Molecular expression patterns in the synovium and their association with advanced symptomatic knee osteoarthritis

Objective: Osteoarthritis (OA) is a major source of knee pain. Mechanisms of OA knee pain are incompletely understood but include synovial pathology. We aimed to identify molecular expression patterns in the synovium associated with symptomatic knee OA.Design: Snap frozen synovia were from people undergoing total knee replacement (TKR) for advanced OA, or from post-mortem (PM) cases who had not sought help for knee pain. Associations with OA symptoms were determined using discovery and validation samples, each comprising TKR and post mortem (PM) cases matched for chondropathy (Symptomatic or Asymptomatic Chondropathy). Associations with OA were determined by comparing age matched TKR and PM control cases. Real-time quantitative PCR for 96 genes involved in inflammation and nerve sensitisation used TaqMan® Array Cards in discovery and validation samples, and protein expression for replicated genes was quantified using Luminex bead assay.Results: Eight genes were differentially expressed between asymptomatic and symptomatic chondropathy cases and replicated between discovery and validation samples (P3-fold change). Of these, matrix metalloprotease (MMP)-1 was also increased whereas interleukin-1 receptor 1 (IL1R1) and vascular endothelial growth factor (VEGF) were decreased at the protein level in the synovium of symptomatic compared to asymptomatic chondropathy cases. MMP1 protein expression was also increased in OA compared to PM controls.Conclusion: Associations of symptomatic OA may suggest roles of MMP1 expression and IL1R1 and VEGF pathways in OA pain. Better understanding of which inflammation-associated molecules mediate OA pain should inform refinement of existing therapies and development of new treatments

Nitric oxide synthase:non-canonical expression patterns

Science can move ahead by questioning established or canonical views and, so it may be with the enzymes, nitric oxide synthases (NOS). Nitric oxide (NO) is generated by NOS isoforms that are often described by their tissue-specific expression patterns. NOS1 (nNOS) is abundant in neural tissue, NOS2 is upregulated in activated macrophages and known as inducible NOS (iNOS), and NOS3 (eNOS) is abundant in endothelium where it regulates vascular tone. These isoforms are described as constitutive or inducible, but in this perspective we question the broad application of these labels. Are there instances where “constitutive” NOS (NOS1 and NOS3) are inducibly expressed; conversely, are there instances where NOS2 is constitutively expressed? NOS1 and NOS3 inducibility may be linked to post-translational regulation, making their actual patterns activity much more difficult to detect. Constitutive NOS2 expression has been observed in several tissues, especially the human pulmonary epithelium where it may regulate airway tone. These data suggest that expression of the three NOS enzymes may include non-established patterns. Such information should be useful in designing strategies to modulate these important enzymes in different disease states

Effects of Flight on Gene Expression and Aging in the Honey Bee Brain and Flight Muscle

Honey bees move through a series of in-hive tasks (e.g., “nursing”) to outside tasks (e.g., “foraging”) that are coincident with physiological changes and higher levels of metabolic activity. Social context can cause worker bees to speed up or slow down this process, and foragers may revert back to their earlier in-hive tasks accompanied by reversion to earlier physiological states. To investigate the effects of flight, behavioral state and age on gene expression, we used whole-genome microarrays and real-time PCR. Brain tissue and flight muscle exhibited different patterns of expression during behavioral transitions, with expression patterns in the brain reflecting both age and behavior, and expression patterns in flight muscle being primarily determined by age. Our data suggest that the transition from behaviors requiring little to no flight (nursing) to those requiring prolonged flight bouts (foraging), rather than the amount of previous flight per se, has a major effect on gene expression. Following behavioral reversion there was a partial reversion in gene expression but some aspects of forager expression patterns, such as those for genes involved in immune function, remained. Combined with our real-time PCR data, these data suggest an epigenetic control and energy balance role in honey bee functional senescence

