Autoregulatory Feedback Research Articles

The c-myb proto-oncogene and microRNA-15a comprise an active autoregulatory feedback loop in human hematopoietic cells

AbstractThe c-myb proto-oncogene encodes an obligate hematopoietic cell transcription factor important for lineage commitment, proliferation, and differentiation. Given its critical functions, c-Myb regulatory factors are of great interest but remain incompletely defined. Herein we show that c-Myb expression is subject to posttranscriptional regulation by microRNA (miRNA)–15a. Using a luciferase reporter assay, we found that miR-15a directly binds the 3′-UTR of c-myb mRNA. By transfecting K562 myeloid leukemia cells with a miR-15a mimic, functionality of binding was shown. The mimic decreased c-Myb expression, and blocked the cells in the G1 phase of cell cycle. Exogenous expression of c-myb mRNA lacking the 3′-UTR partially rescued the miR-15a induced cell-cycle block. Of interest, the miR-15a promoter contained several potential c-Myb protein binding sites. Occupancy of one canonical c-Myb binding site was demonstrated by chromatin immunoprecipitation analysis and shown to be required for miR-15a expression in K562 cells. Finally, in studies using normal human CD34+ cells, we showed that c-Myb and miR-15a expression were inversely correlated in cells undergoing erythroid differentiation, and that overexpression of miR-15a blocked both erythroid and myeloid colony formation in vitro. In aggregate, these findings suggest the presence of a c-Myb–miR-15a autoregulatory feedback loop of potential importance in human hematopoiesis.

Functional characteristics of a double positive feedback loop coupled with autorepression

We study the functional characteristics of a two-gene motif consisting of a double positive feedback loop and an autoregulatory negative feedback loop. The motif appears in the gene regulatory network controlling the functional activity of pancreatic β-cells. The model exhibits bistability and hysteresis in appropriate parameter regions. The two stable steady states correspond to low (OFF state) and high (ON state) protein levels, respectively. Using a deterministic approach, we show that the region of bistability increases in extent when the copy number of one of the genes is reduced from 2 to 1. The negative feedback loop has the effect of reducing the size of the bistable region. Loss of a gene copy, brought about by mutations, hampers the normal functioning of the β-cells giving rise to the genetic disorder, maturity-onset diabetes of the young (MODY). The diabetic phenotype makes its appearance when a sizable fraction of the β-cells is in the OFF state. Using stochastic simulation techniques we show that, on reduction of the gene copy number, there is a transition from the monostable ON to the ON state in the bistable region of the parameter space. Fluctuations in the protein levels, arising due to the stochastic nature of gene expression, can give rise to transitions between the ON and OFF states. We show that as the strength of autorepression increases, the ON → OFF state transitions become less probable whereas the reverse transitions are more probable. The implications of the results in the context of the occurrence of MODY are pointed out.

A Feedback Mechanism Controlling SCRAMBLED Receptor Accumulation and Cell-Type Pattern in Arabidopsis

Cellular pattern formation in the root epidermis of Arabidopsis occurs in a position-dependent manner, generating root-hair (H) cells contacting two underlying cortical cells and nonhair (N) cells contacting one cortical cell. SCRAMBLED (SCM), a leucine-rich repeat receptor-like kinase (LRR-RLK), mediates this process through its effect on a downstream transcription factor regulatory network. After perception of a positional cue, the SCM signaling pathway is proposed to preferentially repress WEREWOLF (WER) transcription factor expression in H cells and thereby bias the outcome of mutual lateral inhibition acting between H and N cells. However, the molecular mechanism responsible for this preferential SCM signaling is unknown. Here, we analyze the distribution of the SCM receptor and the biological effect of altering its accumulation pattern. We find that SCM expression and accumulation in the epidermal cell layer is necessary and sufficient to direct the cell-type pattern. Further, SCM preferentially accumulates in H cells, and this accumulation pattern is dependent on the downstream transcription factors. Thus, SCM participates in an autoregulatory feedback loop, enabling cells engaged in SCM signaling to maintain high levels of SCM receptor, which provides a simple mechanism for reinforcing a bias in receptor-mediated signaling to ensure robust pattern formation.

