Distinct Functional Modes Research Articles

TALE factors use two distinct functional modes to control an essential zebrafish gene expression program.

TALE factors are broadly expressed embryonically and known to function in complexes with transcription factors (TFs) like Hox proteins at gastrula/segmentation stages, but it is unclear if such generally expressed factors act by the same mechanism throughout embryogenesis. We identify a TALE-dependent gene regulatory network (GRN) required for anterior development and detect TALE occupancy associated with this GRN throughout embryogenesis. At blastula stages, we uncover a novel functional mode for TALE factors, where they occupy genomic DECA motifs with nearby NF-Y sites. We demonstrate that TALE and NF-Y form complexes and regulate chromatin state at genes of this GRN. At segmentation stages, GRN-associated TALE occupancy expands to include HEXA motifs near PBX:HOX sites. Hence, TALE factors control a key GRN, but utilize distinct DNA motifs and protein partners at different stages - a strategy that may also explain their oncogenic potential and may be employed by other broadly expressed TFs.

An easily reversible structural change underlies mechanisms enabling desert crust cyanobacteria to survive desiccation

Biological desert sand crusts are the foundation of desert ecosystems, stabilizing the sands and allowing colonization by higher order organisms. The first colonizers of the desert sands are cyanobacteria. Facing the harsh conditions of the desert, these organisms must withstand frequent desiccation–hydration cycles, combined with high light intensities. Here, we characterize structural and functional modifications to the photosynthetic apparatus that enable a cyanobacterium, Leptolyngbya sp., to thrive under these conditions.Using multiple in vivo spectroscopic and imaging techniques, we identified two complementary mechanisms for dissipating absorbed energy in the desiccated state. The first mechanism involves the reorganization of the phycobilisome antenna system, increasing excitonic coupling between antenna components. This provides better energy dissipation in the antenna rather than directed exciton transfer to the reaction center. The second mechanism is driven by constriction of the thylakoid lumen which limits diffusion of plastocyanin to P700. The accumulation of P700+ not only prevents light-induced charge separation but also efficiently quenches excitation energy.These protection mechanisms employ existing components of the photosynthetic apparatus, forming two distinct functional modes. Small changes in the structure of the thylakoid membranes are sufficient for quenching of all absorbed energy in the desiccated state, protecting the photosynthetic apparatus from photoinhibitory damage. These changes can be easily reversed upon rehydration, returning the system to its high photosynthetic quantum efficiency.

Distinct functional modes of SUMOylation for retinoid X receptor alpha

The present study investigated human retinoid X receptor alpha (hRXRα) as a substrate for modification with small ubiquitin like modifier (SUMO) and how members of the protein inhibitor of activated STAT (PIAS) family may impact upon this process. In agreement with a previous study, we validate Ubc9 to facilitate SUMOylation of hRXRα at lysine 108 but note this modification to occur for all isoforms rather than specifically with SUMO1 and to preferentially occur with the unliganded form of hRXRα. SUMOylation of hRXRα is significantly enhanced through PIAS4-mediated activity with lysine 245 identified as a specific SUMO2 acceptor site modified in a PIAS4-dependent fashion. While individual mutations at lysine 108 or 245 modestly increase receptor activity, the combined loss of SUMOylation at both sites significantly potentiates the transcriptional responsiveness of hRXRα suggesting both sites may cooperate in a DNA element-dependent context. Our findings highlight combinatorial effects of SUMOylation may regulate RXRα-directed signalling in a gene-specific fashion.

Top-Down Modulation on Perceptual Decision with Balanced Inhibition through Feedforward and Feedback Inhibitory Neurons

Recent physiological studies have shown that neurons in various regions of the central nervous systems continuously receive noisy excitatory and inhibitory synaptic inputs in a balanced and covaried fashion. While this balanced synaptic input (BSI) is typically described in terms of maintaining the stability of neural circuits, a number of experimental and theoretical studies have suggested that BSI plays a proactive role in brain functions such as top-down modulation for executive control. Two issues have remained unclear in this picture. First, given the noisy nature of neuronal activities in neural circuits, how do the modulatory effects change if the top-down control implements BSI with different ratios between inhibition and excitation? Second, how is a top-down BSI realized via only excitatory long-range projections in the neocortex? To address the first issue, we systematically tested how the inhibition/excitation ratio affects the accuracy and reaction times of a spiking neural circuit model of perceptual decision. We defined an energy function to characterize the network dynamics, and found that different ratios modulate the energy function of the circuit differently and form two distinct functional modes. To address the second issue, we tested BSI with long-distance projection to inhibitory neurons that are either feedforward or feedback, depending on whether these inhibitory neurons do or do not receive inputs from local excitatory cells, respectively. We found that BSI occurs in both cases. Furthermore, when relying on feedback inhibitory neurons, through the recurrent interactions inside the circuit, BSI dynamically and automatically speeds up the decision by gradually reducing its inhibitory component in the course of a trial when a decision process takes too long.

