Concordance of residual dipolar couplings, backbone order parameters and crystallographic B-factors for a small alpha/beta protein: a unified picture of high probability, fast atomic motions in proteins

Using ensemble refinement of the third immunoglobulin binding domain (GB3) of streptococcal protein G (a small alpha/beta protein of 56 residues), we demonstrate that backbone (N-H, N-C', Calpha-Halpha, Calpha-C') residual dipolar coupling data in five independent alignment media, generalized order parameters from 15N relaxation data, and B-factors from a high-resolution (1.1A), room temperature crystal structure are entirely consistent with one another within experimental error. The optimal ensemble size representation is between four and eight, as assessed by complete cross-validation of the residual dipolar couplings. Thus, in the case of GB3, all three observables reflect the same low-amplitude anisotropic motions arising from fluctuations in backbone phi/psi torsion angles in the picosecond to nanosecond regime in both solution and crystalline environments, yielding a unified picture of fast, high-probability atomic motions in proteins. An understanding of these motions is crucial for understanding the impact of protein dynamics on protein function, since they provide part of the driving force for triggered conformational changes that occur, for example, upon ligand binding, signal transduction and enzyme catalysis.     

Batch, fed-batch, and microcarrier cultures with CHO cell lines in a pressure-cycle driven miniaturized bioreactor

Miniaturized bioreactors for suspension cultures of animal cells, such as Chinese Hamster Ovary (CHO) cells, could improve bioprocess development through the ability to cheaply explore a wide range of bioprocess operating conditions. A miniaturized pressure-cycled bioreactor for animal cell cultures, described previously (Diao et al., 2008), was tested with a suspension CHO cell line producing commercially relevant quantities of human IgG. Results from the suspended CHO cell line showed that the cell growth was comparable to conventional flask controls and the target protein production was enhanced in the minibioreactor, which may be due to the relatively high oxygen transfer rate and the moderate shear stress, measured and simulated previously. Microcarrier culture using an anchorage-dependent CHO cell line and Cytodex 3 also showed a similar result: comparable growth and enhanced production of a model protein (secreted alkaline phosphatase or SEAP). Various fed-batch schemes were applied to the CHO cells producing human IgG, yielding cell numbers (1.1 × 10(7) /mL) at day 8 and titers of human IgG (2.3 g/L) at day 14 that are typical industrial values for CHO cell fed-batch cultures. The alteration of the volumetric oxygen transfer coefficient is a key parameter for viability of the CHO cell line producing human IgG. We conclude that the minibioreactor can provide favorable cell culture environments; oxygen transfer coefficient and mixing time can be altered to mimic values in a larger scale system allowing for potential prediction of response during scale-up.     

Quantitative trait loci analysis of osteochondrosis traits in the elbow joint of pigs

Osteochondrosis is a growth disorder in the cartilage of young animals and is characterised by lesions found in the cartilage and bone. This study identified quantitative trait loci (QTLs) associated with six osteochondrosis lesion traits in the elbow joint of finishing pigs. The traits were: thickening of the cartilage, lesion in the subchondral bone, irregular cartilage surface, fissure under the cartilage, an irregular sagittal central groove and depression of the proximal edge of the radius. The study comprised 7172 finishing pigs from crossing 12 Duroc boars with 600 crossbred Landrace × Large White sows and included 462 single nucleotide polymorphism markers. The results showed 18 QTLs exceeding the 5% genome-wide threshold. The QTLs associated with lesions in the medial part of the condylus humeri (assumed to be the four main osteochondrosis traits) were, in most cases, at common locations, whereas the QTLs associated with depression of the proximal edge of the radius in general were on the same chromosomes but at separate locations. The detected QTLs explain a large part of the genetic variation, which is promising for incorporating osteochondrosis into a breeding programme using marker-assisted selection.     

Effects of cloned-cattle meat on reproductive physiology in rats

The influence of the cloned-cattle meat diets upon reproduction in mammals was rarely studied. This study was performed to analyze the effects of the diets containing cloned-cattle (Korean native beef, Hanwoo) meat on the reproductive physiology in rats. The male and female rats were fed with the diets containing 5% or 10% of normal- (N-5 or N-10) or cloned- (C-5 or C-10) cattle meat during test periods. The rats fed with commercial pellets were used as control. Lower food consumption in normal- and cloned-cattle meat diet groups is detected in both male and female rats compared with that of control (P < 0.05, 0.01 and 0.001). No signs of cloned-cattle meat diets on male reproductive parameters are found in all groups, except for lower sperm deformity in C-5 group (P < 0.05) and higher testosterone concentration in C-10 group (P < 0.05), respectively. There are no significant test substance-related differences of Caesarean section and delivery in dams and external examination and physiological development test in neonate compared with control and normal meat groups. Based on these results, it can be postulated that there are no obvious negative effects on the reproductive physiology in rats fed with cloned-cattle meat diets compared to their comparators.     

