NOD1 modulates decidual stromal cell function to maintain pregnancy in the early trimester

We sought to explore the functions and modulated factors of NOD1 in normal decidual stromal cells (DSCs) derived from the first trimester pregnancy and whether existed different expression of NOD1 between normal and unexplained recurrent pregnancy loss (URPL) in DSCs. Twenty‐six patients with normal pregnancies that required abortion and 12 URPL patients at first trimester were enrolled for the study. As a result, we found lower levels of NOD1 in the DSCs derived from URPL compared with those from normal early trimester pregnancy. Furthermore, increased NOD1 expression in the normal DSCs induced apoptosis and increased monocyte chemotactic protein‐1 (MCP‐1) and IL‐1β (interleukin 1 beta) secretion but decreased their invasion capacity. In addition, several cytokines such as IL‐1β, tumour necrosis factor‐alpha (TNF‐α), interferon‐gamma (IFN‐γ), and interleukin‐17 (IL‐17) were present at the maternal‐fetal interface in RPL and were found to regulate NOD1 expression in primary DSCs. Our study indicates that RPL may be associated with NOD1 aberrant expression in DSCs, which plays a significant role in maintaining pregnancy via infection control and regulation of immune responses that might affect the pregnancy outcome. We expect that our results will bring more comprehensively understanding about the connection between NOD1 and RPL for researchers.     

Measuring population differentiation using GST or D? A simulation study with microsatellite DNA markers under a finite island model and nonequilibrium conditions

The genetic differentiation of populations is a key parameter in population genetic investigations. Wright's F(ST) (and its relatives such as G(ST) ) has been a standard measure of differentiation. However, the deficiencies of these indexes have been increasingly realized in recent years, leading to some new measures being proposed, such as Jost's D (Molecular Ecology, 2008; 17, 4015). The existence of these new metrics has stimulated considerable debate and induced some confusion on which statistics should be used for estimating population differentiation. Here, we report a simulation study with neutral microsatellite DNA loci under a finite island model to compare the performance of G(ST) and D, particularly under nonequilibrium conditions. Our results suggest that there exist fundamental differences between the two statistics, and neither G(ST) nor D operates satisfactorily in all situations for quantifying differentiation. D is very sensitive to mutation models but G(ST) noticeably less so, which limits D's utility in population parameter estimation and comparisons across genetic markers. Also, the initial heterozygosity of the starting populations has some important effects on both the individual behaviours of G(ST) and D and their relative behaviours in early differentiation, and this effect is much greater for D than G(ST) . In the early stages of differentiation, when initial heterozygosity is relatively low (<0.5, if the number of subpopulations is large), G(ST) increases faster than D; the opposite is true when initial heterozygosity is high. Therefore, the state of the ancestral population appears to have some lasting impacts on population differentiation. In general, G(ST) can measure differentiation fairly well when heterozygosity is low whatever the causes; however, when heterozygosity is high (e.g. as a result of either high mutation rate or high initial heterozygosity) and gene flow is moderate to strong, G(ST) fails to measure differentiation. Interestingly, when population size is not very small (e.g. N ≥ 1000), G(ST) measures differentiation quite linearly with time over a long duration when gene flow is absent or very weak even if mutation rate is not low (e.g. μ = 0.001). In contrast, D, as a differentiation measure, performs rather robustly in all these situations. In practice, both indexes should be calculated and the relative levels of heterozygosities (especially H(S) ) and gene flow taken into account. We suggest that a comparison of the two indexes can generate useful insights into the evolutionary processes that influence population differentiation.     

Exploring the conformational diversity of loops on conserved frameworks

Loops are structurally variable regions, but the secondary structural elements bracing loops are often conserved. Motifs with similar secondary structures exist in the same and different protein families. In this study, we made an all-PDB-based analysis and produced 495 motif families accessible from the Internet. Every motif family contains some variable loops spanning a common framework (a pair of secondary structures). The diversity of loops and the convergence of frameworks were examined. In addition, we also identified 119 loops with conformational changes in different PDB files. These materials can give some directions for functional loop design and flexible docking.     

