High-throughput Saccharification Assay for Lignocellulosic Materials

Polysaccharides that make up plant lignocellulosic biomass can be broken down to produce a range of sugars that subsequently can be used in establishing a biorefinery. These raw materials would constitute a new industrial platform, which is both sustainable and carbon neutral, to replace the current dependency on fossil fuel. The recalcitrance to deconstruction observed in lignocellulosic materials is produced by several intrinsic properties of plant cell walls. Crystalline cellulose is embedded in matrix polysaccharides such as xylans and arabinoxylans, and the whole structure is encased by the phenolic polymer lignin, that is also difficult to digest ¹. In order to improve the digestibility of plant materials we need to discover the main bottlenecks for the saccharification of cell walls and also screen mutant and breeding populations to evaluate the variability in saccharification ². These tasks require a high throughput approach and here we present an analytical platform that can perform saccharification analysis in a 96-well plate format. This platform has been developed to allow the screening of lignocellulose digestibility of large populations from varied plant species. We have scaled down the reaction volumes for gentle pretreatment, partial enzymatic hydrolysis and sugar determination, to allow large numbers to be assessed rapidly in an automated system.This automated platform works with milligram amounts of biomass, performing ball milling under controlled conditions to reduce the plant materials to a standardised particle size in a reproducible manner. Once the samples are ground, the automated formatting robot dispenses specified and recorded amounts of material into the corresponding wells of 96 deep well plate (Figure 1). Normally, we dispense the same material into 4 wells to have 4 replicates for analysis. Once the plates are filled with the plant material in the desired layout, they are manually moved to a liquid handling station (Figure 2). In this station the samples are subjected to a mild pretreatment with either dilute acid or alkaline and incubated at temperatures of up to 90°C. The pretreatment solution is subsequently removed and the samples are rinsed with buffer to return them to a suitable pH for hydrolysis. The samples are then incubated with an enzyme mixture for a variable length of time at 50°C. An aliquot is taken from the hydrolyzate and the reducing sugars are automatically determined by the MBTH colorimetric method.     

Restoring freshwater ecosystems in riverine landscapes: the roles of connectivity and recovery processes

1. This paper introduces key messages from a number of papers emanating from the Second International Symposium on Riverine Landscapes held in August 2004 in Sweden, focusing on river restoration. Together these papers provide an overview of the science of river restoration, and point out future research needs. 2. Restoration tests the feasibility of recreating complex ecosystems from more simple and degraded states, thereby presenting a major challenge to ecological science. Therefore, close cooperation between practitioners and scientists would be beneficial, but most river restoration projects are currently performed with little or no scientific involvement. 3. Key messages emanating from this series of papers are: The scope, i.e. the maximum and minimum spatial extent and temporal duration of habitat use, of species targeted for restoration should be acknowledged, so that all relevant stages in their life cycles are considered. Species that have been lost from a stream cannot be assumed to recolonise spontaneously, calling for strategies to ensure the return of target species to be integrated into projects. Possible effects of invasive exotic species also need to be incorporated into project plans, either to minimise the impact of exotics, or to modify the expected outcome of restoration in cases where extirpation of exotics is impractical. 4. Restoration of important ecological processes often implies improving connectivity of the stream. For example, longitudinal and lateral connectivity can be enhanced by restoring fluvial dynamics on flood‐suppressed rivers and by increasing water availability in rivers subject to water diversion or withdrawal, thereby increasing habitat and species diversity. Restoring links between surface and ground water flow enhances vertical connectivity and communities associated with the hyporheic zone. 5. Future restoration schemes should consider where in the catchment to locate projects to make restoration most effective, consider the cumulative effects of many small projects, and evaluate the potential to restore ecosystem processes under highly constrained conditions such as in urban areas. Moreover, restoration projects should be properly monitored to assess whether restoration has been successful, thus enabling adaptive management and learning for the future from both successful and unsuccessful restorations.     