Sexual Back Talk With Evolutionary Implications: Stimulation of the Drosophila Sex-Determination Gene Sex-lethal by Its Target transformer

We describe a surprising new regulatory relationship between two key genes of the Drosophila sex-determination gene hierarchy, Sex-lethal (Sxl) and transformer (tra). A positive autoregulatory feedback loop for Sxl was known to maintain somatic cell female identity by producing SXL-F protein to continually instruct the target gene transformer (tra) to make its feminizing product, TRA-F. We discovered the reciprocal regulatory effect by studying genetically sensitized females: TRA-F from either maternal or zygotic tra expression stimulates Sxl-positive autoregulation. We found female-specific tra mRNA in eggs as predicted by this tra maternal effect, but not predicted by the prevailing view that tra has no germline function. TRA-F stimulation of Sxl seems to be direct at some point, since Sxl harbors highly conserved predicted TRA-F binding sites. Nevertheless, TRA-F stimulation of Sxl autoregulation in the gonadal soma also appears to have a cell-nonautonomous aspect, unprecedented for somatic Sxl regulation. This tra-Sxl retrograde regulatory circuit has evolutionary implications. In some Diptera, tra occupies Sxl's position as the gene that epigenetically maintains female identity through direct positive feedback on pre-mRNA splicing. The tra-mediated Sxl feedback in Drosophila may be a vestige of regulatory redundancy that facilitated the evolutionary transition from tra to Sxl as the master sex switch.

PML, YAP, and p73 Are Components of a Proapoptotic Autoregulatory Feedback Loop

p73 has been identified as a structural and functional homolog of the tumor suppressor p53. The transcriptional coactivator Yes-associated protein (YAP) has been demonstrated to interact with and to enhance p73-dependent apoptosis in response to DNA damage. Here, we show the existence of a proapoptotic autoregulatory feedback loop between p73, YAP, and the promyelocytic leukemia (PML) tumor suppressor gene. We demonstrate that PML is a direct transcriptional target of p73/YAP, and we show that PML transcriptional activation by p73/YAP is under the negative control of the proto-oncogenic Akt/PKB kinase. Importantly, we find that PML and YAP physically interact through their PVPVY and WW domains, respectively, causing PML-mediated sumoylation and stabilization of YAP. Hence, we determine a mechanistic pathway in response to DNA damage that could have relevant implications for the treatment of human cancer.

Inhibition of NOTCH1 Signaling and Glucocorticoid Therapy in T-ALL

Activating mutations in NOTCH1 are present in over 50% of T-cell acute lymphoblastic leukemias (T-ALL). Consequently, inhibition of NOTCH1 signaling with small molecule γ-secretase inhibitors (GSIs) has been proposed as a targeted therapy for this disease. However, GSIs fail to induce robust apoptosis in T-ALL cells and their clinical application has been limited by the development of severe gastrointestinal toxicity (mucous diarrhea and goblet cell metaplasia) resulting from systemic inhibition of NOTCH signaling. Here we show that combination therapy with GSIs plus glucocorticoids can reverse both glucocorticoid resistance in T-ALL and the occurrence of GSI-induced gut toxicity in vivo. The development of glucocorticoid resistance in T-ALL has been associated with the loss of a positive auto-regulatory transcriptional feedback loop required for glucocorticoid induced apoptosis. Using gene expression profiling and ChIP-on-chip analysis we demonstrated that HES1, a transcriptional repressor controlled by NOTCH1, inhibits specific regulatory elements in the glucocorticoid receptor promoter required for effective glucocorticoid receptor autoupregulation and glucocorticoid induced cell death. Consequently, downregulation of HES1 via inhibition of NOTCH1 signaling with GSIs or HES1 inactivation via shRNA knockdown restores glucocorticoid receptor autoupregulation and reverses glucocorticoid resistance in T-ALL cell lines and primary patient samples. Consistent with these results, combination therapy with dexamethasone and GSIs was highly effective in a mouse xenograft model of glucocorticoid resistant T-ALL. Surprisingly, these studies demonstrated not only improved antileukemic responses in mice treated with dexamethasone plus a GSI compared with dexamethasone or placebo treated controls (P<0.05), but also decreased mortality associated with GSI-induced gut toxicity in this model (P<0.01). These results suggested that glucocorticoids may have an enteroprotective effect against GSI-induced gut toxicity. Detailed histological analysis demonstrated a block of proliferation and increased goblet cell numbers in the intestine of GSI treated animals and a moderate increase in proliferation accompanied by increased Paneth cell numbers in the dexamethasone treated group. Notably, cotreatment with dexamethasone plus a GSI completely reversed the induction of goblet cell metaplasia typically induced by systemic inhibition of NOTCH signaling with GSIs. Likewise, dexamethasone also protected RBPJ-K conditional knockout mice, a genetic model of loss of NOTCH signaling, from developing goblet cell metaplasia in the gut. Interestingly, gene expression profiling analysis showed a marked upregulation of cyclin D2 expression in the gut of glucocorticoid treated mice. Moreover, dexamethasone treatment failed to protect Ccnd2 knockout animals from developing GSI-induced metaplasia, demonstrating a critical role of Ccnd2 upregulation in the protective effects of dexamethasone against GSI-induced gut toxicity. Overall, these results uncover a NOTCH1-HES1-glucocorticoid receptor regulatory axis in glucocorticoid resistant T-ALL and demonstrate an unanticipated protective effect of glucocorticoids against GSI-induced gut toxicity. Our studies warrant the clinical testing of glucocorticoids plus GSIs in the treatment of glucocorticoid-resistant T-ALL.