Digital gene expression analysis of the zebra finch genome

Background: In order to understand patterns of adaptation and molecular evolution it is important to quantify both variation in gene expression and nucleotide sequence divergence. Gene expression profiling in non-model organisms has recently been facilitated by the advent of massively parallel sequencing technology. Here we investigate tissue specific gene expression patterns in the zebra finch (Taeniopygia guttata) with special emphasis on the genes of the major histocompatibility complex (MHC). Results: Almost 2 million 454-sequencing reads from cDNA of six different tissues were assembled and analysed. A total of 11,793 zebra finch transcripts were represented in this EST data, indicating a transcriptome coverage of about 65%. There was a positive correlation between the tissue specificity of gene expression and non-synonymous to synonymous nucleotide substitution ratio of genes, suggesting that genes with a specialised function are evolving at a higher rate (or with less constraint) than genes with a more general function. In line with this, there was also a negative correlation between overall expression levels and expression specificity of contigs. We found evidence for expression of 10 different genes related to the MHC. MHC genes showed relatively tissue specific expression levels and were in general primarily expressed in spleen. Several MHC genes, including MHC class I also showed expression in brain. Furthermore, for all genes with highest levels of expression in spleen there was an overrepresentation of several gene ontology terms related to immune function. Conclusions: Our study highlights the usefulness of next-generation sequence data for quantifying gene expression in the genome as a whole as well as in specific candidate genes. Overall, the data show predicted patterns of gene expression profiles and molecular evolution in the zebra finch genome. Expression of MHC genes in particular, corresponds well with expression patterns in other vertebrates

Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution II: dynamics.

BackgroundTo accurately describe gene expression and computationally model animal transcriptional networks, it is essential to determine the changing locations of cells in developing embryos.ResultsUsing automated image analysis methods, we provide the first quantitative description of temporal changes in morphology and gene expression at cellular resolution in whole embryos, using the Drosophila blastoderm as a model. Analyses based on both fixed and live embryos reveal complex, previously undetected three-dimensional changes in nuclear density patterns caused by nuclear movements prior to gastrulation. Gene expression patterns move, in part, with these changes in morphology, but additional spatial shifts in expression patterns are also seen, supporting a previously proposed model of pattern dynamics based on the induction and inhibition of gene expression. We show that mutations that disrupt either the anterior/posterior (a/p) or the dorsal/ventral (d/v) transcriptional cascades alter morphology and gene expression along both the a/p and d/v axes in a way suggesting that these two patterning systems interact via both transcriptional and morphological mechanisms.ConclusionOur work establishes a new strategy for measuring temporal changes in the locations of cells and gene expression patterns that uses fixed cell material and computational modeling. It also provides a coordinate framework for the blastoderm embryo that will allow increasingly accurate spatio-temporal modeling of both the transcriptional control network and morphogenesis

Expression Patterns of Phosphate Transporter Gene Ecgpt Associated with the Salt Stress Response in Perennial Eucalypt Tree Hybrid Clones

Salinity effects on plant can often be related to mineral ion content alteration, including phosphate. Under saline conditions, phosphate levels were reported to decrease in plants. Such effects could indirectly affect intracellular phosphate levels, leading to phosphate deficiency, which in turn leads to increased activities of phosphate uptake mechanisms. This research was aimed to investigate the effects of salinity on the expression changes of phosphate transporter genes isolated from E. camaldulensis x E. globulus hybrid clones subjected to salt concentrations of 0 (control), 50, 100, and 150 mMNaCl. Fragments of genes (1164bp long and encodes 304 amino acid polypeptides) known to be involved in phosphate uptake were identified and isolated by RACE from these hybrids, encoding a Phosphate Transporter (Ecg PT). Expression studies using Northern-Blot analysis revealed that the expression of EcgPT was found to be affected by salt, suggesting a direct effect of salinity on phosphate uptake. EcgPT was expressed differently in different clones, indicating different degrees of phosphate transporter activation in order to tolerate salt stress. Molecular data are discussed in relation to measurements of ion levels in different organs of different clones and under various salt regimes during the course of the hydroponic experiment

