The data presented here allow us to outline a model for gene regulatorypathways leading to the differentiation of SynB-positive and serotonergic neurons in the sea urchin embryo (Fig. 7). The most upstream gene, Six3, is activated in early cleavage, probably by maternal factors among those that are sufficient to initiate the APD developmental program throughout the embryo (Yaguchi et al., 2006; Wei et al., 2009; Range et al., 2013). Although Six3 is necessary for differentiation of all neurons in the embryo, its function is neither specific nor sufficient for their production. Instead, it is crucial for development of the APD per se: embryos lacking Six3 fail to produce neurons, the apical ciliary tuft and the cuboidal epithelium characteristic of the APD, whereas global misexpression converts the embryo to an expanded APD (Wei et al., 2009). Downstream of Six3, SoxC and Delta are activated by unknown mechanisms in isolated individual cells that have properties of neural precursors. These are capable of proliferation and probably undergo asymmetric division, with one daughter cell activating Brn1/2/4 and/or Z167 expression. SoxC expression is transient, and it is required for all neurogenesis, but its overexpression is not sufficient to overproduce neurons, indicating that it must operate in parallel with other factors at this point. As SoxC expression declines, Brn1/2/4 and Z167 mRNAs begin to accumulate; their expression also is transient and leads to the activation of differentiated gene products, including SynB, Tph and serotonin.
oversimplification of the lytic mechanism employed by the PFTs. Recent studies have clearly demonstrated that some PFTs may trigger an early acute release of intracellular ATP through the inserted pores, which further activates the ionotropic P2X receptors and consequently leads to later lysis via the increase of overall membrane permeability to cations such as K + and Ca 2+ [22, 26, 27, 34]. This multistep mechanism is supported by studies in which PFT-mediated ATP transport across artificial vesicle membranes (which are devoid of any other channels or transporters) has been observed, whereas the direct lytic activity presented by the PFTs was minimal . In addition, inhibition of cell lysis in the presence of ATP receptor antagonists demonstrated that a purinergic signaling pathway is responsible for the cell damage . Nonetheless, many PFTs have a high potential to affect biological functions simply by introducing large conductance pathways within the cell membrane, thus dissipating the electrochemical gradients, which may cause serious damage and even cell death [37, 38, 40].
combine the functional enrichment results of DM genes, DE genes, and DE miRNAs. The MAPK signaling pathway was most significantly associated with this driver subtype, and is well-known to be affected by NRAS mutations. The “melanoma pathway” ranked in the top 5, where we found three sub-pathways that were enriched with DM genes, DE genes, or target genes of DE miRNAs (Ras/Raf/MEK/ERK, PI3K/AKT, and CDK4/6/ Rb). The PI3K pathway is another well-known pathway that plays an important role in NRAS-mutant melanomas. The CDK4/6/Rb pathway recently has attracted more attention, and clinically active CDK4/6 inhibitors, such as palbociclib (PD-0332991) and LEE011 are being developed. Two ongoing phase I/II clinical trials are proceeding in NRAS-mutant melanoma combining MEK inhibitors with CDK4/6 inhibitors with promising early results: 1) binimetinib and LEE011 and 2) trametinib and palbociclib. In addition, upstream of the CDK4/6/ Rb pathway, we found that MDM2 was differentially expressed, indicating that it might be a potential drug target. In acute myeloid leukemia, a combined MEK/ MDM2 blockade may induce apoptosis .
Although the FDA biosimilar regulatory pathway is generally similar to that of the EMA, some differences do exist. For example, the FDA pathway includes a regulatory designation on interchangeability, which in the USA is the regulatory prerequisite for automatic substitution at the phar- macy level. To be declared interchangeable by the FDA, a biosimilar is expected to have the same clinical result as the reference medicine in any given patient and, if administered more than once to an individual, the risk in terms of safety or diminished efficacy of switching between the biological product and the reference product is not greater than the risk of using the reference medicine alone. The EMA does not have any provision to make assessments of pharmacy-level substitution, rather it is the responsibility of individual states to make this designation. Another difference between the pathways is that the FDA has a requirement for a transition study to grant approval of a biosimilar; in this study, patients who are on the reference medicine are switched to the bio- similar product in development to show that there are no increases in safety events between the pre- and postswitch population. A transition study is not required by the EMA.
