Cryo-EM structure of CtBP2 confirms tetrameric architecture

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Riboswitch Detection Using Profile Hidden Markov Models

Background  

Riboswitches are a type of noncoding RNA that regulate gene expression by switching from one structural conformation to another on ligand binding. The various classes of riboswitches discovered so far are differentiated by the ligand, which on binding induces a conformational switch. Every class of riboswitch is characterized by an aptamer domain, which provides the site for ligand binding, and an expression platform that undergoes conformational change on ligand binding. The sequence and structure of the aptamer domain is highly conserved in riboswitches belonging to the same class. We propose a method for fast and accurate identification of riboswitches using profile Hidden Markov Models (pHMM). Our method exploits the high degree of sequence conservation that characterizes the aptamer domain.     

ADSBET2: Automated Determination of Salt-Bridge Energy-Terms version 2

AvailabilityADSBET2 is freely available at http://sourceforge.net/projects/ADSBET2/ for all users.     

Balancing functions of annexin A6 maintain equilibrium between hypertrophy and apoptosis in cardiomyocytes

Pathological cardiac hypertrophy is a major risk factor associated with heart failure, a state concomitant with increased cell death. However, the mechanism governing progression of hypertrophy to apoptosis at the single-cell level remains elusive. Here, we demonstrate annexin A6 (Anxa6), a calcium (Ca²⁺)-dependent phospholipid-binding protein critically regulates the transition of chronic hypertrophied cardiomyocytes to apoptosis. Treatment of the H9c2(2-1) cardiomyocytes with hypertrophic agonists upregulates and relocalizes Anxa6 with increased cytosolic punctate appearance. Live cell imaging revealed that chronic exposure to hypertrophic agonists such as phenylephrine (PE) compromises the mitochondrial membrane potential (ΔΨ_m) and morphological dynamics. Such chronic hypertrophic induction also activated the caspases 9 and 3 and induced cleavage of the poly-(ADP-ribose) polymerase 1 (Parp1), which are the typical downstream events in the mitochondrial pathways of apoptosis. An increased rate of apoptosis was evident in the hypertrophied cardiomyocytes after 48–72 h of treatment with the hypertrophic agonists. Anxa6 was progressively associated with the mitochondrial fraction under chronic hypertrophic stimulation, and Anxa6 knockdown severely abrogated mitochondrial network and dynamics. Ectopically expressed Anxa6 protected the mitochondrial morphology and dynamics under PE treatment, and also increased the cellular susceptibility to apoptosis. Biochemical analysis showed that Anxa6 interacts with Parp1 and its 89 kDa cleaved product in a Ca²⁺-dependent manner through the N-terminal residues (1–28). Furthermore, expression of Anxa6^S13E, a mutant dominant negative with respect to Parp1 binding, served as an enhancer of mitochondrial dynamics, even under chronic PE treatment. Chemical inhibition of Parp1 activity released the cellular vulnerability to apoptosis in Anxa6-expressing stable cell lines, thereby shifting the equilibrium away from cell death. Taken together, the present study depicts a dual regulatory function of Anxa6 that is crucial for balancing hypertrophy with apoptosis in cardiomyocytes.Complex machineries govern the life and death decisions in mammalian cells through a dynamic equilibrium, which is essential for physiological homeostasis.¹ Such equilibrium is critical for cardiac myocytes because of their terminally differentiated states and low proliferative capacities. Stress response in cardiomyocytes often involves a switch between survival and cell death pathways.^{2, 3, 4} Cardiomyocyte hypertrophy is an adaptive response to stress, which may turn maladaptive and fatal,⁵ as evident in cardiovascular disorders that leads to heart failure.⁶ Hypertrophied phenotypes are also associated with a balance between cell growth and programmed cell death.⁷ These processes are aided by several patrolling proteins, which sense and operate to ameliorate the anomalies.