Accuracy of cDNA microarray methods to detect small gene expression changes induced by neuregulin on breast epithelial cells

Background  

cDNA microarrays are a powerful means to screen for biologically relevant gene expression changes, but are often limited by their ability to detect small changes accurately due to "noise" from random and systematic errors. While experimental designs and statistical analysis methods have been proposed to reduce these errors, few studies have tested their accuracy and ability to identify small, but biologically important, changes. Here, we have compared two cDNA microarray experimental design methods with northern blot confirmation to reveal changes in gene expression that could contribute to the early antiproliferative effects of neuregulin on MCF10AT human breast epithelial cells.     

Mass distributions of a macromolecular assembly based on electrospray ionization mass spectrometric masses of the constituent subunits

Macromolecular assemblies containing multiple protein subunits and having masses in the megadalton (MDa) range are involved in most of the functions of a living cell. Because of variation in the number and masses of subunits, macromolecular assemblies do not have a unique mass, but rather a mass distribution. The giant extracelular erythrocruorins (Ers), ∼ 3.5 MDa, comprized of at least 180 polypeptide chains, are one of the best characterized assemblies. Three-dimensional reconstructions from cryoelectron microscopic images show them to be hexagonal bilayer complexes of 12 subassemblies, each comprised of 12 globin chains, anchored to a subassembly of 36 nonglobin linker chains. We have calculated the most probable mass distributions forLumbricus andRiftia assemblies and their globin and linker subassemblies, based on theLumbricus Er stoichiometry and using accurate subunit masses obtained by electrospray ionization mass spectrometry. The expected masses ofLumbricus andRiftia Ers are 3.517 MDa and 3.284 MDa, respectively, with a possible variation of ∼ 9% due to the breadth of the mass distributions. TheLumbricus Er mass is in astonishingly good agreement with the mean of 23 known masses, 3.524 ± 0.481 MDa.     

The effect of manipulating ecdysteroid signaling on embryonic eye development in the locust<Emphasis Type="Italic"> Schistocerca americana</Emphasis>

Adult body plan differentiation in holometabolous insects depends on global induction and control by ecdysteroid hormones during the final phase of postembryogenesis. Studies in Drosophila melanogaster and Manduca sexta have shown that this pertains also to the development of the compound eye retina. It is unclear whether the hormonal control of postembryonic eye development in holometabolous insects represents evolutionary novelty or heritage from hemimetabolous insects, which develop compound eyes during embryogenesis. We therefore investigated the effect of manipulating ecdysteroid signaling in cultured embryonic eye primordia of the American desert locust Schistocerca americana, in which ecdysteroid level changes are known to induce three rounds of embryonic molt. Although at a considerably reduced rate compared to in vivo development, early differentiation and terminal maturation of the embryonic retina was observed in culture even if challenged with the ecdysteroid antagonist cucurbitacin B. Supplementing cultures with 20-hydroxyecdysone (20E) accelerated differentiation and maturation, and enhanced cell proliferation. Considering these results, and the relation between retina differentiation and ecdysteroid level changes during locust embryogenesis, we conclude that ecdysteroids are not an essential but possibly a modulatory component of embryonic retina development in S. americana. We furthermore found evidence that 20E initiated precocious epithelial morphogenesis of the posterior retinal margin indicating a more general role of ecdysteroids in insect embryogenesis.Electronic Supplementary Material Supplementary material is available in the online version of this article at Edited by C. Desplan     

High-resolution physical map for chromosome 16q12.1-q13, the Blau syndrome locus

Background  

The Blau syndrome (MIM 186580), an autosomal dominant granulomatous disease, was previously mapped to chromosome 16p12-q21. However, inconsistent physical maps of the region and consequently an unknown order of microsatellite markers, hampered us from further refining the genetic locus for the Blau syndrome. To address this problem, we constructed our own high-resolution physical map for the Blau susceptibility region.     