Mdm2 Regulates p53 mRNA Translation through Inhibitory Interactions with Ribosomal Protein L26

Mdm2 regulates the p53 tumor suppressor by promoting its proteasome-mediated degradation. Mdm2 and p53 engage in an autoregulatory feedback loop that maintains low p53 activity in nonstressed cells. We now report that Mdm2 regulates p53 levels also by targeting ribosomal protein L26. L26 binds p53 mRNA and augments its translation. Mdm2 binds L26 and drives its polyubiquitylation and proteasomal degradation. In addition, the binding of Mdm2 to L26 attenuates the association of L26 with p53 mRNA and represses L26-mediated augmentation of p53 protein synthesis. Under nonstressed conditions, both mechanisms help maintain low cellular p53 levels by constitutively tuning down p53 translation. In response to genotoxic stress, the inhibitory effect of Mdm2 on L26 is attenuated, enabling a rapid increase in p53 synthesis. The Mdm2-L26 interaction thus represents an additional important component of the autoregulatory feedback loop that dictates cellular p53 levels and activity.

A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence

Recognition sites for microRNAs (miRNAs) have been reported to be located in the 3' untranslated regions of transcripts. In a computational screen for highly conserved motifs within coding regions, we found an excess of sequences conserved at the nucleotide level within coding regions in the human genome, the highest scoring of which are enriched for miRNA target sequences. To validate our results, we experimentally demonstrated that the let-7 miRNA directly targets the miRNA-processing enzyme Dicer within its coding sequence, thus establishing a mechanism for a miRNA/Dicer autoregulatory negative feedback loop. We also found computational evidence to suggest that miRNA target sites in coding regions and 3' UTRs may differ in mechanism. This work demonstrates that miRNAs can directly target transcripts within their coding region in animals, and it suggests that a complete search for the regulatory targets of miRNAs should be expanded to include genes with recognition sites within their coding regions. As more genomes are sequenced, the methodological approach that we used for identifying motifs with high sequence conservation will be increasingly valuable for detecting functional sequence motifs within coding regions.

Transcriptional Autoregulatory Loops Are Highly Conserved in Vertebrate Evolution

BackgroundFeedback loops are the simplest building blocks of transcriptional regulatory networks and therefore their behavior in the course of evolution is of prime interest.MethodologyWe address the question of enrichment of the number of autoregulatory feedback loops in higher organisms. First, based on predicted autoregulatory binding sites we count the number of autoregulatory loops. We compare it to estimates obtained either by assuming that each (conserved) gene has the same chance to be a target of a given factor or by assuming that each conserved sequence position has an equal chance to be a binding site of the factor.ConclusionsWe demonstrate that the numbers of putative autoregulatory loops conserved between human and fugu, danio or chicken are significantly higher than expected. Moreover we show, that conserved autoregulatory binding sites cluster close to the factors' starts of transcription. We conclude, that transcriptional autoregulatory feedback loops constitute a core transcriptional network motif and their conservation has been maintained in higher vertebrate organism evolution.

