An empirical energy function for threading protein sequence through the folding motif

In this paper we present a new residue contact potantial derived by statistical analysis of protein crystal structures. This gives mean hydrophobic and pairwise contact energies as a function of residue type and distance interval. To test the accuracy of this potential we generate model structures by “threading” different sequences through backbone folding motifs found in the structural data base. We find that conformational energies calculated by summing contact potentials show perfect specificity in matching the correct sequences with each globular folding motif in a 161-protcin data set. They also identify correct models with the core folding motifs of heme-rythrin and immunoglobulin McPC603 V₁-do- main, among millions of alternatives possible when we align subsequences with α-helices and β-strands, and allow for variation in the lengths of intervening loops. We suggest that contact potentials reflect important constraints on nonbonded interaction in native proteins, and that “threading” may be useful for structure prediction by recognition of folding motif. © 1993 Wiley-Liss, Inc.     

Carbohydrate degradation and methane production during fermentation ofLaminaria saccharina (Laminariales,Phaeophyceae)

Anaerobic digestion of the brown algaLaminaria saccharina (L.) Lamour. harvested in spring and autumn was carried out at controlled laboratory conditions in stirred fermentor systems. Due to the normal seasonal variations, the autumn material had a much higher content of carbohydrates such as mannitol and laminaran. Both batch and semi-continuous feeding conditions were investigated for periods up to 800 h, with inoculum provided from previous kelp fermentations. In batch cultures, the methane yield from the autumn material was doubled compared to that of the spring material. Semi-continuous conditions gave more similar methane yields for both raw materials, 0.22 and 0.27 l CH₄ per g VS for spring and autumn material, respectively. In all experiments, mannitol and laminaran were reduced to less than 5 of the initial values within 24–48 hours after inoculation, whereas 30 of the alginate content was detectable even after 30 days. Viscometry revealed that this material was severely depolymerized, and alginate lyase activity was found to develop rapidly in all cultures. Although mannitol and laminaran were fermented much faster than alginate, the total accumulated methane yields seemed to be determined by the total carbohydrate content of the raw material during extended semi-continuous feeding.(*author for correspondence)     

光驱动二氧化碳转化系统的构建、优化与应用

利用光能驱动二氧化碳(carbon dioxide, CO₂)还原生产化学品对于缓解环境压力、解决能源危机具有重要意义。光捕获、光电转化和CO₂固定等作为影响光合作用效率的关键因素,同时也制约着CO₂的资源化利用效率。为了解决上述问题,本文从生物化学与代谢工程相结合的角度,系统总结了光驱动杂合系统的构建、优化与应用,并从酶杂合系统、生物杂合系统以及杂合系统应用3个方面分析了光驱动CO₂还原合成化学品的最新研究进展。在酶杂合系统方面,采用的策略主要有提升酶催化活性、增强酶稳定性等;在生物杂合系统方面,采用的方法主要包括增强生物捕光能力、优化还原力供应以及改善能量再生等;在杂合系统应用方面,主要阐述了光驱动CO₂还原生产一碳含能化合物、生物燃料以及生物食品等。最后,从纳米材料(包括有机材料和无机材料)和生物催化剂(包括酶和微生物)两个方面,展望了人工光合系统的进一步发展方向。     

Natural lignin modulators improve bagasse saccharification of sugarcane and energy cane in field trials

The burgeoning cellulosic ethanol industry necessitates advancements in enzymatic saccharification, effective pretreatments for lignin removal, and the cultivation of crops more amenable to saccharification. Studies have demonstrated that natural inhibitors of lignin biosynthesis can enhance the saccharification of lignocellulose, even in tissues generated several months post-treatment. In this study, we applied daidzin (a competitive inhibitor of coniferaldehyde dehydrogenase), piperonylic acid (a quasi-irreversible inhibitor of cinnamate 4-hydroxylase), and methylenedioxy cinnamic acid (a competitive inhibitor of 4-coenzyme A ligase) to 60-day-old crops of two conventional Brazilian sugarcane cultivars and two energy cane clones, bred specifically for enhanced biomass production. The resultant biomasses were evaluated for lignin content and enzymatic saccharification efficiency without additional lignin-removal pretreatments. The treatments amplified the production of fermentable sugars in both the sugarcane cultivars and energy cane clones. The most successful results softened the most recalcitrant lignocellulose to the level of the least recalcitrant of the biomasses tested. Interestingly, the softest material became even more susceptible to saccharification.     

Constraints on prey size selection by the three-spined stickleback: energy requirements and the capacity and fullness of the gut

An experiment was designed to study how gut fullness and encounter with 5-mm Asellus aquaticus influenced acceptance or rejection of less profitable 8-mm Asellus . 45-mm sticklebacks were found to always accept 5-mm prey whereas 8-mm prey were accepted with an initial probability of about 0.9. This probability decreased as the gut filled. Fish of differing sizes and sex had similar daily energy intakes per unit body size, however the acceptance of 8-mm prey was related to fish size. Whenever a fish orientated to a prey it was followed by pursuit and manipulation independently of prey size. The decision to accept or reject prey occurred after one manipulation, a criterion that was more variable for the larger prey. For one feeding session per day the total energy intake was almost constant despite the changing combination of prey sizes eaten. The fish ate prey with long handling times if the energetic contents of the stomach had not reached 450 J. Calculations were made of how many of each millimetre prey size group would satisfy the 450 J demand and how long the estimated number would take to handle. This showed that the best option is to consume 5-mm prey if given the choice.     

