ISRN Cell Biology The latest articles from Hindawi Publishing Corporation © 2014 , Hindawi Publishing Corporation . All rights reserved. Identification of Unique miRNA Biomarkers in Colorectal Adenoma and Carcinoma Using Microarray: Evaluation of Their Putative Role in Disease Progression Tue, 22 Apr 2014 00:00:00 +0000 MicroRNAs (miRNAs) are known to be dysregulated and play a key role in cancer progression. The present study aims to identify the miRNAs associated with colorectal adenoma and carcinoma to evaluate their role in tumor progression and metastasis using microarray. In silico analysis of miRNAs was performed on five different microarray data sets that represented the genes and miRNAs expressed in colorectal adenoma and carcinoma. We identified 10 different miRNAs that were common to both colorectal adenoma and carcinoma, namely, miR9, miR96, miR135b, miR137, miR147, miR182, miR183, miR196b, miR224, and miR503. Of these, miR135b and miR147 were significantly downregulated in colorectal adenoma but upregulated in carcinoma. In addition, we studied the gene expression profile associated with colorectal adenocarcinoma and identified three genes, namely, ZBED3, SLC10A3, and FOXQ1, that were significantly downregulated in colorectal adenoma compared to carcinoma. Interestingly, of all the miRNAs and genes associated with colorectal adenocarcinoma, the myoglobin (MB) gene was identified to be under the direct influence of miR135b, showing an inverse relationship between them in adenoma and carcinoma. Most of the identified miRNAs and associated genes are involved in signaling pathways of cell proliferation, angiogenesis, and metastasis. The present study has identified putative miRNA targets and their associated gene networks which could be used as potential biomarkers of colon adenocarcinoma. Moreover, the association of miR135b and MB gene is very unique and can be considered as a lead candidate for novel cancer therapeutics. Kothandaraman Narasimhan, Kalamegam Gauthaman, Peter Natesan Pushparaj, Govindasamy Meenakumari, Adeel Gulzar Ahmed Chaudhary, Adel Abuzenadah, Mamdooh Abdullah Gari, Mohammed Al Qahtani, and Jayapal Manikandan Copyright © 2014 Kothandaraman Narasimhan et al. All rights reserved. Nonneuronal Cholinergic System in Breast Tumors and Dendritic Cells: Does It Improve or Worsen the Response to Tumor? Thu, 19 Dec 2013 15:27:15 +0000 Besides being the main neurotransmitter in the parasympathetic nervous system, acetylcholine (ACh) can act as a signaling molecule in nonneuronal tissues. For this reason, ACh and the enzymes that synthesize and degrade it (choline acetyltransferase and acetylcholinesterase) as well as muscarinic (mAChRs) and nicotinic receptors conform the non-neuronal cholinergic system (nNCS). It has been reported that nNCS regulates basal cellular functions including survival, proliferation, adhesion, and migration. Moreover, nNCS is broadly expressed in tumors and in different components of the immune system. In this review, we summarize the role of nNCS in tumors and in different immune cell types focusing on the expression and function of mAChRs in breast tumors and dendritic cells (DCs) and discussing the role of DCs in breast cancer. Marisa Vulcano, María Gabriela Lombardi, and María Elena Sales Copyright © 2013 Marisa Vulcano et al. All rights reserved. Generation of Constitutive Active ERK Mutants as Tools for Cancer Research in Zebrafish Mon, 25 Nov 2013 11:06:37 +0000 The extracellular-signal-regulated-kinase (ERK) signaling pathway is essential for vertebrate development and is frequently deregulated in human and zebrafish tumors. Previously, we cloned and characterized the zebrafish MAPK gene family and showed that ERK2 is crucial for cell migration and early zebrafish embryogenesis. To further study ERK2 function we generated constitutively active mutant forms of the ERK proteins by introducing conserved point mutations. We validated the enhanced protein activity in vitro by transfection of constructs into zebrafish fibroblast (zf4) cells and demonstrated elevated phosphorylation levels of downstream targets P90RSK and CREB, by and specifically. In vivo validation was performed by ectopic expression of corresponding mRNAs in the transgenic zebrafish FGF-ERK2 reporter fish line Tg(Dusp6:d2EGFP). Both mutant ERK2 isoforms induced elevated transgene expression compared to , confirming increased kinase activity in vivo. Phospho-kinomic analysis on peptide microarrays was performed to identify new targets in embryos injected with FGF8 or mRNAs. We detected both FGF8 specific and common signalling targets. Interestingly, with both mRNAs we found increased phosphorylation levels of CDK1, which is