Sequence evolution and sex-specific expression patterns of the C class floral identity gene, <Emphasis Type="Italic">SpAGAMOUS</Emphasis>, in dioecious <Emphasis Type="Italic">Spinacia oleracea</Emphasis> L

Development in dioecious cultivated spinach, Spinacia oleracea, is distinguished by the absence of alternative reproductive organ primordia in male and female flowers. Given the highly derived floral developmental program in spinach, we wished to characterize a spinach C class floral identity gene and to determine the patterns of sequence evolution as well as compare the spatial and temporal expression patterns with those of AGAMOUS. The isolated cDNA sequence clusters phylogenetically within the AGAMOUS/FARINELLI C class clade. In comparison with the SLM1 sequence from the related Silene latifolia, amino acid replacements are highly conservative and non-randomly distributed, being predominantly found in hinge regions or on exposed surfaces of helices. The spinach gene (SpAGAMOUS) appears to be exclusively expressed in reproductive tissues and not in vegetative organs. Initial expression of SpAGAMOUS is similar in male and female floral primordia. However, upon initiation of the first whorl organs, SpAGAMOUS becomes restricted to meristemic regions from which the reproductive primordia will develop. This results in an early gender-specific pattern. Thus, the spinach C class gene is differentially expressed prior to reproductive organ development and is, at least, correlated with, if not directly involved in, the sexual dimorphism in spinach.Electronic Supplementary Material Supplementary material is available for this article at     

Nymphal RNAi: systemic RNAi mediated gene knockdown in juvenile grasshopper

Background  

Grasshopper serves as important model system in neuroscience, development and evolution. Representatives of this primitive insect group are also highly relevant targets of pest control efforts. Unfortunately, the lack of genetics or gene specific molecular manipulation imposes major limitations to the study of grasshopper biology.     

Inhibition of Hedgehog signaling sensitizes NSCLC cells to standard therapies through modulation of EMT-regulating miRNAs

Background

Epidermal growth factor receptor- tyrosine kinase inhibitors (EGFR-TKIs) benefit Non-small cell lung cancer (NSCLC) patients, and an EGFR-TKIi erlotinib, is approved for patients with recurrent NSCLC. However, resistance to erlotinib is a major clinical problem. Earlier we have demonstrated the role of Hedgehog (Hh) signaling in Epithelial-to-Mesenchymal transition (EMT) of NSCLC cells, leading to increased proliferation and invasion. Here, we investigated the role of Hh signaling in erlotinib resistance of TGF-β1-induced NSCLC cells that are reminiscent of EMT cells.

Methods

Hh signaling was inhibited by specific siRNA and by GDC-0449, a small molecule antagonist of G protein coupled receptor smoothened in the Hh pathway. Not all NSCLC patients are likely to benefit from EGFR-TKIs and, therefore, cisplatin was used to further demonstrate a role of inhibition of Hh signaling in sensitization of resistant EMT cells. Specific pre- and anti-miRNA preparations were used to study the mechanistic involvement of miRNAs in drug resistance mechanism.

Results

siRNA-mediated inhibition as well as pharmacological inhibition of Hh signaling abrogated resistance of NSCLC cells to erlotinib and cisplatin. It also resulted in re-sensitization of TGF-β1-induced A549 (A549M) cells as well the mesenchymal phenotypic H1299 cells to erlotinib and cisplatin treatment with concomitant up-regulation of cancer stem cell (CSC) markers (Sox2, Nanog and EpCAM) and down-regulation of miR-200 and let-7 family miRNAs. Ectopic up-regulation of miRNAs, especially miR-200b and let-7c, significantly diminished the erlotinib resistance of A549M cells. Inhibition of Hh signaling by GDC-0449 in EMT cells resulted in the attenuation of CSC markers and up-regulation of miR-200b and let-7c, leading to sensitization of EMT cells to drug treatment, thus, confirming a connection between Hh signaling, miRNAs and drug resistance.

