Improving Brassica napus straw for cellulosic ethanol production

It is likely that a combination of process improvement and plant breeding will be needed to make efficient use of biomass. To achieve this, the main bottlenecks to decomposition must be identified and strategies developed to make the process more efficient. Here, the likely process and genotypic variants relevant to saccharification efficiency of Brassica napus straw were investigated using steam explosion. Screening methods were developed to gather suitable data for association mapping. Areas of the B. napus transcriptome related to processing traits were highlighted and assessed. The results show that autocatalytic pretreatments are effective, but commercial cellulases are poorly adapted to hydrolyse Brassica napus straw. Following pretreatment, saccharification was limited by uronic acids and xylose retention, which impeded cellulase performance. Surprisingly, lignin abundance correlated positively with the proportion of rapidly hydrolysable carbohydrate in the pretreated residues. Cultivars with glucan-rich straw did not necessarily produce higher saccharification or ethanol yields. Instead, variations in the non-cellulosic components were the most important differences between cultivars. Smaller scale methods were developed and rational conditions selected for screening In total, seventy-seven straw accessions were processed using four conditions which allowed processing/genotype interactions to be explored. Cultivars that produced more acetic and formic acid using suboptimal pretreatment conditions obtained higher glucose yields. Associated areas of the transcriptome suggested that genes involved in sugar nucleotide provisioning, the endogenous hydrolysis of cellulose and non-cellulosic polysaccharide synthesis were related to saccharification yields. Candidate genes aid in the development of testable hypotheses related to biomass recalcitrance and provides specific targets to conduct experiments, but molecular markers were sensitive to agronomic conditions. Arabidopsis plants deficient in a selection of candidate genes revealed subtle changes in saccharification performance. Result from this work could be the first steps towards deducing the genetic determinants of biomass recalcitrance, paving the way for further research

From Beads on a String to the Pearls of Regulation: the Structure and Dynamics of Chromatin

The assembly of eukaryotic chromatin, and the bearing of its structural organization on the regulation of gene expression, were the central topics of a recent conference organized jointly by the Biochemical Society and Wellcome Trust. A range of talks and poster presentations covered topical aspects of this research field and illuminated recent advances in our understanding of the structure and function of chromatin. The two-day meeting had stimulating presentations complemented with lively discourse and interactions of participants. In the present paper, we summarize the topics presented at the meeting, in particular highlighting subjects that are reviewed in more detail within this issue of Biochemical Society Transactions. The reports bring to life the truly fascinating molecular and structural biology of chromatin

Element-centric clustering comparison unifies overlaps and hierarchy

Clustering is one of the most universal approaches for understanding complex data. A pivotal aspect of clustering analysis is quantitatively comparing clusterings; clustering comparison is the basis for many tasks such as clustering evaluation, consensus clustering, and tracking the temporal evolution of clusters. In particular, the extrinsic evaluation of clustering methods requires comparing the uncovered clusterings to planted clusterings or known metadata. Yet, as we demonstrate, existing clustering comparison measures have critical biases which undermine their usefulness, and no measure accommodates both overlapping and hierarchical clusterings. Here we unify the comparison of disjoint, overlapping, and hierarchically structured clusterings by proposing a new element-centric framework: elements are compared based on the relationships induced by the cluster structure, as opposed to the traditional cluster-centric philosophy. We demonstrate that, in contrast to standard clustering similarity measures, our framework does not suffer from critical biases and naturally provides unique insights into how the clusterings differ. We illustrate the strengths of our framework by revealing new insights into the organization of clusters in two applications: the improved classification of schizophrenia based on the overlapping and hierarchical community structure of fMRI brain networks, and the disentanglement of various social homophily factors in Facebook social networks. The universality of clustering suggests far-reaching impact of our framework throughout all areas of science

