Structural evolution drives diversification of the large LRR-RLK gene family

Cells are continuously exposed to chemical signals that they must discriminate between and respond to appropriately. In embryophytes, the leucine‐rich repeat receptor‐like kinases (LRR‐RLKs) are signal receptors critical in development and defense. LRR‐RLKs have diversified to hundreds of genes in many plant genomes. Although intensively studied, a well‐resolved LRR‐RLK gene tree has remained elusive. To resolve the LRR‐RLK gene tree, we developed an improved gene discovery method based on iterative hidden Markov model searching and phylogenetic inference. We used this method to infer complete gene trees for each of the LRR‐RLK subclades and reconstructed the deepest nodes of the full gene family. We discovered that the LRR‐RLK gene family is even larger than previously thought, and that protein domain gains and losses are prevalent. These structural modifications, some of which likely predate embryophyte diversification, led to misclassification of some LRR‐RLK variants as members of other gene families. Our work corrects this misclassification. Our results reveal ongoing structural evolution generating novel LRR‐RLK genes. These new genes are raw material for the diversification of signaling in development and defense. Our methods also enable phylogenetic reconstruction in any large gene family

Development of in/outflow boundary conditions for MPM simulation of uniform and non-uniform open channel flows

This paper describes the development and application of inflow and outflow boundary conditions (BCs) for the material point method (MPM) in order to simulate fluid flow problems. This corresponds to velocity and pressure controlled BCs. Due to the coupled Lagrangian and Eulerian description of the fluid motion in MPM it is necessary to add and remove material points, with appropriate kinematic properties, to and from the computational domain. The newly-developed BCs have been used to simulate uniform open channel flow and the phenomenon of free overfall in open channels, which is transient conditions leading to non-uniform flow due to a sudden bed level drop. It is shown that the numerical results predict well the flow geometry including end depth ratio, pressure distribution and accelerations, therefore the velocities and displacements.Fundamental Research Funds for the Central Universities (2017B12214) of the Ministry of Education of China, NWO Project MPM-FLOW: Understanding flowslides in flood defences (Grant No. 13889

Pyrolysis activation energy of cellulosic fibres investigated by a method derived from the first order global model

The pyrolysis kinetics of cellulosic fibres, a natural cotton yarn (NCY) and a mercerized cotton yarn (MCY), has been explored with a modified first order global analysis method (FOG), via a series of non-isothermal experiments, using thermogravimetric analysis (TGA). The modified FOG analysis routine was developed to overcome discrepancy in heating rate and the difference between exact results and approximations in integrals. The intrinsic pyrolysis activation energy, with temperature range tending to zero, was found to be independent of heating rate and approximation used, giving average values of 153 ± 2 kJ/mol for NCY and 192 ± 7 kJ/mol for MCY. This proves the applicability of the reported analysis routine under the conducted TGA measurements. The reasons for different values were hypothesized to be the difference in chemical composition and crystalline structure. The findings provide a new approach in the investigation on pyrolysis kinetics of biomass and factors impacting their pyrolytic behaviour

Three methods to measure the dissolution activation energy of cellulosic fibres using time-temperature superposition

Three methods are established to explore the dissolution kinetics of cellulosic fibres in the ionic liquid 1-ethyl-3-methyl-imidazolium acetate ([C2mim][OAc]), based on optical microscopic images of processed dried cellulose and cellulose hydrogels. The dissolution process for different times at various temperatures was analysed using time-temperature superposition, and from this the dissolution was found to follow an Arrhenius behaviour. Three values for the activation energy of dissolution were obtained from three different quantifying methods; these were found to agree, giving an average value of 73 ± 2 kJ/mol. A new method is developed to determine the swelling ratio of different regions of the processed cellulose samples, along with the different water volume fractions contained therein. The findings will be of interest to researchers making all cellulose composites and those studying the dissolution of cellulose by ionic liquids

The NIH-NIAID Schistosomiasis Resource Center

A bench scientist studying schistosomiasis must make a large commitment to maintain the parasite's life cycle, which necessarily involves a mammalian (definitive) host and the appropriate species of snail (intermediate host). This is often a difficult and expensive commitment to make, especially in the face of ever-tightening funds for tropical disease research. In addition to funding concerns, investigators usually face additional problems in the allocation of sufficient lab space to this effort (especially for snail rearing) and the limited availability of personnel experienced with life cycle upkeep. These problems can be especially daunting for the new investigator entering the field. Over 40 years ago, the National Institutes of Health–National Institute of Allergy and Infectious Diseases (NIH-NIAID) had the foresight to establish a resource from which investigators could obtain various schistosome life stages without having to expend the effort and funds necessary to maintain the entire life cycle on their own. This centralized resource translated into cost savings to both NIH-NIAID and to principal investigators by freeing up personnel costs on grants and allowing investigators to divert more funds to targeted research goals. Many investigators, especially those new to the field of tropical medicine, are only vaguely, if at all, aware of the scope of materials and support provided by this resource. This review is intended to help remedy that situation. Following a short history of the contract, we will give a brief description of the schistosome species provided, provide an estimate of the impact the resource has had on the research community, and describe some new additions and potential benefits the resource center might have for the ever-changing research interests of investigators