How kelp produce blade shapes suited to different flow regimes: A new wrinkle

Many species of macroalgae have flat, strap-like blades in habitats exposed to rapidly flowing water, but have wide, ruffled "undulate" blades at protected sites. We used the giant bull kelp, Nereocystis luetkeana, to investigate how these ecomorphological differences are produced. The undulate blades of N. luetkeana from sites with low flow remain spread out and flutter erratically in moving water, thereby not only enhancing interception of light, but also increasing drag. In contrast, strap-like blades of kelp from habitats with rapid flow collapse into streamlined bundles and flutter at low amplitude in flowing water, thus reducing both drag and interception of light. Transplant experiments in the field revealed that shape of the blade in N. luetkeana is a plastic trait. Laboratory experiments in which growing blades from different sites were subjected to tensile forces that mimicked the hydrodynamic drag experienced by blades in different flow regimes showed that change in shape is induced by mechanical stress. During growth experiments in the field and laboratory, we mapped the spatial distribution of growth in both undulate and strap-like blades to determine how these different morphologies were produced. The highest growth rates occur near the proximal ends of N. luetkeana blades of both morphologies, but the rates of transverse growth of narrow, strap-like blades are lower than those of wide, undulate blades. If rates of longitudinal growth at the edges of a blade exceed the rate of longitudinal growth along the midline of the blade, ruffles along the edges of the blade are produced by elastic buckling. In contrast, flat blades are produced when rates of longitudinal growth are similar across the width of a blade. Because ruffles are the result of elastic buckling, a compliant undulate N. luetkeana blade can easily be pushed into different configurations (e.g., the wavelengths of the ruffles along the edges of the blade can change, and the whole blade can twist into left- and right-handed helicoidal shapes), which may enhance movements of the blade in flowing water that reduce self-shading and increase mass exchange along blade surfaces.     

Activation of AMP-activated protein kinase is required for berberine-induced reduction of atherosclerosis in mice: the role of uncoupling protein 2

Aims

Berberine, a botanical alkaloid purified from Coptidis rhizoma, is reported to activate the AMP-activated protein kinase (AMPK). Whether AMPK is required for the protective effects of berberine in cardiovascular diseases remains unknown. This study was designed to determine whether AMPK is required for berberine-induced reduction of oxidative stress and atherosclerosis in vivo.

Methods

ApoE (ApoE^-/-) mice and ApoE^-/-/AMPK alpha 2^-/- mice that were fed Western diets were treated with berberine for 8 weeks. Atherosclerotic aortic lesions, expression of uncoupling protein 2 (UCP2), and markers of oxidative stress were evaluated in isolated aortas.

Results

In ApoE^-/- mice, chronic administration of berberine significantly reduced aortic lesions, markedly reduced oxidative stress and expression of adhesion molecules in aorta, and significantly increased UCP2 levels. In contrast, in ApoE^-/-/AMPK alpha 2^-/- mice, berberine had little effect on those endpoints. In cultured human umbilical vein endothelial cells (HUVECs), berberine significantly increased UCP2 mRNA and protein expression in an AMPK-dependent manner. Transfection of HUVECs with nuclear respiratory factor 1 (NRF1)-specific siRNA attenuated berberine-induced expression of UCP2, whereas transfection with control siRNA did not. Finally, berberine promoted mitochondrial biogenesis that contributed to up-regulation of UCP2 expression.

Conclusion

We conclude that berberine reduces oxidative stress and vascular inflammation, and suppresses atherogenesis via a mechanism that includes stimulation of AMPK-dependent UCP2 expression.     

