Horizontal and vertical gradients in sediment nutrients on mudflats in the Shannon estuary,Ireland

Spatial variability in nutrient concentrations in the intertidal sediments and pore waters has been studied along downshore transects and in core profiles at three locations in the Shannon estuary on the west coast of Ireland. The parameters measured were N, as Kjeldahl N, NO₃, NO₂, and NH₃, and P as total P and PO₄ along with a range of other environmental variables such as salinity and sediment organic content. The concentrations of all nutrients varied with season, but winter values were generally low in comparison with polluted mainland european estuaries. There was a great deal of variation in nutrient concentrations along the transects, and coefficients of variability of up to 153% (NH₃), 173% (NO₃), 129% (NO₂) and 117% (PO₄) were found. Overall, there was little evidence of any trends in concentration in any of the nutrients from the top to the bottom of the transects, although it was occasionally possible to link particular instances to local conditions such as the presence of the channel or a stream. Sediment core profiles showed typical patterns, with NO₃ concentrations for example being highest in surface sediments, while NH₃ and PO₄ concentrations increased with depth. Rather surprisingly perhaps, NO₃ could still be detected on occasion at depths of up to 20 cm, well below the Redox Potential Discontinuity (RPD) and the limit of oxygen penetration which oxygen microelectrodes had measured as being within a few mm of the surface. This was ascribed to the activities of the macrofauna, in that the oxidised sediment which lined the burrows could clearly be seen in some cores. This study not only shows that nutrient distributions along estuarine gradients are linked to physicochemical factors such as oxygenation and freshwater/marine influence, but also that sediment instability, through random physical events such as storms, and macrofaunal activity play an important role and that these latter factors deserve closer attention.     

Differentiation of Lactobacillus sanfranciscensis strains by randomly amplified polymorphic DNA and pulsed-field gel electrophoresis

Genetic diversity of Lactobacillus sanfranciscensis strains isolated from naturally fermented sourdoughs of different origin was evaluated by using randomly amplified polymorphic DNA (RAPD). Computer-assisted comparison of the RAPD patterns revealed a clear separation of L. sanfranciscensis from other obligately heterofermentative Lactobacillus species closely related or normally present in sourdough. Six clusters, five of them constituted by strains of the same origin, were recognized at a similarity level of 63%. Pulsed-field gel electrophoresis (PFGE) results on strains chosen as representative were generally in good agreement with the grouping obtained by RAPD. Both techniques showed a high degree of discriminatory power and indicated the existence of a remarkable genetic polymorphism within the species. Furthermore, the chromosome size of L. sanfranciscensis was estimated by PFGE to be about 1.4 Mb.     

Identifying differentially expressed genes in meta-analysis via Bayesian model-based clustering

A Bayesian model-based clustering approach is proposed for identifying differentially expressed genes in meta-analysis. A Bayesian hierarchical model is used as a scientific tool for combining information from different studies, and a mixture prior is used to separate differentially expressed genes from non-differentially expressed genes. Posterior estimation of the parameters and missing observations are done by using a simple Markov chain Monte Carlo method. From the estimated mixture model, useful measure of significance of a test such as the Bayesian false discovery rate (FDR), the local FDR (Efron et al., 2001), and the integration-driven discovery rate (IDR; Choi et al., 2003) can be easily computed. The model-based approach is also compared with commonly used permutation methods, and it is shown that the model-based approach is superior to the permutation methods when there are excessive under-expressed genes compared to over-expressed genes or vice versa. The proposed method is applied to four publicly available prostate cancer gene expression data sets and simulated data sets.     

High-school students in university research labs? Implementing an outreach model based on the ‘science as inquiry’ approach

In this study we designed, implemented, and evaluated an outreach programme for high-school biology students rooted in the ‘science as inquiry’ approach. Accordingly, students learn about science from experts in the field, as well as through in-class exposure to the history and philosophy of science. Our sample consisted of 11th graders (n?=?497), ages 16–17, attending advanced biology classes. Our goal was to determine whether this programme had a significant effect on students’ understanding of the ‘nature of science’ (NOS) and on their attitudes towards science. Using a controlled pre-post research design, we asked participants to complete a Likert-like questionnaire. Also, we conducted post-programme semi-structured interviews with 35 of the participants. Results show that completion of the programme significantly enhanced participants’ NOS understanding and improved their attitudes towards science. Participants expressed a deep level of NOS understanding and explicitly stated that the field visits to experts’ labs had changed their attitude towards science. We believe that our outreach programme can be adapted for teaching other sciences and for societies worldwide, as long as there is access to university laboratories and researchers willing to interact with young citizens and potential future scientists.     

Robust regression for clustered data with application to binary responses

Generalized estimating equations (GEE) can be highly influenced by the presence of unusual data points. A generalization of the GEE procedure, which yields parameter estimates and fitted values that are resistant to influential data, is introduced. Resistant generalized estimating equations (REGEE) include weights in the estimating equations to downweight influential observations or clusters. Influential observations are downweighted according to their leverage or residual in an example of correlated binary regression applied to 137 urinary incontinent elderly patients from 38 medical practices.     

Assessing the concept of controlled experiments in science teachers

Biology teachers, attending a post-graduate training course, were given a written test in which they had to identify the controlled set-up in two different experiments. A teaching strategy was designed to help the subjects to construct and consolidate an understanding of controlled experiments, in line with scientific inquiry methods, by following the process of hypothesis, formulation and testing.     

A Comparative Study on the Power of van Lieshout and Baddeley's J-Function

Summary functions such as the empty space function F and the nearest neighbour distance distribution function G are often used as test statistics for point patterns. Van Lieshout and Baddeley recently proposed an alternative statistic, the J-function, which is defined as J = (1 — G)/(1 — F). Theoretical advantages of the J-function over the F- and G-statistics are that it measures the type, strength and range of interaction, and that it can be evaluated explicitly for a larger class of models. In this simulation study we investigate empirically how the power of tests based on J compares to that of tests based on F and G.     

Structure-activity studies of a macrocyclic peptide inhibitor of histone lysine demethylase 4A

The combination of genetic code reprogramming and mRNA display is a powerful approach for the identification of macrocyclic peptides with high affinities to a target of interest. We have previously used such an approach to identify a potent inhibitor (CP2) of the human KDM4A and KDM4C lysine demethylases; important regulators of gene expression. In the present study, we have used genetic code reprogramming to synthesise very high diversity focused libraries (>10¹² compounds) based on CP2 and, through affinity screening, used these to delineate the structure activity relationship of CP2 binding to KDM4A. In the course of these experiments we identified a CP2 analogue (CP2f-7) with ～4-fold greater activity than CP2 in in vitro inhibition assays. This work will facilitate the development of more potent, selective inhibitors of lysine demethylases.     

干细胞与再生医学技术发展态势研究

20世纪以来,干细胞与再生医学技术一直是国际生物医学领域的热点前沿之一,它为保障人类生命健康、改善人类生存质量和延长人类寿命发挥不可替代的巨大作用。因此,美国、欧洲国家、日本和中国等科技大国均将该领域纳入了国家科研与产业发展的重点战略中,并通过专项扶持、政策补贴、立法保障等方式激励该领域的创新发展。通过对近年来国际科技战略和科技研发态势的梳理分析,发现该领域的国际战略布局规律,揭示我国在该领域的领先优势与弱点,为我国未来干细胞与再生医学技术发展提出相关参考建议。