^{8, 9} Understanding the dynamics of such signaling events is vital for the development of novel therapeutic strategies.Anxa6 belongs to the annexin family of calcium (Ca²⁺)/phospholipid-binding proteins.¹⁰ A major cardiac annexin,¹¹ Anxa6 has diverse functions ranging from handling intracellular Ca²⁺ signaling, cholesterol transport,¹² Ras inactivation¹³ and vesicular traffic.¹⁴ Anxa6 mostly functions as an intracellular scaffold.¹⁵ Although mice with targeted depletion of the Anxa6 gene remain viable,¹⁶ functional redundancies within the annexin family have been proposed to compensate for the loss of Anxa6 function.^{17, 18} A 10-fold overexpression of Anxa6 targeted to the heart developed cardiomyopathies in mice, whereas cardiomyocytes from Anxa6-knockout mice exhibited increased contractility and altered Ca²⁺ turnover.^{19, 20} Such contradictory findings may indicate participation of Anxa6 in counterbalancing signaling mechanisms. Moreover, end-stage heart failures have been reported to be associated with downregulation of Anxa6, and, in general, Anxa6 has compensatory roles in chronic pathological conditions.^{20, 21, 22} However, the function of differential Anxa6 expression or dynamics in chronic cardiomyocyte hypertrophy is poorly understood.We have reported the interactions of Anxa6 with the sarcomeric α-actinin and its role in cardiomyocyte contractility.²³ Recently, we have characterized a role of Anxa6 in the antihypertrophic signaling via the regulation of atrial natriuretic peptide (ANP) secretion.²⁴ The mechanistic spectrum of Anxa6 in the earlier study was limited to a short-term (24 h) exposure of H9c2 cardiomyocytes to the α1-adrenergic receptor agonist phenylephrine (PE). The dynamics of Anxa6 within this small window yielded valuable insight into the spatiotemporal regulation of hypertrophic signaling. Here, we extended the study to understand the dynamics of Anxa6 under chronic hypertrophic conditions. The mechanodeficient H9c2(2-1) cardiomyocyte line has been instrumental in our study to rule out the contributions of Anxa6 towards contractility,²³ owing to its multidimensional scaffold activity and functional compensations.^{17, 18} The H9c2 cardiomyocytes have been extensively characterized and ARE an established animal origin-free model for studying signal-transduction pathways in cardiomyocytes, including hypertrophy.^{25, 26}Adrenergic stimulation is crucial in compensatory and pathological cardiac hypertrophy, an early state that may proceed towards heart failure.²⁷ Cardiac hypertrophy at advanced stages (chronic) is associated with mitochondrial dysfunction, which also contributes to cardiac decompensation.²⁸ To explore the temporal events under chronic hypertrophy, we analyzed the effects of adrenergic induction on mitochondrial membrane potential (ΔΨm) and morphological dynamics, parameters that are directly correlated with mitochondrial dysfunction and programmed cell death.^{29, 30, 31} Anxa6 has been reported to be associated with mitochondria in some cell types.^{17, 32, 33} In the present study, we aim to understand the functions of Anxa6 under chronic hypertrophic conditions that may progress towards apoptosis.     

Politics of archiving: hawkers and pavement dwellers in Calcutta

In the last decade, several influential scholars have rigorously worked on the impact of neoliberal globalization on the poor in the cities of the South. But they have yet to provide a comprehensive account of how and why some groups in the margins are seen to successfully negotiate with the new modes of governing populations and increase their visibility as a “category,” while some groups fail to do so. This paper seeks to bridge this research gap by comparing a successful and a failed mobilization in Calcutta. In both cases, use of the footpath has been central. The paper shows how the success of the hawkers in claiming the footpath is tied to the marginalization of the claims of the pavement dwellers that has (a) homogenized the representation of the footpath as only used by pedestrians and hawkers and (b) led to the elision of the pavement dwellers as a governmental category. The paper argues that by arrogating to themselves an archival function—which is conventionally associated with the governmental state—sections of population like the hawkers can become successful in their negotiations with the government.