Our lab previously demonstrated that TRPM2 is expressed and functional in hippocampal pyramidal neurons; however, the physiological role and various pathways regulating TRPM2 had not yet been established (Olah et al., 2009). Substantial evidence demonstrates that TRPM2 plays an important role in cell death (Takahashi et al., 2011). Here, we identified that TRPM2 is required for NMDAR-dependent LTD through the regulation of GSK-3β activity (Xie et al., 2011). We examined TRPM2 currents over time in vitro and provide evidence that TRPM2 currents are enhanced with GSH depletion (Belrose et al., 2012). This raises the possibility that TRPM2 currents may be enhanced with normal aging and in the various neurodegenerative and psychiatric disorders associated with GSH depletion. Furthermore, we demonstrate that cultured hippocampal neurons derived from TRPM2 KO mice show an attenuated loss of cell viability following treatment with Aβ oligomers when compared with WT cultures. We also demonstrate that Fyn kinase is capable of interacting with, and phosphorylating TRPM2. Delivery of recombinant Fyn through the patch pipette potentiates TRPM2 currents. Combined, this data raises the possibility that TRPM2 may play a role in Alzheimer’s disease pathology (Figure 5.3)
Iron regulatory proteins IRP1 and IRP2 have high se- quence identity (57% identical and 79% similar) except for a 73 amino acid insertion in the case of IRP2 (73). IRP1 (formerly termed as iron regulatory factor IRF or iron res- ponsive element binding protein IRE-BP) is 98 kDa bifunc- tional protein of 889 amino acids containing iron-sulfur cluster. When intracellular iron is abundant, protein pos- sess [4Fe-4S] cluster and act as c-acon, while the condition of low intracellular iron level occurs, the cluster somewhat decomposes and acts as IRP1. The disintegration of cluster involves more profound changes than a simple lose of Fe a atom (see previous section and Fig. 4) (16). It should be men- tioned, that m-acon lacks the IRE-binding activity (46). IRP2 (formerly assigned as IRP B ) is a 105 kDa protein (38) containing 963 amino acids (73). It is not composed of iron-sulfur cluster and it lacks aconitase activity (35). Like IRP1 also IRP2 binds to IREs in the state of iron deficien- cy. When iron is in excess, IRP2 is enzymatically degraded (45). Though IRP1 and IRP2 are very similar, they bind va- rious IREs with different affinities: IRP1 affinity to all known IREs was detected to be analogous, but IRP2 binds 10–times more IREs with 3–nucleotide bulge than IREs with single cytosine bulge (45).
The clinical trials process is very different in the US and the EU and the regulatorypathways reflect this. Those wishing to carry out clinical studies in the EU must apply to the relevant competent authorities that operate within each individual member state of the EU in order to receive permission to commence a trial in that country. In the US, the regulations require the manufacturer to gain approval from both the FDA and an institutional review board (IRB) before a clinical trial involving a HCT/P can be commenced. An IRB is the US equivalent of an ethics committee in Europe; therefore IRBs are responsible for ensuring that the welfare and rights of patients are protected during clinical studies. However, the in the EU it must be remembered that each member state will have different ethics committees and different ethical viewpoints, so any potential multi-centre trial will have to be considered with this in mind, especially when ethically divisive technologies are involved in that trial e.g. human ES cells. One advantage in the EU clinical trials process in the EU is the new implementation of a clinical trials facilitation group (CTFG), which has been mandated to harmonise the clinical trials process across the EU, including harmonisation of the clinical trials assessment procedure between the different competent authorities in the EU . Apart from the proliferation of regulations, patient numbers involved in the clinical trials process with these cell- and tissue-based therapies may also be dramatically less than in a traditional pharmaceutical product, and as such the clinical trial design is especially important. Companies may be limited to smaller data sets, and will need creative clinical study designs to gain maximum data from a smaller number of patients, combined with potentially higher costs for the study . This remains an open issue in the design of clinical trials using viable human cells or any other complex biological product.