critical for proper G2/M phase transition and mitotic entry in proliferation control. These results corroborate that constitutive activation of the ERK2 pathway leads to enhanced, possibly oncogenic, proliferation. Hanan Rian, S. F. Gabriel Krens, Herman P. Spaink, and B. Ewa Snaar-Jagalska Copyright © 2013 Hanan Rian et al. All rights reserved. A Microscopic View of the Store-Operated Calcium Entry-Pathway Sun, 10 Nov 2013 13:37:06 +0000 Orai and STIM are the basic components of a highly complex and regulated mechanism for Ca2+ entry into the cell, known as store-operated calcium entry (SOCE). The activation of plasma membrane G-protein-coupled receptors associated with the phospholipase C cascade results in the rapid and massive production of inositol 1,4,5-triphosphate (IP3). This second messenger triggers the massive efflux of Ca2+ from the endoplasmic reticulum and into the cytosol, resulting in the oligomerization of the stromal interacting molecule (STIM1), a sensor of ER Ca2+. STIM1 oligomers (the so-called puncta) activate Orai channels at the plasma membrane, triggering the influx of Ca2+ into the cytosol. Several microscopy techniques have been implemented to study SOCE, resulting in stunning images of protein complexes assembling in real time. However, little attention has been paid to the findings about this complex mechanism from the imaging point of view, some of which appear to produce contradictory results. In the present review we gathered all the information about SOCE obtained with imaging techniques and contrast these findings with those obtained with alternative methods. Jonathan Pacheco and Luis Vaca Copyright © 2013 Jonathan Pacheco and Luis Vaca. All rights reserved. Proteomics Characterization of the Secretome from Rat Pancreatic Stellate Cells with ATP-Binding Cassette Transporters (ABCG2) and NCAM Phenotype Thu, 31 Oct 2013 13:18:57 +0000 We have previously reported the identification of a pancreata mitoxantrone-resistant cell population which expressed the ABCG2 transporter with a pancreatic stellate cells phenotype (PaSC) and ability of secreting insulin after inducing their differentiation. The characterization of the secretome of this cell population by two-dimensional electrophoresis (2D) coupled with mass spectrometry MALDI-TOF was able to identify seventy-six protein spots involved in different cellular processes: development/differentiation, proteases, immune response, and other. Moreover, Ingenuity Pathway Analysis displayed several significant networks and TGFβ1 molecule was identified as a central node of one of them. The effect of this active molecule secreted in the conditioned medium was investigated in ductal cell line (ARIP). The results showed that the conditioned medium inhibited their proliferation without affecting their cell viability. Additionally, they showed an upregulation of PDX1 and downregulation of CK19. The rate of ARIP cell proliferation was recovered, but no effects on the gene expression were observed after using TGFβ1-neutralising antibody. Proteins associated with cell growth, development and differentiation such as PEDF, LIF, and Wnt5b, identified in the secretome, could be involved in the observed transcription changes. These finding may suggest a new paracrine action of PaSCs involved in the proliferation and differentiation pathways not yet identified. Maria Lucas, Eugenia Mato, Silvia Barceló-Batllori, Ramon Gomis, and Anna Novials Copyright © 2013 Maria Lucas et al. All rights reserved. Downregulation of Caspase-2 Expression in Somitic Cells following Coculture with Chicken Notochord Wed, 31 Jul 2013 13:14:43 +0000 Somites are spherical aggregations of mesodermal cells located on either sides of neural tube and are differentiated into sclerotome and dermomyotome. Notochord as an axial mesoderm has a major role in somitic cell survival and differentiation in vivo. Despite secreting the survival factors, how to notochord inhibits somitic cells apoptosis remains to be elusive. So, this study was aimed to investigate downregulation of caspase-2 expression in somitic cells upon coculturing with notochord. By using alginate system to encapsulate the isolated notochord in Somite + Notochord group, the embryonic somites were cocultured with the notochord on different days. Concurrently in somite group, the somites were cultured alone. Survival assay with MTT showed that the rate of viability in somitic cells cocultured with notochord increased from 59% on day 2 to 89.7% on day 6 but decreased to 38.5% on day 10 after coculturing. Reverse transcriptase-polymerase chain reaction and spectrophotometry analysis also confirmed these findings and showed low caspase-2 and high Bcl-2 