Insomnia and Circadian Rhythm Sleep Disorders

&lt;p&gt;All living organisms exhibit endogenous circadian rhythms in physiology and behavior. In mammals, circadian rhythms are generated by a central clock located in the suprachiasmatic nucleus (SCN) of the hypothalamus. The basic molecular mechanism by which SCN neurons generate and maintain a self-sustaining rhythm is via an autoregulatory feedback loop in which oscillating circadian gene products regulate their own expression through a complex system of transcription, translation, and post translational processes. On average, the frequency of this circadian clock oscillation (free-running period) is slightly longer than 24 hours in humans. Therefore, precise alignment between internal circadian rhythms and the 24-hour physical and social environments requires daily adjustments or entrainment by synchronizing agents. Light, physical activity, and melatonin from the pineal gland are the primary synchronizing or entraining agents for the human circadian clock. Of these, light is the most potent entraining agent. &lt;/p&gt; &lt;h4&gt;ABOUT THE AUTHORS&lt;/h4&gt; &lt;p&gt;Phyllis C. Zee, MD, PhD; and Brandon S. Lu, MD, are with the Department of Neurology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois.&lt;/p&gt; &lt;p&gt;Address correspondence to Phyllis C. Zee, MD, PhD, Northwestern University, Feinberg School of Medicine, 710 North Lake Shore Drive, 11th Floor, Abbott Hall, Chicago, Illinois 60611; or e-mail: &lt;a href="mailto:p-zee@northwestern.edu"&gt;p-zee@northwestern.edu&lt;/a&gt;.&lt;/p&gt; &lt;p&gt;Dr. Zee and Lu have disclosed no relevant financial relationships.&lt;/p&gt; &lt;h4&gt;EDUCATIONAL OBJECTIVES&lt;/h4&gt; &lt;ol&gt;&lt;li&gt;Identify the role of the suprachiasmatic nucleus (SCN) in the control of sleep-wake function. &lt;/li&gt; &lt;li&gt;Review the signs and symptoms associated with circadian rhythm sleep disorders (CRSD). &lt;/li&gt; &lt;li&gt;Assess the use of bright light and melatonin of the treatment of CRSD. &lt;/li&gt; &lt;/ol&gt;

Expression and Suppressive Effects of Interleukin-19 on Vascular Smooth Muscle Cell Pathophysiology and Development of Intimal Hyperplasia

Anti-inflammatory cytokines may play a protective role in the progression of vascular disease. The purpose of this study was to characterize interleukin (IL)-19 expression and function in the development of intimal hyperplasia, and discern a potential mechanism of its direct effects on vascular smooth muscle cells (VSMCs). IL-19 is an immunomodulatory cytokine, the expression of which is reported to be restricted to inflammatory cells. In the present study, we found that IL-19 is not expressed in quiescent VSMCs or normal arteries but is induced in human arteries by injury and in cultured human VSMCs by inflammatory cytokines. Recombinant IL-19 significantly reduced VSMC proliferation (37.1 +/- 4.8 x 10(3) versus 72.2 +/- 6.1 x 10(3) cells/cm(2)) in a dose-dependent manner. IL-19 adenoviral gene transfer significantly reduced proliferation and neointimal formation in balloon angioplasty-injured rat carotid arteries (0.172 +/- 29.9, versus 0.333 +/- 71.9, and 0.309 +/- 56.6 microm(2)). IL-19 induced activation of STAT3 as well as the expression of the suppressor of cytokine signaling 5 (SOCS5) in VSMCs. IL-19 treatment significantly reduced the activation of p44/42 and p38 MAPKs in stimulated VSMCs. Additionally, SOCS5 was found to interact with both p44/42 and p38 MAPKs in IL-19-treated human VSMCs. This is the first description of the expression of both IL-19 and SOCS5 in VSMCs and of the functional interaction between SOCS5 and MAPKs. We propose that through induction of SOCS5 and inhibition of signal transduction, IL-19 expression in VSMCs may represent a novel, protective, autocrine response of VSMCs to inflammatory stimuli.