The protein elicitor PevD1, isolated from Verticillium dahlia, could enhance resistance to TMV in tobacco and Verticillium wilt in cotton. Here, the pevd1 gene was over-expressed in wild type (WT) Arabidopsis, and its biological functions were investigated. Our results showed that the transgenic lines were more resistant to Botrytis cinerea and Pseudomonas syringae pv. tomato DC3000 than the WT line was. In transgenic plants, both the germination time and bolting time required were significantly shorter and fresh weights and plant heights were significantly higher than those in the WT line. A transcriptomics study using digital gene expression profiling (DGE) was performed in transgenic and WT Arabidopsis. One hundred and thirty-six differentially expressed genes were identified. In transgenic Arabidopsis, three critical regulators of JA biosynthesis were up-regulated and JA levels were slightly increased. Three important repressors of the ABA-responsive pathway were up-regulated, indicating that ABA signal transduction may be suppressed. One CML and two WRKY TFs involved in Ca 2+ -responsive pathways were
these mechanisms confers risk of disease development. Perhaps it should come as no surprise that some human SLE risk alleles, such as PTPN22R620W, have an impact on these signaling pathways. However, considering the myriad cells and processes that impinge on the immune response, it is surprising that such a large proportion of risk alleles defined to date are operative in regulation of B cell antigen receptor sig- naling. It will be interesting to see whether this trend continues as GWAS define new susceptibility alleles. These findings both underscore the importance of regulation of BCR signaling in preventing autoim- munity and indicate that operative mech- anisms are finely tuned and fragile. Finally, they may reveal fruitful targets for disease prevention and therapy.
Certain phytohormone-related genes can also regulate rice primary root growth. The auxin transporter mutant Osaux1 had a longer primary root and shorter root hairs than the wild type (WT) when grown in hydroponic cul- ture (Yu et al. 2015), while knock-out lines of OsAUXIN RESPONSE FACTOR 12 (OsARF12) had shorter primary roots (Qi et al. 2012). The microRNA miR393 influences auxin signalling to mediate primary root and adventitious root development by regulating its target genes, OsTIR1 and OsAFB2, the rice orthologs of the Arabidopsis auxin receptors TRANSPORT INHIBITOR RESPONSE 1 (TIR1) and AUXIN SIGNALING F-Box 2 (AFB2), which interact with OsIAA1, an AUXIN/INDOLE ACETIC ACID (AUX/ IAA) regulatory protein (Bian et al. 2012). Moreover, silen- cing the expression of DNA TOPOISOMERASE 1 (TOP1), an essential manipulator of DNA topology during RNA transcription and DNA replication, strongly reduced rice root elongation and gravitropism by mis-regulating auxin signalling and its associated transporters (Shafiq et al. 2017). Ethylene (ET) also appears to be involved in root development in rice. OsEIL1, a transcription factor in- volved in the ethylene signalling pathway, promotes rice root elongation (Mao et al. 2006). In addition, a recent study showed that the gain-of-function mutant Osethy- lene responsive factor 2 (Oserf2) formed a shorter root than the WT, while silencing OsERF2 leads to a long-root phenotype. Further experiments revealed that
In this study, a tumor was identified as p53 or Rb pathway inactivation by alteration of even one component of this regulatory pathway, which supports the idea that individual genetic abnormality should be viewed as ways of disrupting the whole cell signaling but not as simply abrogating functions of a single gene [29, 30], also supports the idea that abnormalities of each component may have approximately equivalent effects [11, 29]. Given the significant association between mir- 577/TSGA10 pathway activation and TP53 nuclear accumulation alone, in this study, we also identified a significant association between the mir-577/TSGA10 pathway activation and TP53 mutation, since a good correlation is known to exist between p53 protein accu- mulation and the presence of TP53 gene mutations in ESCC [14, 31, 32]. This novel finding is exciting, since the activation of mir- 577/TSGA10 pathway may give insight into p53 mutation, one of the most frequent genetic lesions associated with ESCC progression . Limitations of mir-577/TSGA10 axis in cell types as well as in biological behaviors of cancers
The quantity and complexity of information about cancer presents a problem. Creation of cell phenotypes involves activities and regulation of groups of genes. More than one mutation is usually needed to make a hit, oncotargets are likely to act in sets, multi-drug combinations are superior to a single drug . Comprehensive therapy based on oncotarget research should be bases on complex system models . Systems biology is an approach to quantitate and visualize the massive information that links molecular biological pathways and their regulations. This modeling could provide a basis for studies of defective controls in cancers . Negative and positive feedback loops  and bifan switching mechanism  have been discovered in cell signaling networks . These can identify oncotargets as for metastasis  and for drug discovery .They are incorporated in stem cell systems .