expressions and low caspase-2 enzyme activity in somitic cells cocultured with notochord, respectively. These results clearly show that the notochord enhances survival of somitic cells in vitro through downregulating of caspase-2 expression along with triggering differentiation of somitic cells to Pax-1 expressing mesenchymal cells. Rezgar Rahbari, Mohammad Mazani, Mohammad Ghasem Golmohammadi, and Mohsen Sagha Copyright © 2013 Rezgar Rahbari et al. All rights reserved. Integrin Signaling as a Cancer Drug Target Wed, 24 Jul 2013 09:06:32 +0000 Integrins are transmembrane receptors that mediate cell adhesion to neighboring cells and to the extracellular matrix. Here, the various modes in which integrin-mediated adhesion regulates intracellular signaling pathways impinging on cell survival, proliferation, and differentiation are considered. Subsequently, evidence that integrins also control crucial signaling cascades in cancer cells is discussed. Lastly, the important role of integrin signaling in tumor cells as well as in stromal cells that support cancer growth, metastasis, and therapy resistance indicates that integrin signaling may be an attractive target for (combined) cancer therapy strategies. Current approaches to target integrins in this context are reviewed. Erik H. J. Danen Copyright © 2013 Erik H. J. Danen. All rights reserved. A C-Terminal Transmembrane Anchor Targets the Nuage-Localized Spermatogenic Protein Gasz to the Mitochondrial Surface Mon, 15 Jul 2013 12:32:45 +0000 Mitochondria, normally tubular and distributed throughout the cell, are instead found in spermatocytes in perinuclear clusters in close association with nuage, an amorphous organelle composed of RNA and RNA-processing proteins that generate piRNAs. piRNAs are a form of RNAi required for transposon suppression and ultimately fertility. MitoPLD, another protein required for piRNA production, is anchored to the mitochondrial surface, suggesting that the nuage, also known as intermitochondrial cement, needs to be juxtaposed there to bring MitoPLD into proximity with the remainder of the piRNA-generating machinery. However, the mechanism underlying the juxtaposition is unknown. Gasz, a multidomain protein of known function found in the nuage in vertebrates, is required for piRNA production and interacts with other nuage proteins involved in this pathway. Unexpectedly, we observed that Gasz, in nonspermatogenic mammalian cells lines, localizes to mitochondria and does so through a previously unrecognized conserved C-terminal mitochondrial targeting sequence. Moreover, in this setting, Gasz is able to recruit some of the normally nuage-localized proteins to the mitochondrial surface. Taken together, these findings suggest that Gasz is a nuage-localized protein in spermatocytes that facilitates anchoring of the nuage to the mitochondrial surface where piRNA generation takes place as a collaboration between nuage and mitochondrial-surface proteins. Yelena Altshuller, Qun Gao, and Michael A. Frohman Copyright © 2013 Yelena Altshuller et al. All rights reserved. Crosstalk between Endoplasmic Reticulum Stress and Protein Misfolding in Neurodegenerative Diseases Thu, 13 Jun 2013 13:16:40 +0000 Under physiological conditions, the endoplasmic reticulum (ER) is a central subcellular compartment for protein quality control in the secretory pathway that prevents protein misfolding and aggregation. Instrumental in protein quality control in the ER is the unfolded protein response (UPR), which is activated upon ER stress to reestablish homeostasis through a sophisticated transcriptionally and translationally regulated signaling network. However, this response can lead to apoptosis if the stress cannot be alleviated. The presence of abnormal protein aggregates containing specific misfolded proteins is recognized as the basis of numerous human conformational disorders, including neurodegenerative diseases. Here, I will highlight the overwhelming evidence that the presence of specific aberrant proteins in Alzheimer’s disease (AD), Parkinson’s disease (PD), Huntington’s disease (HD), prion diseases, and Amyotrophic Lateral Sclerosis (ALS) is intimately associated with perturbations in the ER protein quality control machinery that become incompetent to restore protein homeostasis and shift adaptive programs toward the induction of apoptotic signaling to eliminate irreversibly damaged neurons. Increasing our understanding about the deadly crosstalk between ER dysfunction and protein misfolding in these neurodegenerative diseases may stimulate the development of novel therapeutic strategies able to support neuronal survival and ameliorate disease progression. Cláudia M. F. Pereira Copyright © 2013 Cláudia M. F. Pereira. All rights reserved. Building Spinal and Brain Commissures: Axon Guidance at the Midline Thu, 23 May 2013 10:03:14 +0000 Commissural circuits are brain and spinal cord connections which interconnect the two sides of the central nervous system (CNS). They play essential roles in brain and spinal cord processing, ensuring left-right coordination and synchronization of information and commands. During the formation of neuronal circuits, all commissural neurons of the central nervous system must accomplish a common task, which is to project their axon onto the other side of the nervous system, across the midline that delineates the two halves of the CNS. How this task is accomplished has been the topic of extensive studies over the last past 20 years and remains one of the best models to investigate axon guidance mechanisms. In the first part of this review, I will introduce the commissural circuits, their general role in the physiology of the nervous system, and their recognized or suspected pathogenic properties in human diseases. In the second part of the review, I will concentrate on two commissural circuits, the spinal commissures and the corpus callosum, to detail the cellular and molecular mechanisms governing their formation, mostly during their navigation at the midline. Valérie Castellani Copyright © 2013 Valérie Castellani. All rights reserved. Intra-Golgi Transport: Roles for Vesicles, Tubules, and Cisternae Sun, 24 Feb 2013 08:23:34 +0000 The Golgi complex is considered the central station of the secretory pathway where cargo proteins and lipids are properly modified, classified, packed into specific carriers and delivered to their final destinations. Early electron microscope studies showed the extraordinary structural complexity of this organelle. However, despite the large volume of incoming and outgoing traffic, it is able to maintain its architecture, although it is also flexible enough to adapt to the functional status of the cell. Many components of the molecular machinery involved in membrane traffic and other Golgi functions have been identified. However, some basic aspects of Golgi functioning remain unsolved. For instance, how cargo moves through the stack remains controversial and two classical models have been proposed: vesicular transport and cisternal maturation. Since neither of these models explains all the experimental data, a combination of these models as well as new models have been proposed. In this context, the specific role of the cisternae, vesicles and tubules needs to be clarified. In this review, we summarize our current knowledge of the Golgi organization and function, focusing on the mechanisms of intra-Golgi transport. José A. Martínez-Menárguez Copyright © 2013 José A. Martínez-Menárguez. All rights reserved. Identification of PDZ Domain Containing Proteins Interacting with 1.2 and PMCA4b Thu, 07 Feb 2013 14:24:36 +0000 PDZ (PSD-95/Disc large/Zonula occludens-1) protein interaction domains bind to cytoplasmic protein C-termini of transmembrane proteins. In order to identify new interaction partners of the voltage-gated L-type Ca2+ channel 1.2 and the plasma membrane Ca2+ ATPase 4b (PMCA4b), we used PDZ domain arrays probing for 124 PDZ domains. We confirmed this by GST pull-downs and immunoprecipitations. In PDZ arrays, strongest interactions with 1.2 and PMCA4b were found for the PDZ domains of SAP-102, MAST-205, MAGI-1, MAGI-2, MAGI-3, and ZO-1. We observed binding of the 1.2 C-terminus to PDZ domains of NHERF1/2, Mint-2, and CASK. PMCA4b was observed to interact with Mint-2 and its known interactions with Chapsyn-110 and CASK were confirmed. Furthermore, we validated interaction of 1.2 and PMCA4b with NHERF1/2, CASK, MAST-205 and MAGI-3 via immunoprecipitation. We also verified the interaction of 1.2 and nNOS and hypothesized that nNOS overexpression might reduce Ca2+ influx through 1.2. To address this, we measured Ca2+ currents in HEK 293 cells co-expressing 1.2 and nNOS and observed reduced voltage-dependent 1.2 activation. Taken together, we conclude that 1.2 and PMCA4b bind promiscuously to various PDZ domains, and that our data provides the basis for further investigation of the physiological consequences of these interactions. Doreen Korb, Priscilla Y. Tng, Vladimir M. Milenkovic, Nadine Reichhart, Olaf Strauss, Oliver Ritter, Tobias Fischer, Peter M. Benz, and Kai Schuh Copyright © 2013 Doreen Korb et al. All rights reserved. UV-C Exposure Induces an Apoptosis-Like Process in Euglena gracilis Thu, 17 Jan 2013 14:54:00 +0000 Euglena gracilis is a unicellular, free-living flagellate that inhabits various freshwater environments. Our research shows that exposure