Conceptualising the Global Forest Response to Liana Proliferation

Lianas are woody vines, rooted in the soil, and supported physically by trees. Lianas contribute to forest ecosystem functioning globally, but especially in the tropics and subtropics. However, prolific liana growth following heavy disturbance frequently affects subsequent recovery of forest tree diversity, biomass, structure, and function. Understanding this forest liana dynamic, and its sensitivity to climate and anthropogenic forces, is essential for worldwide forest restoration and climate change mitigation. Here, we synthesise the evidence for both positive and negative effects of lianas on forests and propose a framework that outlines the expected global response of forests to disturbance-induced liana proliferation. Emerging evidence suggests that lianas play a major role in both facilitating and delaying forest recovery following disturbance. At low levels of disturbance and/or where environmental conditions favour tree growth, lianas can facilitate forest recovery by protecting trees from extreme weather, fire, weed invasion and herbivory. However, under conditions where lianas proliferate beyond critical thresholds, positive feedbacks are expected to induce and sustain liana-dominated forest states that can endure for decades or even longer. We conceptualise alternative classes of forest recovery response to disturbance and describe measurement and modelling of liana thresholds.We identify four essential challenges for global change science relating to lianas: (1) incorporation of lianas and sapling stems into forest monitoring and tree stand measurements worldwide; (2) long-term experiments to determine variation in liana-tree competition, and potential drivers across forest successional gradients; (3) identification and prediction of liana thresholds and other alternative forest recovery response classes; and (4) dynamicmechanisticmodelling of forest recovery to determine regional and global variation within and among different recovery response classes, in relation to variation in potential drivers, liana feedbacks and their interactions. Addressing these challenges will determine the importance of lianas in shaping regional and global forest composition, recovery and dynamics

Stops making sense: translational trade-offs and stop codon reassignment

Background Efficient gene expression involves a trade-off between (i) premature termination of protein synthesis; and (ii) readthrough, where the ribosome fails to dissociate at the terminal stop. Sense codons that are similar in sequence to stop codons are more susceptible to nonsense mutation, and are also likely to be more susceptible to transcriptional or translational errors causing premature termination. We therefore expect this trade-off to be influenced by the number of stop codons in the genetic code. Although genetic codes are highly constrained, stop codon number appears to be their most volatile feature. Results In the human genome, codons readily mutable to stops are underrepresented in coding sequences. We construct a simple mathematical model based on the relative likelihoods of premature termination and readthrough. When readthrough occurs, the resultant protein has a tail of amino acid residues incorrectly added to the C-terminus. Our results depend strongly on the number of stop codons in the genetic code. When the code has more stop codons, premature termination is relatively more likely, particularly for longer genes. When the code has fewer stop codons, the length of the tail added by readthrough will, on average, be longer, and thus more deleterious. Comparative analysis of taxa with a range of stop codon numbers suggests that genomes whose code includes more stop codons have shorter coding sequences. Conclusions We suggest that the differing trade-offs presented by alternative genetic codes may result in differences in genome structure. More speculatively, multiple stop codons may mitigate readthrough, counteracting the disadvantage of a higher rate of nonsense mutation. This could help explain the puzzling overrepresentation of stop codons in the canonical genetic code and most variants

Phenotypic and genotypic monitoring of Schistosoma mansoni in Tanzanian schoolchildren five years into a preventative chemotherapy national control programme

We conducted combined in vitro PZQ efficacy testing with population genetic analyses of S. mansoni collected from children from two schools in 2010, five years after the introduction of a National Control Programme. Children at one school had received four annual PZQ treatments and the other school had received two mass treatments in total. We compared genetic differentiation, indices of genetic diversity, and estimated adult worm burden from parasites collected in 2010 with samples collected in 2005 (before the control programme began) and in 2006 (six months after the first PZQ treatment). Using 2010 larval samples, we also compared the genetic similarity of those with high and low in vitro sensitivity to PZQ

Sub-Sets of Cancer Stem Cells Differ Intrinsically in Their Patterns of Oxygen Metabolism

PMCID: PMC3640080This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited