Accurate prediction of protein folding rates from sequence and sequence‐derived residue flexibility and solvent accessibility

Protein folding rates vary by several orders of magnitude and they depend on the topology of the fold and the size and composition of the sequence. Although recent works show that the rates can be predicted from the sequence, allowing for high‐throughput annotations, they consider only the sequence and its predicted secondary structure. We propose a novel sequence‐based predictor, PFR‐AF, which utilizes solvent accessibility and residue flexibility predicted from the sequence, to improve predictions and provide insights into the folding process. The predictor includes three linear regressions for proteins with two‐state, multistate, and unknown (mixed‐state) folding kinetics. PFR‐AF on average outperforms current methods when tested on three datasets. The proposed approach provides high‐quality predictions in the absence of similarity between the predicted and the training sequences. The PFR‐AF's predictions are characterized by high (between 0.71 and 0.95, depending on the dataset) correlation and the lowest (between 0.75 and 0.9) mean absolute errors with respect to the experimental rates, as measured using out‐of‐sample tests. Our models reveal that for the two‐state chains inclusion of solvent‐exposed Ala may accelerate the folding, while increased content of Ile may reduce the folding speed. We also demonstrate that increased flexibility of coils facilitates faster folding and that proteins with larger content of solvent‐exposed strands may fold at a slower pace. The increased flexibility of the solvent‐exposed residues is shown to elongate folding, which also holds, with a lower correlation, for buried residues. Two case studies are included to support our findings. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Production and characterization of an intracellular bioflocculant by Chryseobacterium daeguense W6 cultured in low nutrition medium

A novel intracellular bioflocculant (named MBF-W6) produced by Chryseobacterium daeguense W6 cultured in low nutrition medium was investigated in this study. The effects of carbon source, nitrogen source, C/N ratio, initial pH, inoculum size, culture temperature and shaking speed on MBF-W6 production were studied. Chemical analysis showed that the purified MBF-W6 was mainly composed of 32.4% protein, 13.1% polysaccharide and 6.8% nucleic acid. Fourier-transform infrared (FTIR) spectroscopy indicated the presence of carboxyl, hydroxyl, and methoxyl groups. The elemental analysis of purified MBF-W6 revealed that the mass proportion of C, H, O, N and S was 40.92:6.53:44.01:8.53:1.01 (w/w) correspondingly. MBF-W6 had good flocculating rate in Kaolin suspension without any cation addition. The highest flocculating rate of 96.9% was achieved under the optimal conditions (bioflocculant dosage 1.2 mg l⁻¹, pH 5.6 and temperature 15 °C).     

紫外光诱导苎麻疫霉抗甲霜灵突变及对苎麻疫霉生物学特性的影响

作者研究了紫外光对苎麻疫霉的抗甲霜灵诱变效应及对苎麻疫霉生物学特性的影响。结果表明,供试6个苎麻疫霉野生型菌株经菌丝块紫外光药剂诱变和菌丝块药剂驯化3周后,均获得抗甲霜灵突变体,且紫外光药剂诱变处理角变区出现频率明显高于药剂驯化处理,说明紫外光对苎麻疫霉抗甲霜灵突变有一定促进效应。紫外光显著地抑制苎麻疫霉游动孢子的萌发和菌丝的生长,在一定范围内,处理时间愈长,抑制率愈高。苎麻疫霉耐紫外光菌株(经亚致死剂量的紫外光照射处理后存活的游动孢子所形成的菌株)与野生型亲本相比,对温度和pH的敏感性大致相同,但菌落形态有一定变异,菌丝生长速率、卵孢子产生量均显著下降,表明紫外光对苎麻疫霉的菌丝生长和卵孢子产生量有明显的抑制作用。苎麻疫霉耐紫外光菌株EC50值比野生型亲本菌株EC50值提高了23.21%-56.70%,即耐紫外光菌株对甲霜灵敏感性比野生亲本菌株显著下降,这与紫外光诱变试验结果是相一致的。     

Growth patterns of a stream vertebrate differ between urban and forested catchments

1. Urban development results in the decline of amphibian density and species richness. A logical next step towards understanding why urbanisation negatively impacts amphibians is to track species‐specific demographic responses to urbanisation. 2. We monitored growth of two‐lined salamander (Eurycea cirrigera Green) larvae over two complete cohorts (2006 and 2007) in nine western Georgia, U.S.A. streams. 3. We found that salamanders in streams surrounded by urbanised and developing catchments hatched at the same size as their reference‐stream counterparts, but achieved larger sizes within the first few months of growth. We evaluated the effect of four variables that correlate with the urban‐forest gradient and found that elevated temperatures in the urban environment, coupled with decreased intraspecific competition because of lower survivorship in these same habitats, were two of the most likely explanations for increased growth rates. 4. Such an increase in growth of surviving larvae may maintain population viability in urban areas where it has been shown survival is difficult because of increased in‐channel flow during flood events. Because larvae that do survive in urban streams undergo metamorphosis at large sizes, they may recoup a component of fitness (i.e. increased adult survivorship and reproduction) through growth.     

