A densely interconnected genome-wide network of microRNAs and oncogenic pathways revealed using gene expression signatures

MicroRNAs (miRNAs) are important components of cellular signaling pathways, acting either as pathway regulators or pathway targets. Currently, only a limited number of miRNAs have been functionally linked to specific signaling pathways. Here, we explored if gene expression signatures could be used to represent miRNA activities and integrated with genomic signatures of oncogenic pathway activity to identify connections between miRNAs and oncogenic pathways on a high-throughput, genome-wide scale. Mapping >300 gene expression signatures to >700 primary tumor profiles, we constructed a genome-wide miRNA-pathway network predicting the associations of 276 human miRNAs to 26 oncogenic pathways. The miRNA-pathway network confirmed a host of previously reported miRNA/pathway associations and uncovered several novel associations that were subsequently experimentally validated. Globally, the miRNA-pathway network demonstrates a small-world, but not scale-free, organization characterized by multiple distinct, tightly knit modules each exhibiting a high density of connections. However, unlike genetic or metabolic networks typified by only a few highly connected nodes ("hubs"), most nodes in the miRNA-pathway network are highly connected. Sequence-based computational analysis confirmed that highly-interconnected miRNAs are likely to be regulated by common pathways to target similar sets of downstream genes, suggesting a pervasive and high level of functional redundancy among coexpressed miRNAs. We conclude that gene expression signatures can be used as surrogates of miRNA activity. Our strategy facilitates the task of discovering novel miRNA-pathway connections, since gene expression data for multiple normal and disease conditions are abundantly available.     

Malaria sporozoite antigen‐directed genome‐wide response in transgenic Drosophila

Malaria kills a million people annually. Understanding the relationship between a causative parasite, Plasmodium falciparum, and the mosquito vector might suggest novel prevention approaches. We created and transformed into Drosophila two genes encoding, thrombospondin‐related adhesive protein (TRAP) and circumsporozoite protein (CSP), found on the cell surface of Plasmodium sporozoites. To understand a model insect's response, we induced these proteins separately and together, performing whole genome microarray analysis measuring gene expression changes. Gene ontology classification of responding genes reveals that TRAP and CSP strongly and differentially influence Drosophila genes involved with cell motility and gene regulation, respectively; however, the most striking effects are on the immune system. While immune‐related genes are but modestly elevated compared with responses to sepsis, there is a marked repression of the Toll pathway. This suggests: (1) how Plasmodium infection of the mosquito might use TRAP and CSP to modulate the host insect's physiology to promote sporozoite survival and transmission to man and (2) that approaches to elevate expression of the mosquito's Toll pathway might lead to novel methods of malaria prevention. genesis 47:196–203, 2009. © 2009 Wiley‐Liss, Inc.     

Temporal Coherence of Chlorophyll a during a Spring Phytoplankton Bloom in Xiangxi Bay of Three‐Gorges Reservoir,China

Algal bloom phenomenon was defined as “the rapid growth of one or more phytoplankton species which leads to a rapid increase in the biomass of phytoplankton”, yet most estimates of temporal coherence are based on yearly or monthly sampling frequencies and little is known of how synchrony varies among phytoplankton or of the causes of temporal coherence during spring algal bloom. In this study, data of chlorophyll a and related environmental parameters were weekly gathered at 15 sampling sites in Xiangxi Bay of Three‐Gorges Reservoir (TGR, China) to evaluate patterns of temporal coherence for phytoplankton during spring bloom and test if spatial heterogeneity of nutrient and inorganic suspended particles within a single ecosystem influences synchrony of spring phytoplankton dynamics. There is a clear spatial and temporal variation in chlorophyll a across Xiangxi Bay. The degree of temporal coherence for chlorophyll a between pairs of sites located in Xiangxi Bay ranged from –0.367 to 0.952 with mean and median values of 0.349 and 0.321, respectively. Low levels of temporal coherence were often detected among the three stretches of the bay (Down reach, middle reach and upper reach), while high levels of temporal coherence were often found within the same reach of the bay. The relative difference of DIN between pair sites was the strong predictor of temporal coherence for chlorophyll a in down and middle reach of the bay, while the relative difference in Anorganic Suspended Solids was the important factor regulating temporal coherence in middle and upper reach. Contrary to many studies, these results illustrate that, in a small geographic area (a single reservoir bay of approximately 25 km), spatial heterogeneity influence synchrony of phytoplankton dynamics during spring bloom and local processes may override the effects of regional processes or dispersal. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Rotary torque produced by proton motive force in FoF1 motor

We have attempted direct observation of the light-driven rotation of a FoF(1)-ATP motor. The FoF(1)-ATP motor was co-reconstituted by the deletion-delta subunit of FoF(1)-ATP synthase with bacteriorhodopsins (BRs) into a liposome. The BR converts radiation energy into electrochemical gradient of proton to drive the FoF(1)-ATP motor. Therefore, the light-driven rotation of FoF(1)-ATP motor has been directly observed by a fluorescence microscopy using a fluorescent actin filament connected to beta-subunit as a marker of its orientation. The rotational torque value of the Fo motor was calculated as 27.93+/-1.88pNnm. The ATP motor is expected to be a promising rotary molecular motor in the development of nanodevices.     

甘肃马唧山地区榆中贝母(Fritillaria yuzhongensis)的生态学特性及种子发芽规律的初步研究

榆中贝母(Fritillaria yuzhongensis)生长于马啣山的高山地带,全生育期约100 d左右,是一种生育期较短的类短命植物。在果实成熟时,种子的胚发育不全,具有后熟作用的特点,包括形态后熟和生理后热两个阶段;因此,需要一定时期的低温处理,才能完成后熟过程,以解除休眠,促使种子发芽。本试验表明:榆中贝母完成形态后熟过程的最佳温度是7℃左右,经过100d以上的低温处理才能使原胚发育成熟,继续在7℃低温下处理70d以上,才能完成生理后熟过程。榆中贝母种子休眠时间长,需要经过170d以上的低温处理,种子才能萌发。本试验结果为榆中贝母种子的萌发提出了适宜的温度范围和低温处理时间,为提高种子的出苗率和缩短栽培年限提供了科学依据。     

A potential tocopherol acetate loaded palm oil esters-in-water nanoemulsions for nanocosmeceuticals

Background  

Cosmeceuticals are cosmetic-pharmaceutical hybrids intended to enhance health and beauty of the skin. Nanocosmeceuticals use nano-sized system for the delivery of active ingredients to the targeted cells for better penetration. In this work, nanoemulsion from palm oil esters was developed as a delivery system to produce nanocosmeceuticals. The stability of the resulting formulation was tested using various methods. In addition, the effect of components i.e. Vitamin E and Pluronic F-68 on the formulation was also studied.