Postgenomics data are produced in large volumes by life sciences and clinical applications of novel omics diagnostics and therapeutics for precision medicine. To move from “data-to-knowledge-to-innovation,” a crucial missing step in the current era is, however, our limited understanding of biological and clinical contexts associated with data. Prominent among the emerging remedies to this challenge are the gene set enrichment tools. This study reports on GeneAnalytics™ (), a comprehensive and easy-to-apply gene set analysis tool for rapid contextualization of expression patterns and functional signatures embedded in the postgenomics Big Data domains, such as Next Generation Sequencing (NGS), RNAseq, and microarray experiments. GeneAnalytics' differentiating features include in-depth evidence-based scoring algorithms, an intuitive user interface and proprietary unified data. GeneAnalytics employs the LifeMap Science's GeneCards suite, including the GeneCards®—the human gene database; the MalaCards—the human diseases database; and the PathCards—the biological pathways database. Expression-based analysis in GeneAnalytics relies on the LifeMap Discovery®—the embryonic development and stem cells database, which includes manually curated expression data for normal and diseased tissues, enabling advanced matching algorithm for gene–tissue association. This assists in evaluating differentiation protocols and discovering biomarkers for tissues and cells. Results are directly linked to gene, disease, or cell “cards” in the GeneCards suite. Future developments aim to enhance the GeneAnalytics algorithm as well as visualizations, employing varied graphical display items. Such attributes make GeneAnalytics a broadly applicable postgenomics data analyses and interpretation tool for translation of data to knowledge-based innovation in various Big Data fields such as precision medicine, ecogenomics, nutrigenomics, pharmacogenomics, vaccinomics, and others yet to emerge on the postgenomics horizon.

LifeMap Discovery™ provides investigators with an integrated database of embryonic development, stem cell biology and regenerative medicine. The hand-curated reconstruction of cell ontology with stem cell biology; including molecular, cellular, anatomical and disease-related information, provides efficient and easy-to-use, searchable research tools. The database collates in vivo and in vitro gene expression and guides translation from in vitro data to the clinical utility, and thus can be utilized as a powerful tool for research and discovery in stem cell biology, developmental biology, disease mechanisms and therapeutic discovery. LifeMap Discovery is freely available to academic nonprofit institutions at http://discovery.lifemapsc.com

Early stages of B cell development take place in the bone marrow, resulting in formation of immature B cells, which migrate to the spleen for their final differentiation into mature cells. This final maturation step is essential for B cells to become responsive to antigens and to participate in the immune response. Previously, we showed that the MHC class II chaperone, invariant chain (Ii), controls the differentiation of B cells from the immature to the mature stage. In this study, by generating transgenic mice expressing truncated Ii lacking its luminal domain, we could dissect the chaperonin activity of Ii from its role in B cell maturation. We demonstrate in vivo that Ii N-terminal domain is directly involved in the maturation of B cells and is sufficient to promote B cell differentiation.transgenic mice ͉ N-terminal domain ͉ immature B cell ͉ mature B cell ͉ antigen presentation B cell development involves the ordered progression of a stem cell through a number of stages, ultimately resulting in a mature B cell. There are various selective criteria that the cell must fulfill to complete this program. In the bone marrow, B cell development can be divided into different stages, based on the rearrangement status of the IgH and IgL chain loci (1, 2) and the expression of intracellular and surface-bound markers. This developmental program is controlled largely by a set of transcription factors and signaling pathways. The first cells expressing IgM at their surface during this developmental process are the immature B cells that leave the bone marrow and migrate to the spleen (3, 4). These immature B cells then penetrate the marginal zone sinus and reside in the outer zone of the periarteriolar lymphocytic sheath (5), where they become part of the B cell-rich follicular areas (5, 6). At this site in the spleen, B cells are still immature and can be distinguished from their mature counterparts (3,(7)(8)(9). The transition from immature to mature B cells is characterized by a series of changes in surface marker expression and in the activities of these cells. Recently, this transition stage was characterized further and divided into two populations. Transitional B cells of type 1 (T1) are the recent immigrants from the bone marrow. These cells develop into transitional B cells of type 2 (T2), which cycle and are found exclusively in the primary follicles of the spleen (10). Only 5-10% of the newly generated immature B cells are selected into the pool of long-lived, antigen-responsive mature B cells (9, 11). Why and how only such a small proportion of immature B cells is selected and by what molecular mechanism this selection occurs are largely unknown.Previously, we have shown that invariant chain (Ii), a MHC class II chaperone, plays a crucial role in B cell maturation (12). MHC class II molecules are heterodimeric complexes that present foreign antigenic peptides on the cell surface of antigenpresenting cells (APCs) to CD4 ϩ T cells (13)(14)(15). MHC class II synthesis and assembly begin in the endoplasmic reticul...