VARIABILITY IN NITRATE UPTAKE KINETICS IN THALASSIOSIRA PSEUDONANA (BACILLARIOPHYCEAE)1

Short-term (1–9 min) nitrate uptake kinetics were measured in Thalassiosira pseudonana (Hust.) Hasle & Heimdal grown in nitrate-limited, ammonium-limited, and nitrate-sufficient continuous cultures. For all cultures, maximal nitrate uptake rates did not develop until approximately 3 min after nitrate addition; thereafter, nitrate uptake rates remained constant or declined slightly. The K_s and V_max for the nitrate-limited cultures were higher at any growth rate than those for the ammonium-limited or nitrate-sufficient cultures. Thus, much higher nitrate concentrations would be required to saturate nitrate uptake in nitrate-limited Thalassiosira pseudonana than is usually considered necessary. The lack of data for other species grown under a range of environmental conditions makes it difficult to generalize about the effect of preconditioning on nitrate uptake kinetics.     

Species–energy relationships and habitat complexity in bird communities

Species–energy theory is a commonly invoked theory predicting a positive relationship between species richness and available energy. The More Individuals Hypothesis (MIH) attempts to explain this pattern, and assumes that areas with greater food resources support more individuals, and that communities with more individuals include more species. Using a large dataset for North American birds, I tested these predictions of the MIH, and also examined the effect of habitat complexity on community structure. I found qualitative support for the relationships predicted by the MIH, however, the MIH alone was inadequate for fully explaining richness patterns. Communities in more productive sites had more individuals, but they also had more even relative abundance distributions such that a given number of individuals yielded a greater number of species. Richness and evenness were also higher in structurally complex forests compared to structurally more simple grasslands when controlling for available energy.     

Nutrition and Physical Activity Program to Attenuate Obesity and Promote Physical and Metabolic Fitness in Elementary School Children

Obesity and low levels of physical and metabolic fitness are risk factors for cardiovascular disease and diabetes. The purpose of this investigation was to attenuate obesity and improve physical and metabolic fitness in elementary school children. Schools have the opportunity, mechanisms, and personnel in place to deliver nutrition education, fitness activities, and a school food service that is nutritious and healthy. Cohorts from grades 3 to 5 in two school districts in rural Nebraska (Intervention/Control) participated in a 2-year study of physical activity and modified school lunch program. Data collection for aerobic capacity, body composition, blood chemistry, nutrition knowledge, energy intake, and physical activity was at the beginning and end of each year. Int received enhanced physical activity, grade specific nutrition education, and a lower fat and sodium school lunch program. Con continued with a regular school lunch and team sports activity program. At year 2, Int lunches had significantly less energy (9%), fat (25%), sodium (21%), and more fiber (17%). However, measures of 24-hour energy intake for Int and Con showed significant differences for sodium only. Physical activity in the classroom was 6% greater for Int compared to Con (p < 0.05) but physical activity outside of school was ?16 % less for Int compared to Con (p < 0.05). Body weight and body fat were not different between schools for normal weight or obese children. No differences were found for cholesterol, insulin, and glucose; however, HDL cholesterol was significantly greater and cholesterol/HDL was significantly less for Int compared to Con (p < 0.05). It appears that compensation in both energy intake and physical activity outside of school may be responsible for the lack of differences between Int and Con.     

Molecular Parameterisation and the Theoretical Calculation of Electrode Potentials

The difference in reduction potentials between ortho and para-benzoquinones has been calculated. The employs gas phase ab initio and semi-empirical computations in combination with free energy perturbation theory applied to gas and solution phase Monte Carlo simulations. The effects on calculated results of altering solute electrostatic parameterisation in solution phase simulations is examined. Atom centred charges derived from the molecular electrostatic potentials, MEPs, from optimised ab initio wavefunctions and charges generated by consideration of hydrogen bonded complexes are considered. Parameterisation of hydroxyl torsions in hydroquinone molecules is treated in a physically realistic manner. The coupled torsional system of the ortho-hydrobenzoquinone molecule is described by a potential energy surface calculated using gas phase AM1 semi-empirical computations rather than the simple torsional energy functions frequently employed in such calculations. Calculated differences in electrode potentials show that the electrostatic interactions of quinone and hydroquinone molecules in aqueous solution are not well described by atom centred charges derived from ab initio calculated MEPs. Moreover, results in good agreement with the experimental reduction potential difference can be obtained by employing high level ab initio calculations and solution phase electrostatic parameters developed by consideration of hydrogen bonded complexes.