On the Prediction of Folding Nuclei in Globular Proteins

An approach to predicting folding nuclei in globular proteins with known three-dimensional structures is proposed. This approach is based on the pinpointing of the lowest saddle points on the barrier between the unfolded state and native structure on the free-energy landscape of a protein chain; the proposed technique uses the dynamic programming method. A comparison of calculation results with experimental data on the folding nuclei of 21 proteins shows that the model provides good Φ value predictions for protein structures determined by X-ray analysis and, less successfully, in structures determined by nuclear magnetic resonance. Consideration of the whole ensemble of transition states provides a better prediction of folding nuclei than consideration of only transition states with lowest free energies. In addition, we predict the location of folding nuclei in three-dimensional structures of some proteins whose folding kinetics is being studied, but there is no experimental evidence concerning their folding nuclei.     

How Nature Modulates Inherent Fluctuations for Biological Self-Organization – The Case of Membrane Fusion

Biological systems in nano-scale, due to the weak electrostatic interactions and structural connectivity therein, are flexible so that they undergo conformational transition subject to thermal fluctuations and external noises. In the presence of barriers, nature utilizes the fluctuations to give rise to self-organization, typically accompanied by conformational transitions. In two opposing membranes with like-charges, the cooperative coupling between the undulation and charge fluctuations give rise to a dynamic instability to spontaneous growth of the in-phase membrane undulation, and thus a great reduction of the energy barrier to fusion. The multivalent counter-ions, the Ca²⁺ for example, enhance the necessary charge density fluctuation leading to surface charge inversion and overcondensation.     

Managing vegetation in surface-flow wastewater-treatment wetlands for optimal treatment performance

Constructed wetlands that mimic natural marshes have been used as low-cost alternatives to conventional secondary or tertiary wastewater treatment in the U.S. for at least 30 years. However, the general level of understanding of internal treatment processes and their relation to vegetation and habitat quality has not grown in proportion to the popularity of these systems. We have studied internal processes in surface-flow constructed wastewater-treatment wetlands throughout the southwestern U.S. since 1990. At any given time, the water quality, hydraulics, water temperature, soil chemistry, available oxygen, microbial communities, macroinvertebrates, and vegetation each greatly affect the treatment capabilities of the wetland. Inside the wetland, each of these components plays a functional role and the treatment outcome depends upon how the various components interact. Vegetation plays a uniquely important role in water treatment due to the large number of functions it supports, particularly with regard to nitrogen transformations. However, it has been our experience that vegetation management is critical for achieving and sustaining optimal treatment function. Effective water treatment function and good wildlife quality within a surface-flow constructed wetland depend upon the health and sustainability of the vegetation. We suggest that an effective tool to manage and sustain healthy vegetation is the use of hummocks, which are shallow emergent plant beds within the wetland, positioned perpendicular to the water flow path and surrounded by water sufficiently deep to limit further emergent vegetation expansion. In this paper, we describe the use of a hummock configuration, in conjunction with seasonal water level fluctuations, to manage the vegetation and maintain the treatment function of wastewater-treatment wetlands on a sustainable basis.     

The Influence of the Inoculum Source of Rhizoctonia solani on Development of Black Scurf on Potato

Rhizoctonia solani, the causal agent of stem canker and black scurf on potato, survives as sclerotia on tubers, in soil and in plant residues. The objective of the present study was to evaluate the importance of inoculum source on disease development. Disease‐free minitubers and seed tubers contaminated with low levels of R. solani were planted in fumigated or artificially inoculated growth mixture in greenhouse experiments. Black scurf incidence and severity were significantly higher when the inoculum was present in both seed tubers and soil, compared with either of them separately. The severity of disease symptoms on the subterranean parts of the plant also were significantly higher in plots where both seed tubers and soil were contaminated, compared with plots where the inoculum source was either the seed tubers or the soil. Thus, both major sources of inoculum, seed tubers and soil, are important in disease development. However, when both sources are present, black scurf incidence and severity are increased, leading to economical damage to tuber yield and quality. Additional results from field trials support these findings. Disease incidence and severity on daughter tubers were correlated with levels of contamination in seed tubers and soil. When seed tubers and soil were heavily infested, the levels of black scurf incidence and severity on daughter tubers were very high; when seed tuber and soil infestation were very low, black scurf incidence and severity on progeny were also lower. Disease levels were reduced by in‐furrow fungicide treatment, but were less effective when the initial levels of the fungus on the seed tubers and in the soil were high.     