Security Against Hardware Trojan Attacks Using Key-Based Design Obfuscation

Malicious modification of hardware in untrusted fabrication facilities, referred to as hardware Trojan, has emerged as a major security concern. Comprehensive detection of these Trojans during post-manufacturing test has been shown to be extremely difficult. Hence, it is important to develop design techniques that provide effective countermeasures against hardware Trojans by either preventing Trojan attacks or facilitating detection during test. Obfuscation is a technique that is conventionally employed to prevent piracy of software and hardware intellectual property (IP). In this work, we propose a novel application of key-based circuit structure and functionality obfuscation to achieve protection against hardware Trojans triggered by rare internal circuit conditions. The proposed obfuscation scheme is based on judicious modification of the state transition function, which creates two distinct functional modes: normal and obfuscated. A circuit transitions from the obfuscated to the normal mode only upon application of a specific input sequence, which defines the key. We show that it provides security against Trojan attacks in two ways: (1) it makes some inserted Trojans benign, i.e. they become effective only in the obfuscated mode; and (2) it prevents an adversary from exploiting the true rare events in a circuit to insert hard-to-detect Trojans. The proposed design methodology can thus achieve simultaneous protection from hardware Trojans and hardware IP piracy. Besides protecting ICs against Trojan attacks in foundry, we show that it can also protect against malicious modifications by untrusted computer-aided design (CAD) tools in both SoC and FPGA design flows. Simulation results for a set of benchmark circuits show that the scheme is capable of achieving high levels of security against Trojan attacks at modest area, power and delay overhead.

An interactive software tool for system identification

The paper describes the conceptual basis, main features and functionality of an interactive software tool developed in support of system identification education and discovery. This Interactive Tool for System Identification Education (ITSIE) has been developed using Sysquake, a Matlab-like language with fast execution and excellent facilities for interactive graphics, and is deliverd as a stand-alone executable that is readily accessible to students and engineers. ITSIE provides two distinct functional modes that are very useful from an educational and industrial point of view. The simulation mode enables the user to evaluate the main stages of system identification, from input signal design through model validation, simultaneously and interactively in one screen on a user-specified dynamical system. The real data mode allows the user to load experimental data obtained externally and identify suitable models in an interactive fashion. The interactive tool enables students and engineers in industry to discover a myriad of fundamental system identification concepts with a much lower learning curve than existing methods.

Teaching System Identification Through Interactivity

The paper describes the main features of an interactive software tool developed in support of system identification education. This Interactive Tool for System Identification Education (ITSIE) provides two distinct functional modes that are very useful from an educational point of view. The simulation mode enables the student to evaluate the main stages of system identification, from input signal design through model validation, simultaneously and interactively in one screen on a user-specified dynamical system. The real data mode allows the user to load experimental data obtained externally and identify suitable models in an interactive fashion. The interactive tool enables students to discover a myriad of fundamental system identification concepts with a much lower learning curve than existing methods.

Hypertonicity-induced cation channels rescue cells from staurosporine-elicited apoptosis.

Cell shrinkage is one of the earliest events during apoptosis. Cell shrinkage also occurs upon hypertonic stress, and previous work has shown that hypertonicity-induced cation channels (HICCs) underlie a highly efficient mechanism of recovery from cell shrinkage, called the regulatory volume increase (RVI), in many cell types. Here, the effects of HICC activation on staurosporine-induced apoptotic volume decrease (AVD) and apoptosis were studied in HeLa cells by means of electronic cell sizing and whole-cell patch-clamp recording. It was found that hypertonic stress reduces staurosporine-induced AVD and cell death (associated with caspase-3/7 activation and DNA fragmentation), and that this effect was actually due to activation of the HICC. On the other hand, staurosporine was found to significantly reduce osmotic HICC activation. It is concluded that AVD and RVI reflect two fundamentally distinct functional modes in terms of the activity and role of the HICC, in a shrunken cell. Our results also demonstrate, for the first time, the ability of the HICC to rescue cells from the process of programmed cell death.