Suprachiasmatic nucleus and melatonin

AA-NAT= : aryl alkylamine N-acetyltransferase; AD= : Alzheimer disease; AVP= : arginine vasopressin; Ca2+= : calcium; CaMK= : calmodulin kinase; cAMP= : cyclic adenosine monophosphate; CREB= : cyclic adenosine monophosphate (cAMP) responsive element binding protein; GABA= : γ-aminobutyric acid; HI-OMT= : hydroxyl indol-O-methyltransferase; 5-HTP= : 5-hydroxytryptophan; IML= : intermediolateral cell column; MT= : melatonin; NE= : norepinephrine; NO= : nitric oxide; PAC2= : pituitary adenylate cyclase activating polypeptide receptor 2; PCACP= : pituitary adenylate cyclase activating polypeptide; PKA= : protein kinase A; PVN= : paraventricular nucleus; RAI1 = : retinoic acid induced gene 1; RHT= : retinohypothalamic tract; SCG= : superior cervical ganglion; SCN= : suprachiasmatic nucleus. Melatonin is a ubiquitous molecule that has a major role in regulation of sleep and other cyclical bodily activities. The suprachiasmatic nucleus contains neurons that exhibit a circadian pattern of activity and regulate melatonin secretion by the pineal gland in response to the environmental light/dark cycle. Melatonin signals both the time of the day (a “clock” function) and the time of the year (a “calendar” function) to all tissues of the body. Recent evidence indicates that abnormalities in the circadian control of melatonin secretion may have an important role in sleep disorders associated with aging, Alzheimer disease, and other degenerative and developmental disorders. Because of its antioxidant properties, melatonin may also have potential neuroprotective effects. There are several recent reviews on the mechanisms controlling circadian rhythms and melatonin secretion and functions.1–9 ### Suprachiasmatic nucleus activity and its entrainment by light. The suprachiasmatic nucleus (SCN) of the anterior hypothalamus is the master clock controlling circadian rhythms in mammals.1–3 The SCN neurons have a near-24-hour rhythm of electrical activity, even in the absence of environmental cues. This circadian activity reflects the rhythmic pattern of expression of core genes, called clock genes, that are regulated transcriptionally, translationally, and post-translationally by autoregulatory feedback loops.1–3 The circadian influences of SCN neurons are distributed throughout different target organs of the body by efferent neural and humoral signals, particularly circulating melatonin. The SCN controls melatonin secretion via a multisynaptic pathway1,6 (figure 1). Figure 1 Pathway involving entrainment of melatonin secretion by light The circadian regulation of melatonin secretion depends on an indirect pathway that originates from photosensitive ganglion cells of the retina and reaches, via the retinohypothalamic tract to the suprachiasmatic nucleus, which is the circadian pacemaker. The suprachiasmatic nucleus, via an inhibitory projection to the paraventricular nucleus of the hypothalamus, controls the sympathetic output to the pineal gland that is …

RNA Interference of the Clock Gene period Disrupts Circadian Rhythms in the Cricket Gryllus bimaculatus

Periodic expression of so-called clock genes is an essential part of the circadian clock. In Drosophila melanogaster the cyclic expression of per and tim through an autoregulatory feedback loop is believed to play a central role in circadian rhythm generation. However, it is still elusive whether this hypothesis is applicable to other insect species. Here it is shown that per gene plays a key role in the rhythm generation in the cricket Gryllus bimaculatus. Measurement of per mRNA levels in the optic lobe revealed the rhythmic expression of per in light cycles with a peak in the late day to early night, persisting in constant darkness. A single injection of per double-stranded RNA (dsRNA) into the abdomen of the final instar nymphs effectively knocked down the mRNA levels as adult to about 50% of control animals. Most of the per dsRNA-injected crickets completely lost the circadian locomotor activity rhythm in constant darkness up to 50 days after the injection, whereas those injected with DsRed2 dsRNA as a negative control clearly maintained it. The electrical activity of optic lobe efferents also became arrhythmic in the per dsRNA-injected crickets. These results not only suggest that per plays an important role in the circadian rhythm generation also in the cricket but also show that RNA interference is a powerful tool to dissect the molecular machinery of the cricket circadian clock.