Towards a Crowd-Sourced WordNet for Colloquial English

Princeton WordNet is one of the most widely-used resources for natural language processing, but is updated only infrequently and cannot keep up with the fast-changing usage of the English language on social media platforms such as Twitter. The Colloquial WordNet aims to provide an open platform whereby anyone can contribute, while still following the structure of WordNet. Many crowdsourced lexical resources often have significant quality issues, and as such care must be taken in the design of the interface to ensure quality. In this paper, we present the development of a platform that can be opened on the Web to any lexicographer who wishes to contribute to this resource and the lexicographic methodology applied by this interfac

Conditions for the spectrum associated with a leaky wire to contain the interval [− α2/4, ∞)

The method of singular sequences is used to provide a simple and, in some respects, a more general proof of a known spectral result for leaky wires. The method introduces a new concept of asymptotic straightness

Multiple imputation for an incomplete covariate that is a ratio.

We are concerned with multiple imputation of the ratio of two variables, which is to be used as a covariate in a regression analysis. If the numerator and denominator are not missing simultaneously, it seems sensible to make use of the observed variable in the imputation model. One such strategy is to impute missing values for the numerator and denominator, or the log-transformed numerator and denominator, and then calculate the ratio of interest; we call this 'passive' imputation. Alternatively, missing ratio values might be imputed directly, with or without the numerator and/or the denominator in the imputation model; we call this 'active' imputation. In two motivating datasets, one involving body mass index as a covariate and the other involving the ratio of total to high-density lipoprotein cholesterol, we assess the sensitivity of results to the choice of imputation model and, as an alternative, explore fully Bayesian joint models for the outcome and incomplete ratio. Fully Bayesian approaches using Winbugs were unusable in both datasets because of computational problems. In our first dataset, multiple imputation results are similar regardless of the imputation model; in the second, results are sensitive to the choice of imputation model. Sensitivity depends strongly on the coefficient of variation of the ratio's denominator. A simulation study demonstrates that passive imputation without transformation is risky because it can lead to downward bias when the coefficient of variation of the ratio's denominator is larger than about 0.1. Active imputation or passive imputation after log-transformation is preferable

Fine-scale cryogenic sampling of planktonic microbial communities: Application to toxic cyanobacterial blooms

A lack of fine-scale methods for sampling planktonic microbial populations hinders advancement in understanding the responses of these communities to environmental conditions. Current methods provide resolution at scales of centimeters to meters, but not at the millimeter-scale required to understand highly stratified communities. To address this we developed two cryogenic sampling tools to collect spatially-precise samples from aquatic environments while simultaneously preserving the microbial communities. The application of these samplers was examined over a 5.5 h period using a cyanobacterial scum (Microcystis) formed in experimental mesocosms. A cryogenic “surface snatcher” collected a discrete layer (ca. 1 mm) of surface water. Compared to conventional surface sampling methods, the surface snatcher samples contained up to 22-times more microcystin, indicating that less underlying water was incorporated into the sample. A cryogenic “cold finger” sampler was used to collect vertical profiles of the upper 40 mm of the water column. This profiler provided new insights into the fine-scale structure of Microcystis scums, demonstrating that more microcystin-producing Microcystis was contained in the surface 5 mm than the 35 mm below. The results also showed that upregulation of microcystin production was highly localized in the top 2.5 mm of the Microcystis scum. Our results demonstrate that extreme changes in cyanobacterial communities can occur over small distances, and indicate that sampling resolution is of great importance for improving knowledge on cyanobacterial blooms and toxin production. While this study focused on microcystin-producing Microcystis, the cryogenic sampling tools described here could be applied to any planktonic microbial community

Charge-transfer dynamics at the dye-semiconductor interface of photocathodes for solar energy applications

This article describes a comparison between the photophysical properties of two charge-transfer dyes adsorbed onto NiO via two different binding moieties. Transient spectroscopy measurements suggest that the structure of the anchoring group affects both the rate of charge recombination between the dye and NiO surface and the rate of dye regeneration by an iodide/triiodide redox couple. This is consistent with the performance of the dyes in p-type dye sensitised solar cells. A key finding was that the recombination rate differed in presence of the redox couple. This has important implications on the study of electron transfer at dye|semiconductor interfaces for solar energy applications