Fundulus as the premier teleost model in environmental biology: opportunities for new insights using genomics

A strong foundation of basic and applied research documents that the estuarine fish Fundulus heteroclitus and related species are unique laboratory and field models for understanding how individuals and populations interact with their environment. In this paper we summarize an extensive body of work examining the adaptive responses of Fundulus species to environmental conditions, and describe how this research has contributed importantly to our understanding of physiology, gene regulation, toxicology, and ecological and evolutionary genetics of teleosts and other vertebrates. These explorations have reached a critical juncture at which advancement is hindered by the lack of genomic resources for these species. We suggest that a more complete genomics toolbox for F. heteroclitus and related species will permit researchers to exploit the power of this model organism to rapidly advance our understanding of fundamental biological and pathological mechanisms among vertebrates, as well as ecological strategies and evolutionary processes common to all living organisms.     

The total cavopulmonary connection resistance: a significant impact on single ventricle hemodynamics at rest and exercise

Little is known about the impact of the total cavopulmonary connection (TCPC) on resting and exercise hemodynamics in a single ventricle (SV) circulation. The aim of this study was to elucidate this mechanism using a lumped parameter model of the SV circulation. Pulmonary vascular resistance (1.96+/-0.80 WU) and systemic vascular resistances (18.4+/-7.2 WU) were obtained from catheterization data on 40 patients with a TCPC. TCPC resistances (0.39+/-0.26 WU) were established using computational fluid dynamic simulations conducted on anatomically accurate three-dimensional models reconstructed from MRI (n=16). These parameters were used in a lumped parameter model of the SV circulation to investigate the impact of TCPC resistance on SV hemodynamics under resting and exercise conditions. A biventricular model was used for comparison. For a biventricular circulation, the cardiac output (CO) dependence on TCPC resistance was negligible (sensitivity=-0.064 l.min(-1).WU(-1)) but not for the SV circulation (sensitivity=-0.88 l.min(-1).WU(-1)). The capacity to increase CO with heart rate was also severely reduced for the SV. At a simulated heart rate of 150 beats/min, the SV patient with the highest resistance (1.08 WU) had a significantly lower increase in CO (20.5%) compared with the SV patient with the lowest resistance (50%) and normal circulation (119%). This was due to the increased afterload (+35%) and decreased preload (-12%) associated with the SV circulation. In conclusion, TCPC resistance has a significant impact on resting hemodynamics and the exercise capacity of patients with a SV physiology.     

Assessing the impact of Ascariasis and Trichuriasis on weight gain using a porcine model

BackgroundInfections with Ascaris lumbricoides and Trichuris trichiura remain significant contributors to the global burden of neglected tropical diseases. Infection may in particular affect child development as they are more likely to be infected with T. trichiura and/or A. lumbricoides and to carry higher worm burdens than adults. Whilst the impact of heavy infections are clear, the effects of moderate infection intensities on the growth and development of children remain elusive. Field studies are confounded by a lack of knowledge of infection history, nutritional status, presence of co-infections and levels of exposure to infective eggs. Therefore, animal models are required. Given the physiological similarities between humans and pigs but also between the helminths that infect them; A. suum and T. suis, growing pigs provide an excellent model to investigate the direct effects of Ascaris spp. and Trichuris spp. on weight gain.Methods and resultsWe employed a trickle infection protocol to mimic natural co-infection to assess the effect of infection intensity, determined by worm count (A. suum) or eggs per gram of faeces (A. suum and T. suis), on weight gain in a large pig population (n = 195) with variable genetic susceptibility. Pig body weights were assessed over 14 weeks. Using a post-hoc statistical approach, we found a negative association between weight gain and T. suis infection. For A. suum, this association was not significant after adjusting for other covariates in a multivariable analysis. Estimates from generalized linear mixed effects models indicated that a 1 kg increase in weight gain was associated with 4.4% (p = 0.00217) decrease in T. suis EPG and a 2.8% (p = 0.02297) or 2.2% (p = 0.0488) decrease in A. suum EPG or burden, respectively.ConclusionsOverall this study has demonstrated a negative association between STH and weight gain in growing pigs but also that T. suis infection may be more detrimental that A. suum on growth.     