Genetic and phenotypic parameters of age at first mating, litter size and animal size in Finnish mink

Mink skin size in Finland, as well as in other countries, has increased considerably during last decade. However, there are signs that selection for large body size has a negative impact on litter size (LS) and also for survival of kits. Therefore, it is important to study the genetic relationships among fertility traits and animal size (AS). The variance components for age at first mating (AFM) and first three parity LS and AS were estimated using multi-trait restricted maximum likelihood animal model. Data included 82 945 animals born during 1990 to 2004, originating from nine farms. Heritability estimates for the fertility traits were from 0.10 to 0.15. For AS, heritability was estimated to be 0.18. Genetic correlation between AS and all fertility traits was estimated to be negative (varying from -0.004 to -0.38). It is important to recognize this antagonistic relationship and include the reproductive traits into breeding goals to maintain good reproductive performance when selecting for increased body size and hence larger pelts in fur animals. Genetic correlations between the traits should be accounted in breeding value evaluations by using a multi-trait model. Including AFM into breeding value estimation would also improve the accuracy of breeding value estimation for fertility, because females missing the first LS still have record on AFM.     

低温胁迫对番茄种子萌发的影响

在人工气候箱中模拟3个低温处理(24h最低/最高温度分别设定为7℃/12℃、5℃/10℃和3℃/8℃),分析了播种后不同天数低温胁迫对番茄种子萌发的影响。结果表明:与对照(18℃/25℃)相比,低温胁迫处理的温度越低影响越大,当日最低温度达到5.0℃、日均温低于10.0℃(相当于低温胁迫处理7℃/12℃)时,对番茄种子萌发的影响较为严重;播种后越早经受低温影响越大,播种后3d内经受低温胁迫,番茄种子发芽势、发芽指数和萌发率均有较大的下降,播种6d后低温胁迫对其萌发指标的影响较小;低温胁迫影响种子萌发的原因主要是低温导致了α-淀粉酶活性下降,相对离子渗漏率增加,从而减缓了番茄种子贮藏物质的降解,影响了番茄种子萌发初期的物质与能量代谢,并增强了细胞膜的透性,导致外渗物增多。     

Three-dimensional biofilm image reconstruction for assessing structural parameters

Parameters representing three-dimensional (3D) biofilm structure are quantified from confocal laser-scanning microscope (CLSM) images. These 3D parameters describe the distribution of biomass pixels within the space occupied by a biofilm; however, they lack a direct connection to biofilm activity. As a result, researchers choose a handful of parameters without there being a consensus on a standard set of parameters. We hypothesized that a select 3D parameter set could be used to reconstruct a biofilm image and that the reconstructed and original biofilm images would have similar activities. To test this hypothesis, an algorithm was developed to reconstruct a biofilm image with parameters identical to those of the original CLSM image. We introduced an objective method to assess the reconstruction algorithm by comparing the activities of the original and reconstructed biofilm images. We found that biofilm images with identical structural parameters showed nearly identical activities and substrate concentration profiles. This implies that the set containing all common structural parameters can successfully describe biofilm structure. This finding is significant, as it opens the door to the next step, of finding a smaller standard set of biofilm structural parameters that can be used to compare biofilm structure.     

Melatonin-related mitochondrial respiration responses are associated with growth promotion and cold tolerance in plants