Short‐period Effects of Zirconia and Titanium on Osteoblast MicroRNAs

MicroRNAs (miRNAs) are a class of small, functional, noncoding RNAs of 19 to 23 nucleotides which induce degradation of specific messenger RNAs (mRNAs), thus controlling the translational process (ie, synthesis of proteins from mRNAs). In addition, mRNAs regulate the promoter of specific miRNAs activating an autoregulatory feedback loop. Titanium and zirconium dioxide ceramics (ZDCs) are used to make dental implants. Because the molecular mechanism by which ZDC and Ti act on osteoblasts is incompletely understood, we attempted to get more information by comparing the effect of ZDC and Ti on osteoblast miRNAs. By using miRNA microarray technique, we identified in osteoblast-like cell line (MG63) grown on grade 3 Ti and ZDC disks several miRNAs whose expression was modified. We collected mRNAs after 24 hours of cell culturing to better understand molecular events related to early bone healing around inserted implants. An mRNA microarray technique was then performed as a control. There were six up- and four down-regulated miRNAs. Because every miRNA regulates hundreds of genes, we focused only on those related to bone formation. Among them, the most notable are BMP4 and 7, which are both up-regulated in osteoblasts cultured on Ti disks. The detected miRNAs differentially expressed in osteoblast-like cells grown on ZDC versus Ti act on a limited number of miRNAs and bone-related genes. The most notable are BMP4 and 7, which are more expressed in osteoblasts exposed to Ti surface. Consequently, we suggest that Ti surfaces could provide some advantages to immediate load implantology.

Trim11 modulates the function of neurogenic transcription factor Pax6 through ubiquitin–proteosome system

The transcription factor Pax6 is an important developmental regulator. Spatiotemporal control of Pax6 expression during embryogenesis is crucial for regulating distinct aspects of cortical development. Here, we report that Trim11, a member of the TRIM/RBCC protein family of E3 ubiquitin ligases, interacts with Pax6 and mediates Pax6 degradation via the ubiquitin-proteasome system. Trim11 overexpression decreases endogenous Pax6 protein levels and represses Pax6 functions, including Pax6-dependent transactivation and neurogenesis. Abrogation of endogenous Trim11 expression in the developing cortex increases the level of insoluble forms of Pax6 and enhances apoptosis. We provide evidence that the B30.2 domain of Trim11 is essential for the clearance of insoluble cell proteins. Furthermore, we show that the expression of Trim11 is directly regulated by Pax6 in developing cortex in vivo. Our findings indicate that an autoregulatory feedback loop between Trim11 and Pax6 maintains a balance between the levels of Pax6 and Trim11 proteins in cortical progenitors, having an essential role for the Pax6-dependent neurogenesis.

Proteasome-dependent autoregulation of Bruton tyrosine kinase (Btk) promoter via NF-κB

AbstractBruton tyrosine kinase (Btk) is critical for B-cell development. Btk regulates a plethora of signaling proteins, among them nuclear factor-[κ]B (NF-κB). Activation of NF-κB is a hallmark of B cells, and NF-κB signaling is severely compromised in Btk deficiency. We here present strong evidence indicating that NF-κB is required for efficient transcription of the Btk gene. First, we found that proteasome blockers and inhibitors of NF-κB signaling suppress Btk transcription and intracellular expression. Similar to Btk, proteasome inhibitors also reduced the expression of other members of this family of kinases, Itk, Bmx, and Tec. Second, 2 functional NF-κB–binding sites were found in the Btk promoter. Moreover, in live mice, by hydrodynamic transfection, we show that bortezomib (a blocker of proteasomes and NF-κB signaling), as well as NF-κB binding sequence-oligonucleotide decoys block Btk transcription. We also demonstrate that Btk induces NF-κB activity in mice. Collectively, we show that Btk uses a positive autoregulatory feedback mechanism to stimulate transcription from its own promoter via NF-κB.