to UV-C light can trigger some form of programmed cell death. Cells exposed to UV-C light underwent delayed changes that were strongly reminiscent of apoptosis in mammalian cells, including cell shrinkage and DNA fragmentation that produced the characteristic ladder pattern commonly seen with apoptosis. DNA fragmentation could be inhibited by pretreatment with Z-VAD-FMK and also independently induced by exposure to staurosporine. In addition, Euglena possess proteins that cross-reacted with antibodies raised against human caspases 3 and 9. Given that Euglena are extremely easy to culture and represent a lineage positioned near the base of the eukaryotic tree, they will be an excellent model system for comparative analyses with apoptotic-like death processes in other eukaryotic microbes. Michael J. Bumbulis and Brian M. Balog Copyright © 2013 Michael J. Bumbulis and Brian M. Balog. All rights reserved. Impact of Salmonella enterica Type III Secretion System Effectors on the Eukaryotic Host Cell Mon, 31 Dec 2012 19:30:21 +0000 Type III secretion systems are molecular machines used by many Gram-negative bacterial pathogens to inject proteins, known as effectors, directly into eukaryotic host cells. These proteins manipulate host signal transduction pathways and cellular processes to the pathogen’s advantage. Salmonella enterica possesses two virulence-related type III secretion systems that deliver more than forty effectors. This paper reviews our current knowledge about the functions, biochemical activities, host targets, and impact on host cells of these effectors. First, the concerted action of effectors at the cellular level in relevant aspects of the interaction between Salmonella and its hosts is analyzed. Then, particular issues that will drive research in the field in the near future are discussed. Finally, detailed information about each individual effector is provided. Francisco Ramos-Morales Copyright © 2012 Francisco Ramos-Morales. All rights reserved. Molecular Biomarkers of Response to Antiangiogenic Therapy for Cancer Mon, 17 Dec 2012 17:35:13 +0000 Antiangiogenic therapy for cancer has gone from an intriguing hypothesis in the 1970s to an accepted treatment approach for many cancer types. It has also become a standard of care for certain eye diseases. Yet, despite the use of molecularly targeted drugs with well defined targets, to date there are no biomarkers to guide the use of antiangiogenic therapy in patients. The mechanisms of action of these drugs are also being debated. This paper discusses some of the emerging biomarker candidates for this type of cancer therapy, which have provided mechanistic insight and might be useful in the future for optimizing cancer treatment. Dan G. Duda Copyright © 2012 Dan G. Duda. All rights reserved. Mitochondrial Regulation by PINK1-Parkin Signaling Mon, 17 Dec 2012 14:10:15 +0000 Two genes responsible for the juvenile Parkinson’s disease (PD), PINK1 and Parkin, have been implicated in mitochondrial quality control. The inactivation of PINK1, which encodes a mitochondrial kinase, leads to age-dependent mitochondrial degeneration in Drosophila. The phenotype is closely associated with the impairment of mitochondrial respiratory chain activity and defects in mitochondrial dynamics. Drosophila genetic studies have further revealed that PINK1 is an upstream regulator of Parkin and is involved in the mitochondrial dynamics and motility. A series of cell biological studies have given rise to a model in which the activation of PINK1 in damaged mitochondria induces the selective elimination of mitochondria in cooperation with Parkin through the ubiquitin-proteasome and autophagy machineries. Although the relevance of this pathway to PD etiology is still unclear, approaches using stem cells from patients and animal models will help to understand the significance of mitochondrial quality control by the PINK1-Parkin pathway in PD and in healthy individuals. Here I will review recent advances in our understanding of the PINK1-Parkin signaling and will discuss the roles of PINK1-Parkin signaling for mitochondrial maintenance and how the failure of this signaling leads to neurodegeneration. Yuzuru Imai Copyright © 2012 Yuzuru Imai. All rights reserved. Peroxisome Dynamics: Molecular Players, Mechanisms, and (Dys)functions Wed, 14 Nov 2012 16:36:32 +0000 Peroxisomes are remarkably versatile cell organelles whose size, shape, number, and protein content can vary greatly depending on the organism, the developmental stage of the organism’s life cycle, and the environment in which the organism lives. The main functions usually associated with peroxisomes include the metabolism of lipids and reactive oxygen