Temperature dependence of the free energy landscape of the src-SH3 protein domain

The temperature dependence of the free energy landscape of the src-SH3 protein domain is investigated through fully atomic simulations in explicit solvent. Simulations are performed above and below the folding transition temperature, enabling an analysis of both protein folding and unfolding. The transition state for folding and unfolding, identified from the free energy surfaces, is found to be very similar, with structure in the central hydrophobic sheet and little structure throughout the rest of the protein. This is a result of a polarized folding (unfolding) mechanism involving early formation (late loss) of the central hydrophobic sheet at the transition state. Unfolding simulations map qualitatively well onto low-temperature free energy surfaces but appear, however, to miss important features observed in folding simulations. In particular, details of the folding mechanism involving the opening and closing of the hydrophobic core are not captured by unfolding simulations performed under strongly denaturing conditions. In addition, free energy surfaces at high temperatures do not display a desolvation barrier found at lower temperatures, involving the expulsion of water molecules from the hydrophobic core.     

Expression and function of cyclooxygenase and lipoxygenase enzymes in human islets of Langerhans

Arachidonic acid (AA) is generated in pancreatic beta-cells through the activation of Ca2+-dependent cytosolic phospholipase A2 (cPLA2) and the consequent hydrolysis of membrane phospholipids in the sn-2 position of the glycerophospholipid backbone. AA acts as a second messenger in beta-cells to elevate cytosolic Ca2+ levels and stimulate insulin secretion, but it is not clear whether these are direct effects of AA or are dependent on its metabolism by cyclooxygenase (COX) and/or lipoxygenase (LOX) enzymes. In addition, much of the published data in this area have been generated using insulin-secreting cell lines or rodent islets, with very little information on AA generation and metabolism in human islets of Langerhans. This short review examines cPLA2, COX and LOX expression and function in insulin- secreting cell lines and rodent and human islets.     

Genome sequence of duck pathogen Mycoplasma anatis strain 1340

Mycoplasma anatis, a member of the class Mollicutes, is the causative agent of a contagious infectious disease of domestic ducklings, wild birds, and eggs. Increasing reports show that coinfection of M. anatis with Escherichia coli results in substantial economic impacts on the duck farms in China. Here, we announce the first genome sequence of M. anatis.     

An NF-kappaB-sensitive micro RNA-146a-mediated inflammatory circuit in Alzheimer disease and in stressed human brain cells

Human brains retain discrete populations of micro RNA (miRNA) species that support homeostatic brain gene expression functions; however, specific miRNA abundance is significantly altered in neurological disorders such as Alzheimer disease (AD) when compared with age-matched controls. Here we provide evidence in AD brains of a specific up-regulation of an NF-kappaB-sensitive miRNA-146a highly complementary to the 3'-untranslated region of complement factor H (CFH), an important repressor of the inflammatory response of the brain. Up-regulation of miRNA-146a coupled to down-regulation of CFH was observed in AD brain and in interleukin-1beta, Abeta42, and/or oxidatively stressed human neural (HN) cells in primary culture. Transfection of HN cells using an NF-kappaB-containing pre-miRNA-146a promoter-luciferase reporter construct in stressed HN cells showed significant up-regulation of luciferase activity that paralleled decreases in CFH gene expression. Treatment of stressed HN cells with the NF-kappaB inhibitor pyrollidine dithiocarbamate or the resveratrol analog CAY10512 abrogated this response. Incubation of an antisense oligonucleotide to miRNA-146a (anti-miRNA-146a; AM-146a) was found to restore CFH expression levels. These data indicate that NF-kappaB-sensitive miRNA-146a-mediated modulation of CFH gene expression may in part regulate an inflammatory response in AD brain and in stressed HN cell models of AD and illustrate the potential for anti-miRNAs as an effective therapeutic strategy against pathogenic inflammatory signaling.     

Effect of rock fragments on the percolation and evaporation of forest soil in Liupan Mountains, China

The water-retaining capacity, percolation and evaporation of stony soil in Liupan Mountains, China, were measured in order to understand the effect of rock fragments on soil hydrological processes. The results indicated that the effective water-retaining capacity of soil is positively related with the volumetric content of rock fragments, but there is no relation between saturated water-retaining capacity and rock fragment content. For the soil layers within 0–40 cm, the steady infiltration rate increases with increasing volumetric content of rock fragments until it reaches the range of 15%–20%, and then it decreases when the rock fragment content further increases. For the soil layers below 40 cm, the steady infiltration rate always increases with increasing rock fragment content. The soil evaporation rate decreases with increasing volumetric content of rock fragments when it varies in the range of 0–20%, while the soil evaporation rate keeps basically stable when the rock fragment content is higher than 20%. The soil evaporation rate shows a rising tendency with increasing size of rock fragments.     