Bilayer interaction and localization of cell penetrating peptides with model membranes: A comparative study of a human calcitonin (hCT)-derived peptide with pVEC and pAntp(43-58)

Cell-penetrating peptides (CPPs) are able to translocate problematic therapeutic cargoes across cellular membranes. The exact mechanisms of translocation are still under investigation. However, evidence for endocytic uptake is increasing. We investigated the interactions of CPPs with phospholipid bilayers as first step of translocation. To this purpose, we employed four independent techniques, comprising (i) liposome buffer equilibrium dialysis, (ii) Trp fluorescence quenching, (iii) fluorescence polarization, and (iv) determination of ζ-potentials. Using unilamellar vesicles (LUVs) of different phospholipid composition, we compared weakly cationic human calcitonin (hCT)-derived peptides with the oligocationic CPPs pVEC and penetratin (pAntp). Apparent partition coefficients of hCT-derived peptides in neutral POPC LUVs were dependent on amino acid composition and secondary structure; partitioning in negatively charged POPC/POPG (80:20) LUVs was increased and mainly governed by electrostatic interactions. For hCT(9-32) and its derivatives, D values raised from about 100-200 in POPC to about 1000 to 1500 when negatively charged lipids were present. Localization profiles of CPPs obtained by Trp fluorescence quenching were dependent on the charge density of LUVs. In POPC/POPG, hCT-derived CPPs were located on the bilayer surface, whereas pVEC and pAntp resided deeper in the membrane. In POPG LUVs, an increase of fluorescence polarization was observed for pVEC and pAntp but not for hCT-derived peptides. Generally, we found strong peptide-phospholipid interactions, especially when negatively charged lipids were present.     

Cu(II) organizes beta-2-microglobulin oligomers but is released upon amyloid formation

beta-2-Microglobulin (beta2m) is deposited as amyloid fibrils in the bones and joints of patients undergoing long-term dialysis treatment as a result of kidney failure. Previous work has shown that biologically relevant amounts of Cu(II) can cause beta2m to be converted to amyloid fibrils under physiological conditions in vitro. In this work, dynamic light scattering, mass spectrometry, and size-exclusion chromatography are used to characterize the role that Cu plays in the formation of oligomeric intermediates that precede fibril formation. Cu(II) is found to be necessary for the stability of the dimer and an initial form of the tetramer. The initially formed tetramer then undergoes a structural change to a state that no longer binds Cu(II) before progressing to a hexameric state. Based on these results, we propose that the lag phase associated with beta2m fibril formation is partially accounted for by the structural transition of the tetramer that results in Cu(II) loss. Consistent with this observation is the determination that the mature beta2m amyloid fibrils do not contain Cu. Thus, Cu(II) appears to play a catalytic role by enabling the organization of the necessary oligomeric intermediates that precede beta2m amyloid formation.     

Optimal moult strategies in migratory birds

Avian migration, which involves billions of birds flying vast distances, is known to influence all aspects of avian life. Here we investigate how birds fit moult into an annual cycle determined by the need to migrate. Large variation exists in moulting patterns in relation to migration: for instance, moult can occur after breeding in the summer or after arrival in the wintering quarters. Here we use an optimal annual routine model to investigate why this variation exists. The modelled bird's decisions depend on the time of year, its energy reserves, breeding status, experience, flight feather quality and location. Our results suggest that the temporal and spatial variations in food are an important influence on a migratory bird's annual cycle. Summer moult occurs when food has a high peak on the breeding site in the summer, but it is less seasonal elsewhere. Winter moult occurs if there is a short period of high food availability in summer and a strong winter peak at different locations (i.e. the food is very seasonal but in opposite phase on these areas). This finding might explain why only long-distance migrants have a winter moult.     