Annealing Robust Fuzzy Neural Networks for Modeling of Molecular Autoregulatory Feedback Loop Systems

In this paper, the annealing robust fuzzy neural networks (ARFNNs) are proposed to improve the problems of fuzzy neural networks for modeling of the molecular autoregulatory feedback loop systems with outliers. Firstly, the support vector regression (SVR) approach is proposed to determine the initial structure of the ARFNNs. Because of a SVR approach is equivalent to solving a linear constrained quadratic programming problem under a fixed structure of SVR, the number of hidden nodes, the initial parameters and the initial weights of the ARFNNs are easy obtained via the SVR approach. Moreover, the results of the SVR are used as initial structure in the ARFNNs. At the same time, an annealing robust learning algorithm (ARLA) is used as the learning algorithm for the ARFNNs, and applied to adjust the parameters in the membership function as well as weights of the ARFNNs. That is, an ARLA is proposed to overcome the problems of initialization and the cut-off points in the robust learning algorithm. Hence, when an initial structure of the ARFNNs are determined by a SVR approach, the ARFNNs with the ARLA have fast convergence speed and robust against outliers for the modeling of the molecular autoregulatory feedback loop systems.

Comment on causality and pathway search in microarray time series experiment

Abstract Contact: nagarajanradhakrish@uams.edu

Aberrant activation of nuclear factor of activated T cell 2 in lamina propria mononuclear cells in ulcerative colitis

To investigate the role of nuclear factor of activated T cell 2 (NFAT2), the major NFAT protein in peripheral T cells, in sustained T cell activation and intractable inflammation in human ulcerative colitis (UC). We used two-dimensional gel-electrophoresis, immunohistochemistry, double immunohistochemical staining, and confocal microscopy to inspect the expression of NFAT2 in 107, 15, 48 and 5 cases of UC, Crohn's disease (CD), non-specific colitis, and 5 healthy individuals, respectively. Up-regulation with profound nucleo-translocation/activation of NFAT2 of lamina propria mononuclear cells (LPMC) of colonic mucosa was found specifically in the affected colonic mucosa from patients with UC, as compared to CD or NC (P < 0.001, Kruskal-Wallis test). Nucleo-translocation/activation of NFAT2 primarily occurred in CD8+T, but was less prominent in CD4+ T cells or CD20+B cells. It was strongly associated with the disease activity, including endoscopic stage (tau = 0.2145, P = 0.0281) and histologic grade (tau = 0.4167, P < 0.001). We disclose for the first time the nucleo-translocation/activation of NFAT2 in lamina propria mononuclear cells in ulcerative colitis. Activation of NFAT2 was specific for ulcerative colitis and highly associated with disease activity. Since activation of NFAT2 is implicated in an auto-regulatory positive feedback loop of sustained T-cell activation and NFAT proteins play key roles in the calcium/calcineurin signaling pathways, our results not only provide new insights into the mechanism for sustained intractable inflammation, but also suggest the calcium-calcineurin/NFAT pathway as a new therapeutic target for ulcerative colitis.

Robust and sensitive control of a quorum‐sensing circuit by two interlocked feedback loops

The quorum-sensing (QS) response of Vibrio fischeri involves a rapid switch between low and high induction states of the lux operon over a narrow concentration range of the autoinducer (AI) 3-oxo-hexanoyl-L-homoserine lactone. In this system, LuxR is an AI-dependent positive regulator of the lux operon, which encodes the AI synthase. This creates a positive feedback loop common in many bacterial species that exhibit QS-controlled gene expression. Applying a combination of modeling and experimental analyses, we provide evidence for a LuxR autoregulatory feedback loop that allows LuxR to increase its concentration in the cell during the switch to full lux activation. Using synthetic lux gene fragments, with or without the AI synthase gene, we show that the buildup of LuxR provides more sensitivity to increasing AI, and promotes the induction process. Elevated LuxR levels buffer against spurious variations in AI levels ensuring a robust response that endows the system with enhanced hysteresis. LuxR autoregulation also allows for two distinct responses within the same cell population.