The miR-200 family includes miR-200a, miR- 200b, miR-200c, miR-141, and miR-429, all of which are significantly downregulated in PCa. Each of these miRNAs has been reported to suppress PCa metastasis via EMT inhibition. miR-200 inhibits Platelet-Derived Growth Factor-D (PDGF-D) induced EMT in PC3 cells by targeting and repressing Zeb1, Zeb2, and Slug expression (Figure 1) . Similarly, miR-200b significantly inhibited tumor growth and cell proliferation in PC-3 cells due to inhibition of EMT . Slabakova et al showed that miR-200 can counteract TGFβ1-induced EMT in benign prostate hyperplasia (BPH) cells . Liu et al identified that miR-200 along with miR-1 act as negative regulators of EMT in Pten and TP53 null murine models . miR-1 and miR-200 repress EMT by targeting Slug, which plays an important regulatory role in mesenchymal differentiation. Further, Slug was found as a direct repressor of miR-1 and miR-200 transcription suggesting
The adipocyte fatty acid–binding protein aP2 regulates systemic glucose and lipid metabolism. We report that aP2, in addition to being abundantly expressed by adipocytes, is also expressed by human airway epithelial cells and shows a striking upregulation following stimulation of epithelial cells with the Th2 cytokines IL-4 and IL-13. Regulation of aP2 mRNA expression by Th2 cytokines was highly dependent on STAT6, a transcription factor with a major regulatory role in allergic inflammation. We examined aP2-deficient mice in a model of allergic airway inflammation and found that infiltration of leukocytes, especially eosinophils, into the airways was highly dependent on aP2 function. T cell priming was unaffected by aP2 deficiency, suggesting that aP2 was acting locally within the lung, and analysis of bone marrow chimeras implicated non-hematopoietic cells, most likely bronchial epithelial cells, as the site of action of aP2 in allergic airway inflammation. Thus, aP2 regulates allergic airway inflammation and may provide a link between fatty acid metabolism and asthma.
Methylation of CpG cg05575921 at the aryl hydrocarbon receptor repressor (AHRR) gene locus was associated with tobacco smoking in numerous studies (6–9,11–14,26). Smoking during pregnancy also affected methylation at the same CpG site in newborns (15). We reported an association of this CpG site with blood circulating 4-vinylphenol, supporting the function of AHRR as a mediator of dioxin toxicity (25). Similarly, the robustly replicated associations of diabetes and obesity with differential CpG methylation near the genes that encode TXNIP (cg19693031), ABCG1 (cg06500161) and CPT1A (cg00574958) (3–5,17) likely reflect a gene regulatory response to diabetes and obesity induced metabolic dysregulations. TXNIP, for instance, plays an important role in glucose regulation by directly suppressing glucose uptake through binding to the glucose transporter GLUT1 (27). This idea is supported by our previously reported association of these three CpG sites with a diabetes- specific metabolic phenotype (metabotype), including changes in the well-established T2D biomarkers alpha-hydroxybutyrate (AHB), 3-methyl-2-oxovalerate, glycine and several diabetes-associated lipids (5,25). A recent obesity Mendelian randomization (MR) study by Wahl et al. (22) showed that adiposity was causal for changes in methylation of multiple CpG sites near obesity-related genes. Interestingly, several of the CpG sites identified in that study were also within a set of 20 CpG sites that we previously identified in an EWAS with blood metabolites (25) (Table 1).