You are what your mother eats: evidence for maternal preconception diet influencing foetal sex in humans

Facultative adjustment of sex ratios by mothers occurs in some animals, and has been linked to resource availability. In mammals, the search for consistent patterns is complicated by variations in mating systems, social hierarchies and litter sizes. Humans have low fecundity, high maternal investment and a potentially high differential between the numbers of offspring produced by sons and daughters: these conditions should favour the evolution of facultative sex ratio variation. Yet little is known of natural mechanisms of sex allocation in humans. Here, using data from 740 British women who were unaware of their foetus's gender, we show that foetal sex is associated with maternal diet at conception. Fifty six per cent of women in the highest third of preconceptional energy intake bore boys, compared with 45% in the lowest third. Intakes during pregnancy were not associated with sex, suggesting that the foetus does not manipulate maternal diet. Our results support hypotheses predicting investment in costly male offspring when resources are plentiful. Dietary changes may therefore explain the falling proportion of male births in industrialized countries. The results are relevant to the current debate about the artificial selection of offspring sex in fertility treatment and commercial 'gender clinics'.     

Impact of wheat grinding and pelleting in a wheat–rapeseed meal diet on amino acid ileal digestibility and endogenous losses in pigs

The purpose of the current experiment was to investigate the impacts of grinding and pelleting procedures applied to wheat in a wheat–rapeseed meal diet on the coefficients of standardized ileal digestibility, i.e., apparent digestibility corrected for basal endogenous losses (CSID), and true ileal digestibility, i.e., apparent digestibility corrected for total endogenous losses (CTID), of nitrogen (N) and amino acids (AA) in pigs. Ileal digestibility was measured by collecting digesta from pigs fitted with ileorectal anastomoses. Four diets, involving four technological treatments applied to wheat, were compared in vivo according to a 4 × 4 Latin square design (four pigs each fed four diets during four successive periods of 1 week). The technological treatments of wheat were two grinding procedures and two pelleting processes. Wheat was ground to obtain mean flour particle sizes of 1000 and 500 μm, leading after mixing with rapeseed meal and minerals-vitamins premix to the first and second diets named “coarse” and “fine”, respectively. Part of the 500 μm wheat flour was pelleted through dies of same screen diameter (4 mm) but different thicknesses, 16 and 20 mm, inducing a low and high compression ratio, leading after mixing with rapeseed meal and premix to the third and fourth diets named “LCR” and “HCR”, respectively. Basal endogenous losses were determined by feeding a protein-free diet during the 5th week of the experiment. Total endogenous losses were measured by way of the isotopic dilution method using ¹⁵N-labeled wheat and rapeseed meal. Decreasing wheat particle size from 1000 to 500 μm improved (P<0.05) the coefficient of ileal digestibility of dietary energy (0.707 versus 0.665), organic matter (0.718 versus 0.677) and dry matter (0.681 versus 0.645), but neither AA CSID nor N retention. The pelleting processes did not further increase (P>0.10) energy or organic matter digestibility but improved (P<0.05) N and AA CSID (0.785 versus 0.759 for N and 0.725 versus 0.679 for lysine, with HCR versus fine diet, respectively). Pelleting wheat flour at higher compression ratio (HCR versus LCR diet) was more efficient to improve dietary N and AA digestibility values due to a significant decrease in ileal specific, i.e., total minus basal, N and AA endogenous losses (P<0.05) associated with an increase in CTID. It is concluded that pelleting wheat fine flour at high compression ratio allows maximizing AA digestibility and availability of a wheat–rapeseed meal diet.