Genetic structure of Brandt’s vole (<Emphasis Type="Italic">Lasiopodomys brandtii</Emphasis>) populations in Inner Mongolia,China, based on microsatellite analysis

Brandt’s vole (Lasiopodomys brandtii) distribution is discontinuous in Inner Mongolia with some populations isolated from others. Recently, some isolated populations have suffered extinction, and the factors responsible remain elusive. Genetic drift is one of the processes affecting population genetic differentiation, and can play a substantial role in the divergence of small, isolated populations. Using seven microsatellite markers, we genotyped four geographically isolated populations of Brandt’s vole, all of which exhibit episodic fluctuations in population density. The results showed a strong genetic differentiation among the geographically distinct populations (total F _ST = 0.124) and in particular, one population (Zhengxiangbaiqi) was isolated from all others (F _ST values were greatest between Zhengxiangbaiqi and other populations). Furthermore, high levels of inbreeding (F _IS values ranged from 0.205 to 0.290) within each distinct population suggest that inbreeding has and is likely occurring in Brandt’s vole populations. These processes can decrease average individual fitness and consequently increase the risk of extinction of the species.     

Large‐scale gene expression reveals different adaptations of Hyalopterus persikonus to winter and summer host plants

Host alternation, an obligatory seasonal shifting between host plants of distant genetic relationship, has had significant consequences for the diversification and success of the superfamily of aphids. However, the underlying molecular mechanism remains unclear. In this study, the molecular mechanism of host alternation was explored through a large‐scale gene expression analysis of the mealy aphid Hyalopterus persikonus on winter and summer host plants. More than four times as many unigenes of the mealy aphid were significantly upregulated on summer host Phragmites australis than on winter host Rosaceae plants. In order to identify gene candidates related to host alternation, the differentially expressed unigenes of H. persikonus were compared to salivary gland expressed genes and secretome of Acyrthosiphon pisum. Genes involved in ribosome and oxidative phosphorylation and with molecular functions of heme–copper terminal oxidase activity, hydrolase activity and ribosome binding were potentially upregulated in salivary glands of H. persikonus on the summer host. Putative secretory proteins, such as detoxification enzymes (carboxylesterases and cytochrome P450s), antioxidant enzymes (peroxidase and superoxide dismutase), glutathione peroxidase, glucose dehydrogenase, angiotensin‐converting enzyme, cadherin, and calreticulin, were highly expressed in H. persikonus on the summer host, while a SCP GAPR‐1‐like family protein and a salivary sheath protein were highly expressed in the aphids on winter hosts. These results shed light on phenotypic plasticity in host utilization and seasonal adaptation of aphids.     

Genetic distances revealed by morphological characters,isozymes, proteins and RAPD markers and their relationships with hybrid performance in oilseed rape (<Emphasis Type="Italic">Brassica napus</Emphasis> L.)

Genetic distances (GDs) based on morphological characters, isozymes and storage proteins, and random amplified polymorphic DNAs (RAPD) were used to predict the performance and heterosis of crosses in oilseed rape (Brassica napus L.). Six male-sterile lines carrying the widely used Shaan2A cytoplasm were crossed with five restorer lines to produce 30 F₁ hybrids. These 30 hybrids and their parents were evaluated for seven agronomically important traits and their mid-parent heterosis (MPH) at Yangling, Shaanxi province in Northwest China for 2 years. Genetic similarity among the parents based on 34 isozyme and seven protein markers was higher than that based on 136 RAPDs and/or 48 morphological markers. No significant correlation was detected among these three sets of data. Associations between the different estimates of GDs and F₁ performance for some agronomic traits were significant, but not for seed yield. In order to enhance the predicting efficiency, we selected 114 significant markers and 43 favoring markers following statistical comparison of the mean values of the yield components between the heterozygous group (where the marker is present only in one parent of each hybrid) and the homozygous group (where the marker is either present or absent in both parents of each hybrid) of the 30 hybrids. Parental GD based on total polymorphic markers (GD_total, indicating general heterozygosity), significant markers (GD_sign, indicating specific heterozygosity) and favoring markers (GD_favor, indicating favoring-marker heterozygosity) were calculated. The correlation between GD_favor or GD_sign and hybrid performance was higher than the correlation between GD_total and hybrid performance. GD_sign and GD_favor significantly correlated with plant height, seeds per silique and seed yield, but not with the MPH of the other six agronomic traits with the exception of plant height. The information obtained in this study on the genetic diversity of the parental lines does not appear to be reliable for predicting F₁ yield and heterosis.