large‐ and fine‐scale population structure in the European hake (Merluccius merluccius), a widely distributed demersal species of high priority for the European fishery. Analysis of 850 individuals from 19 locations across the entire distribution range showed evidence for several outlier loci, with significantly higher resolving power. While 299 putatively neutral SNPs confirmed the genetic break between basins (F_CT = 0.016) and weak differentiation within basins, outlier loci revealed a dramatic divergence between Atlantic and Mediterranean populations (F_CT range 0.275–0.705) and fine‐scale significant population structure. Outlier loci separated North Sea and Northern Portugal populations from all other Atlantic samples and revealed a strong differentiation among Western, Central and Eastern Mediterranean geographical samples. Significant correlation of allele frequencies at outlier loci with seawater surface temperature and salinity supported the hypothesis that populations might be adapted to local conditions. Such evidence highlights the importance of integrating information from neutral and adaptive evolutionary patterns towards a better assessment of genetic diversity. Accordingly, the generated outlier SNP data could be used for tackling illegal practices in hake fishing and commercialization as well as to develop explicit spatial models for defining management units and stock boundaries.     

A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions

Identification of three-dimensional (3D) interactions between regulatory elements across the genome is crucial to unravel the complex regulatory machinery that orchestrates proliferation and differentiation of cells. ChIA-PET is a novel method to identify such interactions, where physical contacts between regions bound by a specific protein are quantified using next-generation sequencing. However, determining the significance of the observed interaction frequencies in such datasets is challenging, and few methods have been proposed. Despite the fact that regions that are close in linear genomic distance have a much higher tendency to interact by chance, no methods to date are capable of taking such dependency into account. Here, we propose a statistical model taking into account the genomic distance relationship, as well as the general propensity of anchors to be involved in contacts overall. Using both real and simulated data, we show that the previously proposed statistical test, based on Fisher''s exact test, leads to invalid results when data are dependent on genomic distance. We also evaluate our method on previously validated cell-line specific and constitutive 3D interactions, and show that relevant interactions are significant, while avoiding over-estimating the significance of short nearby interactions.     

Mitochondrial DNA sequence variation in whiting Merlangius merlangus in the North East Atlantic

Genetic variation in whiting Merlangius merlangus was examined using a 621 base pair fragment of the cytochrome c oxidase subunit I mitochondrial gene in 138 individuals sampled from Iceland, Norway and the North Sea. In total 10 segregating sites were observed defining 12 haplotypes. Three of the haplotypes were found at high frequencies (>5 %). All but one mutations were synonymous and the nonsynonymous mutation was found as a singleton. This suggests weak or no natural selection acting on the observed polymorphism making it useful for examination of population breeding structure. The genetic variation suggests that the whiting population has undergone sudden expansion in the past, estimated to have started 70 Kyr ago, during the last glacial period. Spatial genetic analysis reveals genetic uniformity across long geographic distances suggesting high level of gene flow. The long pelagic phase at early age, allowing for high dispersal rate, may partly explain the observed pattern.     

Breast cancer stromal elastosis is associated with mammography screening detection,low Ki67 expression and favourable prognosis in a population-based study

Squamous cell carcinomas (SCCs) are uncommon, high-grade tumors, predominantly composed of round cells in the prepuce. The aim of this study is to better define the clinicopathologic features of this neoplasm. We conducted cyto-histopathologic analysis on the manifestations of the prepuce SCC by H &; E staining in a terrier mix dog. Grossly, tumor was large, multiple erythematous patch, and ulcerated masses frequently affecting the prepuce and deeply invading to distal prepuce out from the ventro-lateral of penis and the tumor covered by a necrotic discharge. Cytological evaluation of fine-needle aspirates from the cutaneous mass from the prepuce comprised of round nuclei, coarse chromatin pattern, distinct nucleoli and nuclear pleomorphism. Furthermore, the neoplastic cells were pleomorphic, round to caudate in shape, exhibiting prominent anisokaryosis and anisocytosis with rare mitotic features. Microscopically, the lesions were predominantly composed of atypical round cells disposed in interlacing fascicles. Frequent findings include keratin formation, horn pearls, mitoses and cellular atypia. The cells showed distinct borders, ranged from polygonal to round or elongate and had moderate amounts of eosinophilic cytoplasm. The histopathologic features coupled with the cytopathology findings led to a diagnosis of squamous cell carcinoma. To the authors’ knowledge, this is the first time that multiple erythematous plaques have undergone malignant transformation in a terrier mix dog. The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/5748771971272873     

The influence of carbon sources and morphology on nystatin production by Streptomyces noursei

Carbon source nutrition and morphology were examined during cell growth and production of nystatin by Streptomyces noursei ATCC 11455. This strain was able to utilise glucose, fructose, glycerol and soluble starch for cell growth, but failed to grow on media supplemented with galactose, xylose, maltose, sucrose, lactose and raffinose. Utilisation of glucose had a negative influence on production of nystatin independent of the specific growth rate when phosphate and ammonium was in excess. Consumption of carbon sources was related to the specific growth rate. S. noursei ATCC 11455 formed mainly mycelial clumps during cultivation, while pellet growth dominated the culture of the morphologically altered high producing mutant S. noursei NG7.19. When the pellet size increased above a critical size, cell growth and nystatin production terminated. Fluorescent staining of hyphae revealed that this coincided with loss of activity inside the core of the pellets, probably due to diffusion limitation of oxygen or other nutrients.     

Effect of dietary vegetable oils on the fatty acid profile of plasma lipoproteins in dairy cows

The aim of this study was to elucidate the effect of dietary supplementation of soybean oil (SO) and hydrogenated palm oil (HPO) on the transport of fatty acids (FA) within plasma lipoproteins in lactating and non-lactating cows. Three lactating and three non-lactating Holstein cows were used in two different 3 × 3 Latin square experiments that included three periods of 21 d. Dietary treatments for lactating cows consisted of a basal diet (control; no fat supplement) and fat-supplemented diets containing SO (500 g/d per cow) or HPO (500 g/d per cow). For non-lactating cows, dietary treatments consisted of a basal diet (control; no fat supplement) and fat-supplemented diets containing SO (170 g/d per cow) or HPO (170 g/d per cow). Compared with the control and SO diet, HPO addition increased (p < 0.05) the concentration of C16:0, C18:0, C18:2cis-9,12, C18:3cis-9,12,15 and total saturated and polyunsaturated FA in the plasma of lactating cows. In non-lactating cows, the SO addition increased the plasma concentration of C18:1trans-11. In lactating cows, concentrations of C16:0, C18:0 and total saturated FA were increased (p < 0.05) by HPO addition in the high-density lipoprotein (HDL). Total saturated FA were increased (p < 0.05) by HPO in very-low-density lipoprotein (VLDL). In non-lactating cows, the concentration of C18:0 was increased (p < 0.05) by HPO in HDL, whereas C18:1trans-11 was increased (p < 0.05) by SO in the low-density lipoprotein. Overall, it was found that distribution and transport of FA within the bovine plasma lipoproteins may be influenced by chain length and degree of unsaturation of dietary lipids. Also, the distribution of individual FA isomers such as C18:1trans-11 and C18:2cis-9,trans-11 may vary depending on the physiological state of the cow (lactating or non-lactating), and are increased in plasma (lactating cows) and the HDL (non-lactating cows) when cows are fed SO.