Melatonin has the ability to improve plant growth and strengthened plant tolerance to environmental stresses; however, the effects of melatonin on mitochondrial respiration in plants and the underlying biochemical and molecular mechanisms are still unclear. The objective of the study is to determine possible effects of melatonin on mitochondrial respiration and energy efficiency in maize leaves grown under optimum temperature and cold stress and to reveal the relationship between melatonin-induced possible alterations in mitochondrial respiration and cold tolerance. Melatonin and cold stress, alone and in combination, caused significant increases in activities and gene expressions of pyruvate dehydrogenase, citrate synthase, and malate dehydrogenase, indicating an acceleration in the rate of tricarboxylic acid cycle. Total mitochondrial respiration rate, cytochrome pathway rate, and alternative respiration rate were increased by the application of melatonin and/or cold stress. Similarly, gene expression and protein levels of cytochrome oxidase and alternative oxidase were also enhanced by melatonin and/or cold stress. The highest values for all these parameters were obtained from the seedlings treated with the combined application of melatonin and cold stress. The activity and gene expression of ATP synthase and ATP concentration were augmented by melatonin under control and cold stress. On the other hand, cold stress reduced markedly plant growth parameters, including root length, plant height, leaf surface area, and chlorophyll content and increased the content of reactive oxygen species (ROS), including superoxide anion and hydrogen peroxide and oxidative damage, including malondialdehyde content and electrolyte leakage level; however, melatonin significantly promoted the plant growth parameters and reduced ROS content and oxidative damage under control and cold stress. These data revealed that melatonin-induced growth promotion and cold tolerance in maize is associated with its modulating effect on mitochondrial respiration.     

家蝇幼虫肠道细菌对其取食选择性和生长发育的影响

目的探究家蝇幼虫肠道细菌对幼虫取食与发育的影响,进而明确肠道细菌的部分功能。方法取3日龄家蝇幼虫,采用细菌传统分离法分离纯化其肠道内可培养细菌并进行分子鉴定,利用这些肠道细菌进行家蝇幼虫爬行选择实验,测定幼虫对不同细菌的选择性;利用这些肠道细菌发酵液与麦麸混合饲养家蝇幼虫,记录家蝇幼虫发育过程中的生物学参数,分别以LB培养原液与麦麸混合饲养的幼虫为阴性对照,以无菌水与麦麸混合饲养的幼虫为空白对照。结果在家蝇幼虫肠道中共分离出9个属10种细菌,分别为霍氏肠杆菌(Enterobacter hormaechei)、肺炎克雷伯菌(Klebsiella pneumoniae)、铜绿假单胞菌(Pseudomonas aeruginosa)、别雷斯不动杆菌(Acinetobacter bereziniae)、斯氏普罗威登斯菌(Providencia stuartii)、阴沟肠杆菌(Enterobacter cloacae)、乳酸乳球菌(Lactococcus lactis)、纺锤形赖氨酸芽胞杆菌(Lysinibacillus fusiformis)、居幼虫普罗威登斯菌(Providencia vermicola)和沙福芽胞杆菌(Bacillus safensis)。其中,除铜绿假单胞菌和斯氏普罗威登斯菌外,其余8种细菌对幼虫有显著吸引作用;除铜绿假单胞菌对家蝇生长有明显抑制作用以外,其余9种细菌对家蝇幼虫生长均有一定的促进作用,其中霍氏肠杆菌和别雷斯不动杆菌对其生长有显著促进作用。结论明确了家蝇幼虫肠道细菌的组成,确定了8种家蝇幼虫肠道细菌对其取食有吸引作用,9种细菌对其生长发育有促进作用。霍氏肠杆菌和别雷斯不动杆菌可作为添加剂用于家蝇的规模化饲养,以提高养殖效率。铜绿假单胞菌可作为生长抑制剂用于家蝇幼虫的防治。     

A systematic review and meta-analysis of higher expression of folate receptor alpha (FOLR1) predicts poor cancer prognosis

Abstract

Folate receptor alpha (FOLR1), a glycosylphosphatidylinositol-linked protein, is a well characterized folate transporter. However, the prognostic power of FOLR1 in cancer remains controversial. We conducted a meta-analysis to assess the prognostic roles of FOLR1 on different cancers. Twelve studies involving 4471 patients were included in this meta-analysis. The pooled analysis indicated that high FOLR1 significantly predicted poor overall survival (OS) (pooled hazard ratio (HR)?=?0.78, 95% confidence interval (CI)?=?0.64–0.94, p?=?0.009) and the disease-free survival (DFS) (HR?=?1.25, 95% CI?=?1.07–1.47, p?=?0.005). Subgroup analyses based on tumour type found that high FOLR1 level was associated with poor OS in breast cancer (HR?=?2.66, 95% CI?=?1.54–4.59, p?=?0.0005) and endometrial carcinoma (HR?=?1.30, 95% CI?=?1.05–1.61, p?=?0.02). However, FOLR1 has relatively weakly correlation with gender, tumour size and chemotherapy. Additionally, overexpression of FOLR1 was correlated with grade, FIGO stage, vital status and nodule status. The present meta-analysis indicated that the high expression of FOLR1 is associated with the poor survival of cancer patients, which is helpful for the clinical decision-making process.