Dicer-1, but not Loquacious, is critical for assembly of miRNA-induced silencing complexes

Double-stranded RNA-binding proteins (dsRBPs), such as R2D2 and Loquacious (Loqs), function in tandem with Dicer (Dcr) enzymes in RNA interference (RNAi). In Drosophila, Dcr-1/Loqs and Dcr-2/R2D2 complexes generate microRNAs (miRNAs) and small interfering RNAs (siRNAs), respectively. Although R2D2 does not regulate siRNA production, R2D2 and Dcr-2 coordinately bind siRNAs to promote assembly of the siRNA-induced silencing (siRISC) complexes. Conversely, Loqs enhances miRNA production. It is uncertain if Dcr-1 and Loqs facilitate miRNA loading onto the miRISC complexes. Here we used loqs knockout (KO) flies to characterize the physiological functions of Loqs in the miRNA pathway. Northern analysis revealed consistent accumulation of precursor (pre)-miRNAs in loqs(KO) flies. However, the lack of Loqs had differential effects on mature miRNAs: some are diminished, whereas others maintain wild-type levels. Importantly, the data suggest that miRNA production is not the rate-limiting step of the miRNA pathway. We show that Dcr-1, but not Loqs, is critical for assembly of miRISCs by using dcr-1 or loqs null egg extract. Consistent with this, recombinant Dcr-1 could efficiently interact with miRNA duplex in the absence of Loqs. Together, our results indicate that Loqs plays a prominent role in miRNA biogenesis, but is largely dispensable for miRISC assembly. Thus, Loqs and R2D2 represent two distinct functional modes for dsRBPs in the RNAi pathways.

Smooth muscle sparklet Cav channels defined: 1.2 is the number

Systemic blood pressure and tissue blood flow are regulated by the contractile status of smooth muscle cells located within the wall of small arteries and arterioles. One important signal that regulates arterial smooth muscle cell contractility is the intracellular calcium ion (Ca2+) concentration. Although Ca2+ was once considered to act only as a global intracellular signaling element, research performed over the past decade has revealed Ca2+ to act in a far more dynamic and versatile manner than previously thought possible.

Collision-induced signal enhancement: a method to increase product ion intensities in MS/MS and MSn experiments.

Collision-induced signal enhancement (CISE), a new technique to enhance the MSn capabilities of the quadrupole ion trap, is demonstrated. CISE is based on the chemistry, i.e., the dissociation pathways, of the analyte examined. Polysaccharides up to hexamers are used to demonstrate the capabilities of CISE to enhance signal in two distinct functional modes. Mode 1 CISE is designed to enhance the signal of an ion desired for MSn analysis. Mode 2 CISE is designed to enhance structurally significant product ions in an MS/MS spectrum. Two different approaches can be utilized to effect the two functional modes of CISE. Both approaches use conventional resonant excitation techniques to effect dissociation, which is performed nonanalytically, i.e., without isolation of the ions to be dissociated. The two approaches are (1) single-frequency resonance excitation, and (2) broad-band wave form resonant excitation. Experimental results for Mode 1 CISE analysis demonstrate up to a 17.3-fold signal increase for the single-frequency approach and 5.3-fold using broad-band excitation. Mode 2 CISE analysis shows up to a 16.3-fold increase in signal strength with single-frequency excitation and 3.3-fold using broad-band excitation.

Effector contributions to G beta gamma-mediated signaling as revealed by muscarinic potassium channel gating.

Receptor-mediated activation of heterotrimeric G proteins leading to dissociation of the G alpha subunit from G beta gamma is a highly conserved signaling strategy used by numerous extracellular stimuli. Although G beta gamma subunits regulate a variety of effectors, including kinases, cyclases, phospholipases, and ion channels (Clapham, D.E., and E.J. Neer. 1993. Nature (Lond.). 365:403-406), few tools exist for probing instantaneous G beta gamma-effector interactions and little is known about the kinetic contributions of effectors to the signaling process. In this study, we used the atrial muscarinic K + channel, which is activated by direct interactions with G beta gamma subunits (Logothetis, D.E., Y. Kurachi J. Galper, E.J. Neer, and D.E. Clap. 1987. Nature (Lond.). 325:321-326; Wickman, K., J. A. Iniguez-Liuhi, P.A. Davenport, R. Taussig, G.B. Krapivinsky, M.E. Linder, A.G. Gilman, and D.E. Clapham. 1994. Nature (Lond.). 366: 654-663; Huang, C.-L., P.A. Slesinger, P.J. Casey, Y.N. Jan, and L.Y. Jan. 1995. Neuron. 15:1133-1143), as a sensitive reporter of the dynamics of G beta gamma-effector interactions. Muscarinic K+ channels exhibit bursting behavior upon G protein activation, shifting between three distinct functional modes, characterized by the frequency of channel openings during individual bursts. Acetylcholine concentration (and by inference, the concentration of activated G beta gamma) controls the fraction of time spent in each mode without changing either the burst duration or channel gating within individual modes. The picture which emerges is of a G beta gamma effector with allosteric regulation and an intrinsic "off" switch which serves to limit its own activation. These two features combine to establish exquisite channel sensitivity to changes in G beta gamma concentration, and may be indicative of the factors regulating other G beta gamma-modulated effectors.