Community-wide assessment of protein-interface modeling suggests improvements to design methodology

The CAPRI (Critical Assessment of Predicted Interactions) and CASP (Critical Assessment of protein Structure Prediction) experiments have demonstrated the power of community-wide tests of methodology in assessing the current state of the art and spurring progress in the very challenging areas of protein docking and structure prediction. We sought to bring the power of community-wide experiments to bear on a very challenging protein design problem that provides a complementary but equally fundamental test of current understanding of protein-binding thermodynamics. We have generated a number of designed protein-protein interfaces with very favorable computed binding energies but which do not appear to be formed in experiments, suggesting that there may be important physical chemistry missing in the energy calculations. A total of 28 research groups took up the challenge of determining what is missing: we provided structures of 87 designed complexes and 120 naturally occurring complexes and asked participants to identify energetic contributions and/or structural features that distinguish between the two sets. The community found that electrostatics and solvation terms partially distinguish the designs from the natural complexes, largely due to the nonpolar character of the designed interactions. Beyond this polarity difference, the community found that the designed binding surfaces were, on average, structurally less embedded in the designed monomers, suggesting that backbone conformational rigidity at the designed surface is important for realization of the designed function. These results can be used to improve computational design strategies, but there is still much to be learned; for example, one designed complex, which does form in experiments, was classified by all metrics as a nonbinder.     

de novo转录组学分析华南地区入侵植物五爪金龙代谢特征

为探究华南地区严重入侵植物五爪金龙(Ipomoea cairica)生物入侵的分子机制,对五爪金龙及其近缘种七爪金龙(I. digitata)和裂叶牵牛(I. nil)进行de novo转录组测序和组装,得到56551条unigenes,其中56522条得到注释,7815条GO注释,15615条COG注释,180201条KEGG数据库注释。转录组分析结果表明,五爪金龙氮代谢通路关键酶基因的表达高于对照。次生代谢关键酶(PAL、4CL、CAD、查耳酮合酶、苯基丙乙烯酮异构酶、槲皮黄3-O-甲基转移酶等)基因在五爪金龙与七爪金龙及裂叶牵牛中均得到协同性的差异表达,而这些代谢通路指导的产物合成对五爪金龙的抗逆境能力、生长、化感作用等均起关键作用。关键基因的RT-qPCR验证结果与转录组结果具有一致性。因此,这从分子生物学层面上对解释五爪金龙在华南地区的入侵机制提供了新的证据。     

Repeated call sequences and behavioural context in long-finned pilot whales off Cape Breton,Nova Scotia,Canada

Repeated calls are part of the vocal repertoire of a diverse array of species, often presented in sequences that take time and effort on the part of the signal producer. Rhythmic repeated call sequences make up a significant portion of long-finned pilot whale (Globicephala melas) vocal production, yet the function of these sequences has not been investigated until now. In this study, we explored the relationship between behavioural context and the presence of these vocal sequences using recordings of a population of pilot whales found off Cape Breton, Nova Scotia, Canada. We used a binomial logit-link generalized linear model to look for possible predictors of the presence of repeated call sequences. They were more common in recordings of socializing whales than in those of whales in other behavioural states, and least common in resting whales. These vocal repetitions were also more common with larger group size. These results suggest that sequences function in maintaining contact and cohesion within this social species, possibly also serving in individual or group identification. The context of repeated call sequences indicate that they are not primarily mother–calf interactions, as they are heard just as commonly from groups without young. Future studies of pilot whale repeated call sequences should include individual-level behaviour and detailed acoustic calling context.