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The expression patterns in Meishan- and Yorkshire-derived endometrium during early (gestational day 15) and mid-gestation (gestational days 26 and 50) were investigated, respectively. Totally, 689 and 1649 annotated genes were identified to be differentially expressed in Meishan and Yorkshire endometrium during the three gestational stages, respectively. Hierarchical clustering analysis identified that, of the annotated differentially expressed genes (DEGs), 73 DEGs were unique to Meishan endometrium, 536 DEGs were unique to Yorkshire endometrium, and 228 DEGs were common in Meishan and Yorkshire endometriums. Subsequently, DEGs in each of the three types of expression patterns were grouped into four distinct categories according to the similarities in their temporal expression patterns. The expression patterns identified from the microarray analysis were validated by quantitative RT-PCR. The functional enrichment analysis revealed that the common DEGs were enriched in pathways of steroid metabolic process and regulation of retinoic acid receptor signaling. These unique DEGs in Meishan endometrium were involved in cell cycle and adherens junction. The DEGs unique to Yorkshire endometrium were associated with regulation of Rho protein signal transduction, maternal placenta development and cell proliferation. This study revealed the different gene expression patterns or pathways related to the endometrium remodeling in Meishan and Yorkshire pigs, respectively. These unique DEGs in either Meishan or Yorkshire endometriums may contribute to the divergence of the endometrium environment in the two pig breeds.

Objective: Retinal neovascularization is an iconic change in retinopathies. Vascular Endothelial Growth Factor (VEGF) and α-crystallins have been identified to mediate the pathogenesis of retinopathy. However, the special and temporal changes in their expression associated with retinal neovascularization have not yet been determined. Therefore, we examined the expression and distribution of VEGF, αA- and αB-crystallins in the retina using a mouse model of oxygen-induced retinopathy (OIR)., Methods: 90 C57/BL mice were randomly divided into the OIR and control groups. The OIR group at postnatal day 7 (P7) were kept at high oxidation state (75 ± 5%) for 5 days before returned to normal environment. Retinal tissue was cut into sections. Oxygen induced retinal neovascularization and vascular structural changes were evaluated using retinal fluorescein angiography. The number of endothelial cell nuclei breaking through the retinal internal limiting membrane was counted after H&E staining. The mRNA expression levels of VEGF, αA- and αB-crystallins in the mouse retina were determined using real-time RT-PCR. The distribution of αA- and αB-crystallins in the retina was detected by fluorescent immunohistochemistry staining., Results: Oxygen induction triggered new blood vessel formation in the retina and impaired the structure of the retinal vascular network. The number of endothelial cell nuclei breaking through the retinal internal limiting membrane was significantly increased in the OIR group compared to the control group at P13, P17 and P21 (P < 0.01), reaching the peak on P17. The expression levels of VEGF, αA- and αB-crystalllins were also significantly different between the OIR and control groups. VEGF expression was highest on P15, αA-crystallin expression was highest on P17, whereas αB-crystallin expression kept increasing during the time frame of our study. Both αA- and αB-crystallins were expressed in the ganglion cell layer and the inner nuclear cell layer. While αA- and αB-crystallins were only located on the cell membrane in the outer ganglion cell layer, they were observed both on the cell membrane and in the cytoplasm in the inner layer of cells., Conclusion: Using our mouse model of oxygen-induced retinopathy, we showed that the expression patterns of VEGF, αA- and αB-crystallins during retinal neovascularization in both spatially and temporally manners, providing significant insights into the molecular mechanisms of retinopathy and the associated neovascularization.

In the studies of Drosophila embryogenesis, a large number of two-dimensional digital images of gene expression patterns have been produced to build an atlas of spatio-temporal gene expression dynamics across developmental time. Gene expressions captured in these images have been manually annotated with anatomical and developmental ontology terms using a controlled vocabulary (CV), which are useful in research aimed at understanding gene functions, interactions, and networks. With the rapid accumulation of images, the process of manual annotation has become increasingly cumbersome, and computational methods to automate this task are urgently needed. However, the automated annotation of embryo images is challenging. This is because the annotation terms spatially correspond to local expression patterns of images, yet they are assigned collectively to groups of images and it is unknown which term corresponds to which region of which image in the group. In this paper, we address this problem using a new machine learning framework, Multi-Instance Multi-Label (MIML) learning. We first show that the underlying nature of the annotation task is a typical MIML learning problem. Then, we propose two support vector machine algorithms under the MIML framework for the task. Experimental results on the FlyExpress database (a digital library of standardized Drosophila gene expression pattern images) reveal that the exploitation of MIML framework leads to significant performance improvement over state-of-the-art approaches. [ABSTRACT FROM PUBLISHER]

Here we provide the first genome-wide in vivo analysis of the Na+/Ca2+ exchanger family in the model system Caenorhabditis elegans. We source all members of this family within the Caenorhabditis genus and reconstruct their phylogeny across humans and Drosophila melanogaster. Next, we provide a description of the expression pattern for each exchanger gene in C. elegans, revealing a wide expression in a number of tissues and cell types including sensory neurons, interneurons, motor neurons, muscle cells, and intestinal tissue. Finally, we conduct a series of behavioral and functional analyses through mutant characterization in C. elegans. From these data we demonstrate that, similar to mammalian systems, the expression of Na+/Ca2+ exchangers in C. elegans is skewed toward excitable cells, and we propose that C. elegans may be an ideal model system for the study of Na+/Ca2+ exchangers.