Conclusions

We demonstrate that Hh pathway, through EMT-induction, leads to reduced sensitivity to EGFR-TKIs in NSCLCs. Therefore, targeting Hh pathway may lead to the reversal of EMT phenotype and improve the therapeutic efficacy of EGFR-TKIs in NSCLC patients.

     

番茄交替氧化酶基因的克隆和表达

利用简并PCR扩增产物做探针筛选番茄cDNA基因文库获得一个全长交替氧化酶cDNA基因LeAoxlau.经序列分析得出,该基因全长1 418bp,编码区序列长1 077 bp,编码约40 kD的前体蛋白.该蛋白在转运到线粒体时被加工成32kD的成熟蛋白.Southern印迹杂交分析结果显示该基因以单拷贝形式存在于番茄的基因组中RT-PCR显示,该基因在在番茄植株的根、茎、叶和子叶中表达.重组表达实验表明该基因能在大肠杆菌中表达.     

Characterization of <Emphasis Type="Italic">SpAPETALA3</Emphasis> and <Emphasis Type="Italic">SpPISTILLATA</Emphasis>, B class floral identity genes in <Emphasis Type="Italic">Spinacia oleracea</Emphasis>, and their relationship to sexual dimorphism

Floral organ identity B class genes are generally recognized as being required for development of petals and stamens in angiosperm flowers. Spinach flowers are distinguished in their complete absence of petals in both sexes, and the absence of a developed stamen whorl in female flowers. As such, we hypothesized that differential expression of B class floral identity genes is integral to the sexual dimorphism in spinach flowers. We isolated two spinach orthologs of Arabidopsis B class genes by 3 and 5 RACE. Homology assignments were tested by comparisons of percent amino acid identities, searches for diagnostic consensus amino acid residues, conserved motifs, and phylogenetic groupings. In situ hybridization studies demonstrate that both spinach B class genes are expressed throughout the male floral meristem in early stages, and continue to be expressed in sepal primordia in reduced amounts at later stages of development. They are also highly expressed in the third whorl primordia when they arise and continue to be expressed in these tissues through the development of mature anthers. In contrast, neither gene can be detected in any stage in female flowers by in situ analyses, although northern blot experiments indicate low levels of SpAP3 within the inflorescence. The early, strong expressions of both B class floral identity genes in male floral primordia and their absence in female flowers demonstrate that B class gene expression precedes the origination of third whorl primordia (stamen) in males and is associated with the establishment of sexual floral dimorphism as it initiates in the first (sepal) whorl. These observations suggest that regulation of B class floral identity genes has a role in the development of sexual dimorphism and dioecy in spinach rather than being a secondary result of organ abortion.Electronic Supplementary Material Supplementary material is available for this article at Edited by G. Jürgens     

Projected drought effects on the demography of Ashe juniper populations inferred from remote measurements of tree canopies

Tree mortality from drought is anticipated to increase as climate change promotes more frequent or severe water limitation. Ecosystem impacts of woody mortality depend on both the number and sizes of trees that die, but a limited capacity to predict mortality risk for individual trees hinders the capacity to forecast drought effects on tree population demography and ecosystem processes. We remotely measured leaf area of living Ashe juniper trees at three savanna sites in central Texas, USA to characterize the frequency-size distribution (FSD) of juniper populations and evaluate mortality risk from drought as a function of tree size. Mortality risk of individuals was assessed from the deviation in leaf area per tree from that of a similarly sized individual with near maximal leaf area using correlations among leaf area, growth rate, and mortality measured during a prior drought. We found that the FSD of juniper trees is bell-shaped at each site. Mortality risk from drought exceeded 25% of emergent (>?4 m height) trees in savanna juniper populations, but was highest for largest trees. Mortality risk was greatest at a grazed savanna, exceeding 50% of trees with projected canopy area >?20 m². Results imply that severe drought could kill a large fraction (18–85%) of intermediate- to large-sized Ashe juniper trees in central Texas savannas. Our analysis demonstrates a novel use of remote measurements of canopy foliation to link mortality risk from drought to the demography of Ashe juniper populations through properties of individual trees.