Virtual in situs: Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression

Complex spatial and temporal patterns of gene expression underlie embryo differentiation, yet methods do not yet exist for the efficient genome-wide determination of spatial expression patterns during development. In situ imaging of transcripts and proteins is the gold-standard, but it is difficult and time consuming to apply to an entire genome, even when highly automated. Sequencing, in contrast, is fast and genome-wide, but is generally applied to homogenized tissues, thereby discarding spatial information. It is likely that these methods will ultimately converge, and we will be able to sequence RNAs in situ, simultaneously determining their identity and location. As a step along this path, we developed methods to cryosection individual blastoderm stage Drosophila melanogaster embryos along the anterior-posterior axis and sequence the mRNA isolated from each 25 micron slice. The spatial patterns of gene expression we infer closely match patterns previously determined by in situ hybridization and microscopy. We applied this method to generate a genome-wide timecourse of spatial gene expression from shortly after fertilization through gastrulation. We identify numerous genes with spatial patterns that have not yet been described in the several ongoing systematic in situ based projects. This simple experiment demonstrates the potential for combining careful anatomical dissection with high-throughput sequencing to obtain spatially resolved gene expression on a genome-wide scale.Comment: 6 pages, 3 figures, 7 supplemental figures (available on request from [email protected]

Which Regular Expression Patterns are Hard to Match?

Regular expressions constitute a fundamental notion in formal language theory and are frequently used in computer science to define search patterns. A classic algorithm for these problems constructs and simulates a non-deterministic finite automaton corresponding to the expression, resulting in an $O(mn)$ running time (where $m$ is the length of the pattern and $n$ is the length of the text). This running time can be improved slightly (by a polylogarithmic factor), but no significantly faster solutions are known. At the same time, much faster algorithms exist for various special cases of regular expressions, including dictionary matching, wildcard matching, subset matching, word break problem etc. In this paper, we show that the complexity of regular expression matching can be characterized based on its {\em depth} (when interpreted as a formula). Our results hold for expressions involving concatenation, OR, Kleene star and Kleene plus. For regular expressions of depth two (involving any combination of the above operators), we show the following dichotomy: matching and membership testing can be solved in near-linear time, except for "concatenations of stars", which cannot be solved in strongly sub-quadratic time assuming the Strong Exponential Time Hypothesis (SETH). For regular expressions of depth three the picture is more complex. Nevertheless, we show that all problems can either be solved in strongly sub-quadratic time, or cannot be solved in strongly sub-quadratic time assuming SETH. An intriguing special case of membership testing involves regular expressions of the form "a star of an OR of concatenations", e.g., $[a|ab|bc]^*$. This corresponds to the so-called {\em word break} problem, for which a dynamic programming algorithm with a runtime of (roughly) $O(n\sqrt{m})$ is known. We show that the latter bound is not tight and improve the runtime to $O(nm^{0.44\ldots})$

Heart enhancers with deeply conserved regulatory activity are established early in zebrafish development.

During the phylotypic period, embryos from different genera show similar gene expression patterns, implying common regulatory mechanisms. Here we set out to identify enhancers involved in the initial events of cardiogenesis, which occurs during the phylotypic period. We isolate early cardiac progenitor cells from zebrafish embryos and characterize 3838 open chromatin regions specific to this cell population. Of these regions, 162 overlap with conserved non-coding elements (CNEs) that also map to open chromatin regions in human. Most of the zebrafish conserved open chromatin elements tested drive gene expression in the developing heart. Despite modest sequence identity, human orthologous open chromatin regions recapitulate the spatial temporal expression patterns of the zebrafish sequence, potentially providing a basis for phylotypic gene expression patterns. Genome-wide, we discover 5598 zebrafish-human conserved open chromatin regions, suggesting that a diverse repertoire of ancient enhancers is established prior to organogenesis and the phylotypic period