Prevalence, risk factors for and impact of subclinical endometritis in repeat breeder dairy cows

The aim of this study was to determine the prevalence and risk factors for subclinical endometritis (SE) and its effects on fertility in repeat breeder dairy cows. Dairy cows of parity 1 to 5 that were artificially inseminated (AI) 3 or more times (selected cows were artificially inseminated an average of 3.9 times) were examined at 190 ± 40 days in milk, and clinically normal cows (n = 77) were selected based on the absence of abnormal discharges on external inspection and the absence of abnormal findings on transrectal palpation and ultrasonographic examination. Endometrial samples were collected from the uterus by using the lavage technique in the luteal phase of the estrus cycle. Collected samples were centrifuged and a drop of sediment was streaked on to a clean microscopic slide and stained with Giemsa. The percentage of polymorphonuclear cells (neutrophils) was counted for each specimen. The analysed data showed that the average amount of neutrophils was 3.1% (0-9) in the selected cows. Abnormal calving (dystocia, twin births, and abortion), retained placenta, and postpartum uterine infections were associated with an increase in prevalence of SE. Subsequently, SE was significantly associated with a decrease in conception rate in the next AI. Conception rate in the next AI was 5% for cows (n = 38) with SE (≥ 3% neutrophil), and 47% for cows (n = 34) without SE (< 3% neutrophil) (P = 0.001). The prevalence of cytologically diagnosed SE (≥ 3% neutrophil) was 52.7% (n = 38). In conclusion, abnormal calving, retained placenta, and postpartum uterine infections may be associated with an increase in prevalence of SE and subsequently, SE may decrease reproductive performance and increase the incidence of repeat breeder syndrome.     

Common trade‐offs between xylem resistance to cavitation and other physiological traits do not hold among unrelated Populus deltoides ×Populus nigra hybrids

We examined the relationships between xylem resistance to cavitation and 16 structural and functional traits across eight unrelated Populus deltoides×Populus nigra genotypes grown under two contrasting water regimes. The xylem water potential inducing 50% loss of hydraulic conductance (Ψ₅₀) varied from ?1.60 to ?2.40 MPa. Drought‐acclimated trees displayed a safer xylem, although the extent of the response was largely genotype dependant, with Ψ₅₀ being decreased by as far as 0.60 MPa. At the tissue level, there was no clear relationship between xylem safety and either xylem water transport efficiency or xylem biomechanics; the only structural trait to be strongly associated with Ψ₅₀ was the double vessel wall thickness, genotypes exhibiting a thicker double wall being more resistant. At the leaf level, increased cavitation resistance was associated with decreased stomatal conductance, while no relationship could be identified with traits associated with carbon uptake or bulk leaf carbon isotope discrimination, a surrogate of intrinsic water‐use efficiency. At the whole‐plant level, increased safety was associated with higher shoot growth potential under well‐irrigated regime only. We conclude that common trade‐offs between xylem resistance to cavitation and other physiological traits that are observed across species may not necessarily hold true at narrower scales.     

Density dependence and population dynamics of black rhinos (Diceros bicornis michaeli) in Kenya’s rhino sanctuaries

Density‐dependent feedback mechanisms provide insights into the population dynamics and interactions of large herbivores with their ecosystem. Sex ratio also has particularly important implications for growth rates of many large mammal populations through its influence on reproductive potential. Therefore, the interrelationships between density‐dependent factors, comprising density, sex ratio and underlying growth rates (r) were examined for the Eastern black rhino (Diceros bicornis michaeli) living in three rhino sanctuaries in Kenya using four population models. The exponential and logistic models gave similar results and the former were accepted because they better portrayed the actual situation on the ground. Sex ratios in all sanctuary populations were positively correlated with r but interpreted with realization of other factors also affecting r. We caution that the results of population models should be interpreted alongside ground‐truthed observations. We recommend that future translocation strategies should take into account sex and age structures of the donor population, while future studies of density dependence should take into account both biotic and abiotic factors.     

A pathogenic mutation in cytochrome c oxidase results in impaired proton pumping while retaining O2-reduction activity

In this work we have investigated the effect of a pathogenic mitochondrial DNA mutation found in human colon cells, at a functional-molecular level. The mutation results in the amino-acid substitution Tyr19His in subunit I of the human CytcO and it is associated with respiratory deficiency. It was introduced into Rhodobacter sphaeroides, which carries a cytochrome c oxidase (cytochrome aa₃) that serves as a model of the mitochondrial counterpart. The residue is situated in the middle of a pathway that is used to transfer substrate protons as well as protons that are pumped across the membrane. The Tyr33His (equivalent residue in the bacterial CytcO) structural variant of the enzyme was purified and its function was investigated. The results show that in the structurally altered CytcO the activity decreased due to slowed proton transfer; proton transfer from an internal proton donor, the highly-conserved Glu286, to the catalytic site was slowed by a factor of ∼ 5, while reprotonation of the Glu from solution was slowed by a factor of ∼ 40. In addition, in the structural variant proton pumping was completely impaired. These results are explained in terms of introduction of a barrier for proton transfer through the D pathway and changes in the coordination of water molecules surrounding the Glu286 residue. The study offers an explanation, at the molecular level, to the link between a specific amino-acid substitution and a pathogenic phenotype identified in human colon cells.     

Prevention of a systematic underestimation of antioxidant activity in competition assays. The impact of unspecific reactions of the reactive species

In antioxidant competition assays, an antioxidant (A) and a detector compound (D) compete for a reactive species (R). In the evaluation of these assays, it is tacitly assumed that all of R is captured by either D or A. Due to the - by definition - high reactivity of R, unspecific reactions of R are likely to occur and neglecting these reactions will result in a systematic underestimation of antioxidant activity. It was shown that in the standard hydroxyl radical scavenging assay this was indeed the case; the inaccurate mathematical evaluation resulted in an underestimation of antioxidant activity of 25% in this competition assay. The systematic underestimation of antioxidant activity can be prevented by using an adjusted Stern-Volmer equation that takes into account that only part of R is captured by D or A.