Background: Because of the heterogeneity of human mesenchymal stem cells (MSCs), methods for cell expansion in culture and the effects on gene expression are critical factors that need to be standardized for preparing MSCs. We investigated gene expression patterns of MSCs with different seeding densities and culture times., Methods: Bone marrow-derived MSCs were plated at densities from 200 cells/cm(2) to 5,000 cells/cm(2), and the gene expression patterns were evaluated over time using a reverse-transcription polymerase chain reaction assay., Results: The mRNA levels of factors that play a critical role in cell migration and tissue regeneration, such as podocalyxin-like protein (PODXL), α4-integrin, α6-integrin, and leukemia inhibitory factor (LIF), were higher in MSCs plated at 200 cells/cm(2) than in MSCs plated at 5,000 cells/cm(2). The mRNA levels of these factors gradually increased for 10 days and then decreased by day 15 in culture. MSCs seeded at 200 cells/cm(2) that were cultured for 10 days expressed high levels of Oct-4 and Nanog. Indoleamine 2,3-dioxygenase, cyclooxygenase-1, and hepatocyte growth factor expression were upregulated in the presence of the proinflammatory cytokine interferon-γ in these cells., Conclusion: We found differences in the gene expression patterns of MSCs under different culture conditions. MSCs from 10-day cultures seeded at a low density were efficiently expanded, expressed PODXL, α6-integrin, α4-integrin, and LIF, and maintained properties like stemness and immunomodulation. Therefore, ex vivo expansion of MSCs maintained for an adequate culture time after plating at low cell density can provide an effective regenerative medicinal strategy for cell therapies using MSCs.

An important goal in neuroscience is to understand gene expression patterns in the brain. The recent availability of comprehensive and detailed expression atlases for mouse and human creates opportunities to discover global patterns and perform cross-species comparisons. Recently we reported that the major source of variation in gene transcript expression in the adult normal mouse brain can be parsimoniously explained as reflecting regional variation in glia to neuron ratios, and is correlated with degree of connectivity and location in the brain along the anterior-posterior axis. Here we extend this investigation to two gene expression assays of adult normal human brains that consisted of over 300 brain region samples, and perform comparative analyses of brain-wide expression patterns to the mouse. We performed principal components analysis (PCA) on the regional gene expression of the adult human brain to identify the expression pattern that has the largest variance. As in the mouse, we observed that the first principal component is composed of two anti-correlated patterns enriched in oligodendrocyte and neuron markers respectively. However, we also observed interesting discordant patterns between the two species. For example, a few mouse neuron markers show expression patterns that are more correlated with the human oligodendrocyte-enriched pattern and vice-versa. In conclusion, our work provides insights into human brain function and evolution by probing global relationships between regional cell type marker expression patterns in the human and mouse brain.

Our present work focuses on the set of genes, which are involved in primary brain tumors - the glioma pathway. These gliomas are mostly malignant (cancerous) in nature and are difficult to be cured and that's why they attract the attention of all the workers. To understand the relative functionality of these genes, we analyzed the expression pattern of all genes, using gene expression data, at genomic level, and then to check their universality in all other cancers, we compared their expression levels and patterns in all other types of cancers by using gene expression graphs, and observed their expression levels in all these cancers, whether they are over or under expressed. We found that every gene has its own unique expression pattern and level and on that basis it can be classified. We also found that oncogenes and tumor suppressor genes that were involved in the glioma pathway were showing similar expression patterns in other cancers too but their expression level is low.

Posttraumatic stress disorder (PTSD) is associated with decreased activity in the dorsolateral prefrontal cortex (DLPFC), the brain region that regulates working memory and preparation and selection of fear responses. We investigated gene expression profiles in DLPFC Brodmann area (BA) 46 of postmortem patients with (n=6) and without PTSD (n=6) using human mitochondria-focused cDNA microarrays. Our study revealed PTSD-specific expression fingerprints of 800 informative mitochondria-focused genes across all of these 12 BA46 samples, and 119 (+/->1.25, p<0.05) and 42 (+/->1.60, p<0.05) dysregulated genes between the PTSD and control samples. Quantitative RT-PCR validated the microarray results. These fingerprints can essentially distinguish the PTSD DLPFC BA46 brains from controls. Of the 119 dysregulated genes (+/-> or =125%, p<0.05), the highest percentages were associated with mitochondrial dysfunction (4.8%, p=6.61 x 10(-6)), oxidative phosphorylation (3.8%, p=9.04 x 10(-4)), cell survival-apoptosis (25.2%, p<0.05) and neurological diseases (23.5%, p<0.05). Fifty (50) dysregulated genes were present in the molecular networks that are known to be involved in neuronal function-survival and contain 7 targets for neuropsychiatric drugs. Thirty (30) of the dysregulated genes are associated with a number of neuropsychiatric disorders. Our results indicate mitochondrial dysfunction in the PTSD DLPFC BA46 and provide the expression fingerprints that may ultimately serve as biomarkers for PTSD diagnosis and the drugs and molecular targets that may prove useful for development of remedies for prevention and treatment of PTSD.