Fig.·1. Cartoon illustrating the hypertonic stress response of animal cells. Exposure to hypertonic media causes rapid water loss and cell shrinkage. Cells respond to shrinkage by activating regulatory volume increase (RVI) salt uptake mechanisms. Osmotically obliged water follows salt uptake and cell volume returns to its original value. Over a period of several hours, cells replace inorganic ions accumulated during RVI with organic osmolytes. Accumulation of organic osmolytes is mediated either by energy-dependent transport from the external medium or by changes in the rates of osmolyte synthesis and degradation. Hypertonic stress typically increases the expression of both organic osmolyte transporters and key enzymes involved in their synthesis. Cells also repair molecular damage including DNA breaks and protein denaturation induced by the initial cell shrinkage and elevation cell inorganic ion levels.
Both epithelial and vascular lumens rely on the molecular crosstalk between cell-cell and cell-matrix adhesion pathways (Iruela-Arispe and Davis, 2009). These connections provide the information required for the acquisition of cell polarity, a crucial prerequisite for lumen formation. Polarization results in the segregation of cell-cell contacts to the lateral aspects of the cell, while associations with the extracellular matrix (ECM) become exclusive to the basal side. The distribution of these cell surface molecules is concurrent with polarization of the centrosomes and, through an as yet unclear mechanism, regulates the orientation of cell division (Taylor et al., 2010; Zovein et al., 2010). This is crucial because cell divisions in the plane of the lumen wall result in stratification, whereas division orthogonal to this plane will lead to enlargement of the tube.
Remarkably, metabolic analysis of the nagA mutant revealed GlcNAc-6P accumulation after induction with GlcN, which would suggest that GlcN metabolism leads to GlcNAc-6P formation through a yet unde ined route (preliminary data, not shown). The double mutant nagAB accumulated both GlcN-6P and GlcNAc-6P when media were supplemented with GlcN, suggesting that multiple pathways may be available for GlcN metabolism. However the effect of PG recycling cannot be ruled out. Another interesting discovery was that mutants lacking the nagK gene produced an unknown compound with a mass of m/z 256.06 after induction with GlcN (preliminary metabolomic data, not shown). Though further investigation is needed to elucidate this unknown compound, we hypothesise that it may well be an oxidized form of GlcN-6P (m/z 258.04) which could present a novel feature of GlcN metabolism. It remains to be determined how the metabolome of these mutants responds to GlcNAc induction and how this compares to GlcN metabolism. It would also be valuable to track the metabolism of labelled aminosugars to distinguish other possible sources of the pathway metabolic intermediates, such as those generated during PG recycling. Also, more research is needed to understand how the deletion of nagK may relieve GlcNAc toxicity to the nagB mutant under conditions presumed to involve PTS transport of the sugar. This may well suggest that a portion of GlcNAc is located intracellularly, via alternative transporters or PG recycling, and that blocking its phosphorylation aids in the prevention of the toxic accumulation of GlcN-6P or related metabolites.
In all three models the importance of legitimacy and trust are considered critical to achieving socially acceptable and sustainable natural resource development and management outcomes. Legitimacy can be defined as the perceived fairness and procedural justice associated with processes and their outcomes. This definition combines an empirical measure of legitimacy (acceptance of a rule or institution as authoritative) and a normative argument concerning whether the authority possesses legitimacy (providing reasons that justify it; Bernstein 2005). Trust means that an entity has confidence that the behavior of some other entity will match their expectations (Cook 2001). Trust in regulatory processes is centered on believing in the reliability, truth, or ability of the regulatory agency (Pirson and Malhotra 2011) and the people that construct it, and is a core issue that deeply influences the level of faith in a regulatory process. The relationship between trust and legitimacy is not straightforward. For instance, there may be lack of legitimacy even when trust is present. Further, conflict frequently arises where legitimacy and/or trust have been eroded (Stern and Baird 2015). This erosion in trust and legitimacy can run in parallel to an increase in societal pressure for natural resource developments to obtain SLO. If legitimacy and trust are strengthened through more formal, transparent, clear, and predictable processes, this can enhance their development between all relevant stakeholders. Navigating trust has become increasingly complex, however, as human interactions expand over multiple spatial, demographic, and information scales, and this has raised the related question on the legitimacy of activities. Trust dynamics in regulatory relationships are under-researched, and surprisingly little empirical research on trust has been conducted in the context of regulator-regulated or citizen-regulator relationships (Lange and Gouldson 2010).