Binding of phosphorothioate oligonucleotides with RNase H1 can cause conformational changes in the protein and alter the interactions of RNase H1 with other proteins

We recently found that toxic PS-ASOs can cause P54nrb and PSF nucleolar mislocalization in an RNase H1-dependent manner. To better understand the underlying mechanisms of these observations, here we utilize different biochemical approaches to demonstrate that PS-ASO binding can alter the conformations of the bound proteins, as illustrated using recombinant RNase H1, P54nrb, PSF proteins and various isolated domains. While, in general, binding of PS-ASOs or ASO/RNA duplexes stabilizes the conformations of these proteins, PS-ASO binding may also cause the unfolding of RNase H1, including both the hybrid binding domain and the catalytic domain. The extent of conformational change correlates with the binding affinity of PS-ASOs to the proteins. Consequently, PS-ASO binding to RNase H1 induces the interaction of RNase H1 with P54nrb or PSF in a 2′-modification and sequence dependent manner, and toxic PS-ASOs tend to induce more interactions than non-toxic PS-ASOs. PS-ASO binding also enhances the interaction between P54nrb and PSF. However, the interaction between RNase H1 and P32 protein can be disrupted upon binding of PS-ASOs. Together, these results suggest that stronger binding of PS-ASOs can cause greater conformational changes of the bound proteins, subsequently affecting protein–protein interactions. These observations thus provide deeper understanding of the molecular basis of PS-ASO-induced protein mislocalization or degradation observed in cells and advance our understanding of why some PS-ASOs are cytotoxic.     

Calpain activation by Wingless-type murine mammary tumor virus integration site family, member 5A (Wnt5a) promotes axonal growth

Axon development involves spatial-temporal cytoskeletal reorganization. However, how the cytoskeleton remodeling is modulated by extracellular cues is unclear. Here, we report a role of Wnt/Ca(2+) signaling in regulating actin and growth cone dynamics. We found that treatment of cultured cortical neurons with Wnt5a, a non-canonical Wnt, either globally or locally, caused an increase in the activity of calpain, a calcium-dependent protease responsible for the cleavage of several actin binding proteins, including spectrin. Treatment with Wnt5a promoted growth cone advance, as well as axonal growth, and these effects were prevented by chelating intracellular calcium, inhibition or down-regulation of calpain, or blockade of spectrin cleavage by competitive peptides. Interestingly, both Wnt5a and activated calpain were found to be mainly distributed in the axon-rich intermediate zone of neocortex. Down-regulating calpain expression interfered with the growth of callosal axons in vivo. Thus, Wnt5a serves as a physiological cue to stimulate localized calpain activity, which in turn promotes growth cone advance and axonal growth.     

Proteomics-based identification of autoantibodies in the sera of healthy Chinese individuals from Beijing

The identification of panels of tumor antigens that elicit an antibody response may have utility in cancer screening, diagnosis and in establishing prognosis. However, autoantibodies normally exist in sera of healthy individuals and are enormously diversified. To explore the reservoir of autoantibody in healthy population, we performed a proteomics investigation of autoantibody profiles in the sera of 36 healthy Chinese individuals from Beijing, which may provide valuable reference information to the identification of disease-specific autoantibodies. The results showed that autoantibody profiles varied individually, but some autoantibodies were identified at a high frequency in the healthy population. The autoantibodies against alpha-enolase and those against heterogeneous nuclear ribonucleoprotein L were positive in more than 50% of the sera samples. The autoantibodies identified in more than 20% of samples included those against annexin II, F-actin capping protein beta subunit and calreticulin. Some of these autoantibodies have been previously reported to be involved in autoimmune conditions and cancers. Autoantibodies in the healthy population are important as a foundation from which disease-specific autoantibodies can be defined. Thus our report on autoantibodies in healthy individuals may be useful as a reference for defining new autoantibody biomarkers.     

A protocol for differential display of mRNA expression using either fluorescent or radioactive labeling

Since its invention in the early 1990s, differential display (DD) has become one of the most commonly used techniques for identifying differentially expressed genes at the mRNA level. Unlike other genomic approaches, such as DNA microarrays, DD systematically detects changes in mRNA profiles among multiple samples being compared without the need of any prior knowledge of genomic information of the living organism being studied. Here, we present an optimized DD protocol with a fluorescent digital readout as well as traditional radioactive labeling. The resulting streamlined fluorescent DD process offers an unprecedented accuracy, sensitivity and throughput in comprehensive and quantitative analysis of eukaryotic gene expression. Results usually can be obtained within days using a limited number of primer combinations, but a comprehensive DD screen may take weeks or months to accomplish, depending on gene coverage required and the number of differentially expressed genes present within a biological system being compared.