The study determined whether there were gender differences in the expression of hippocampal genes in adult rats in association with dissimilarity in their behavior, and how these were affected by prenatal stress. Pregnant Wistar rats were subjected to varied stress once daily on days 14-20 of gestation. Adult female offspring of control rats showed significantly less anxiogenic behavior in the elevated plus maze and better discrimination between a novel and familiar object than males in the object recognition test. These gender differences in behavior were markedly attenuated by prenatal stress. Using Affymetrix DNA chip technology on hippocampal extracts prepared from littermates of the offspring used for behavioral tests, we found that 1,680 genes were differentially expressed in control males and females. The gender difference in gene expression was decreased to 11% (191 genes) by prenatal stress. In both sexes, processes like the translational machinery, mitochondrial activity, and cation transport were downregulated compared to controls, but there was a greater suppression of genes involved in vesicle trafficking, regulation of synaptic plasticity, and neurogenesis in females than in males. This was compensated by a higher expression of other components of vesicle trafficking, microtubule-based processes, and neurite development. Prenatal stress decreased the expression of 19 Rab proteins in females and five Rabs in males, but a compensatory increase of Rab partner proteins and effectors only occurred in females. Exposure to stress decreased the expression of synaptic proteins, synaptophysin, and synaptopodin in prenatally stressed males and females and increased those of PSD-95 and NR1 subunit of the N-methyl-D-aspartic acid (NMDA) glutamate receptor only in females. The study provides an unbiased view of key genes and proteins that act as gender dependent molecular sensors. The disruption of their expression by adverse early life stress may explain the alterations that occur in behavior.

Exposure of pregnant women or animals to stress during a critical period of foetal brain development increases the likelihood of anxiety, depression and learning deficits that are associated with structural alterations in the offspring hippocampus. In this study, we report the effect of gestational stress in rats on anxiogenic behaviour and hippocampal gene expression of their 23-day-old female offspring. As the rat brain continues to develop after birth, we also used the procedure of handling (H) during the first 10 days of life to reverse the anxiogenic behaviour of prenatally stressed (PS) rats. By means of micro-array analysis on hippocampal extracts, we found that the expression of about 6.1% of 9505 valid genes was significantly altered by prenatal stress (p < 0.05). Of these, 48% were over-expressed and 52% under-expressed. The latter included 300 genes that participate in axonal growth, regulation of ion channels and transporters, trafficking of synaptic vesicles and neurotransmitter release. About 30% of the genes that were down-regulated in PS rats were restored to control levels by H. These include genes that play a role in pre-synaptic organization and function. Our results provide a possible relationship between hippocampal gene expression and changes in behaviour resulting from prenatal stress.

Embryonal carcinoma P19 cells provide an ideal model to study molecular programs along differentiation. Upon induction by retinoic acid (RA), the cells undergo a program of differentiation that generates functioning neurons within 60 h. RA induced cells that were plated as sparse (1000 cells/mm(2)) or dense (4000 cells/mm(2)) cultures showed a marked difference in the culture morphology with the dense cultures exhibiting rapid maturation and accelerated neurite outgrowth. The protein expression levels of the sparse and dense cultures were compared 48 h following RA. Cell extracts were separated by 1-DE and 2-DE and differential expression (>four-fold) proteins were identified by MS. Here, we focus on 20 proteins associated with cytoskeletal regulation and stress-dependent protein refolding. The first group includes drebrin, cofilin, alpha-internexin, vimentin, and nestin. Among the proteins in the second group are subunits of the TCP-1, and several chaperones of the Hsp70 and Hsp90 families. We show that coordinated remodeling of the cytoskeleton and modulations in chaperone activity underlie the change in neurite extension rate. Furthermore, a proteomics-based analysis applied on P19 neurons demonstrated pathways underlying neuronal outgrowth, suggesting that a malfunction of such pathways leads to neuropathological conditions.

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Oogenesis produces functional eggs and is essential for fertility, embryonic development, and reproduction. The zebrafish ovary is an excellent model to study oogenesis in vertebrates, and recent studies have identified multiple regulators in oocyte development through forward genetic screens, as well as reverse genetics by CRISPR mutagenesis. However, many developmental steps in oogenesis, in zebrafish and other species, remain poorly understood, and their underlying mechanisms are unknown. Here, we take a genomic approach to systematically uncover biological activities throughout oogenesis. We performed transcriptomic analysis on five stages of oogenesis, from the onset of oocyte differentiation through Stage III, which precedes oocyte maturation. These transcriptomes revealed thousands of differentially expressed genes across stages of oogenesis. We analyzed trends of gene expression dynamics along oogenesis, as well as their expression in pair-wise comparisons between stages. We determined their functionally enriched terms, identifying uniquely characteristic biological activities in each stage. These data identified two prominent developmental phases in oocyte differentiation and traced the accumulation of maternally deposited embryonic regulator transcripts in the developing oocyte. Our analysis provides the first molecular description for oogenesis in zebrafish, which we deposit online as a resource for the community. Further, the presence of multiple gene paralogs in zebrafish, and the exclusive curation by many bioinformatic tools of the single paralogs present in humans, challenge zebrafish genomic analyses. We offer an approach for converting zebrafish gene name nomenclature to the human nomenclature for supporting genomic analyses generally in zebrafish. Altogether, our work provides a valuable resource as a first step to uncover oogenesis mechanisms and candidate regulators and track accumulating transcripts of maternal regulators of embryonic development.