species. However, in recent years, it has become clear that these organelles may also act as intracellular signaling platforms that mediate developmental decisions by modulating extraperoxisomal concentrations of several second messengers. To fulfill their functions, peroxisomes physically and functionally interact with other cell organelles, including mitochondria and the endoplasmic reticulum. Defects in peroxisome dynamics can lead to organelle dysfunction and have been associated with various human disorders. The purpose of this paper is to thoroughly summarize and discuss the current concepts underlying peroxisome formation, multiplication, and degradation. In addition, this paper will briefly highlight what is known about the interplay between peroxisomes and other cell organelles and explore the physiological and pathological implications of this interorganellar crosstalk. Marc Fransen Copyright © 2012 Marc Fransen. All rights reserved. Senescence-Accelerated Mice P8: A Tool to Study Brain Aging and Alzheimer's Disease in a Mouse Model Wed, 14 Nov 2012 09:59:15 +0000 The causes of aging remain unknown, but they are probably intimately linked to a multifactorial process that affects cell networks to varying degrees. Although a growing number of aging and Alzheimer’s disease (AD) animal models are available, a more comprehensive and physiological mouse model is required. In this context, the senescence-accelerated mouse prone 8 (SAMP8) has a number of advantages, since its rapid physiological senescence means that it has about half the normal lifespan of a rodent. In addition, according to data gathered over the last five years, some of its behavioral traits and histopathology resemble AD human dementia. SAMP8 has remarkable pathological similarities to AD and may prove to be an excellent model for acquiring more in-depth knowledge of the age-related neurodegenerative processes behind brain senescence and AD in particular. We review these facts and particularly the data on parameters related to neurodegeneration. SAMP8 also shows signs of aging in the immune, vascular, and metabolic systems, among others. Mercè Pallàs Copyright © 2012 Mercè Pallàs. All rights reserved. Cytoskeleton-Associated Protein 4: Functions Beyond the Endoplasmic Reticulum in Physiology and Disease Wed, 31 Oct 2012 11:35:52 +0000 Cytoskeleton-associated protein 4 (CKAP4; also known as p63, CLIMP-63, or ERGIC-63) is a 63 kDa, reversibly palmitoylated and phosphorylated, type II transmembrane (TM) protein, originally identified as a resident of the endoplasmic reticulum (ER)/Golgi intermediate compartment (ERGIC). When localized to the ER, a major function of CKAP4 is to anchor rough ER to microtubules, organizing the overall structure of ER with respect to the microtubule network. There is also steadily accumulating evidence for diverse roles for CKAP4 localized outside the ER, including data demonstrating functionality of cell surface forms of CKAP4 in various cell types and of CKAP4 in the nucleus. We will review the recent studies that provide evidence for the existence of CKAP4 in multiple cellular compartments (i.e., ER, plasma membrane, and the nucleus) and discuss CKAP4’s role in the regulation of various physiological and pathological processes, such as interstitial cystitis, drug-induced cytotoxicity, pericullar proteolytic activity, and lung lipid homeostasis. Kevin M. Tuffy and Sonia Lobo Planey Copyright © 2012 Kevin M. Tuffy and Sonia Lobo Planey. All rights reserved. Hematopoietic Microenvironment in the Fetal Liver: Roles of Different Cell Populations Tue, 23 Oct 2012 09:36:27 +0000 Hematopoiesis is the main function of the liver during a considerable period of mammalian prenatal development. Hematopoietic cells of the fetal liver exist in a specific microenvironment that controls their proliferation and differentiation. This microenvironment is created by different cell populations, including epitheliocytes, macrophages, various stromal elements (hepatic stellate cells, fibroblasts, myofibroblasts, vascular smooth muscle and endothelial cells, mesenchymal stromal cells), and also cells undergoing epithelial-to-mesenchymal transition. This paper considers the involvement of these cell types in the regulation of fetal liver hematopoiesis. Olga V. Payushina Copyright © 2012 Olga V. Payushina. All rights reserved. Autophagy Mechanism, Regulation, Functions, and Disorders Thu, 06 Sep 2012 09:43:04 +0000 Autophagy is a self-digesting mechanism responsible for removal of damaged organelles, malformed proteins during biosynthesis, and nonfunctional long-lived proteins by lysosome. Autophagy has been divided into three general types depending on the mechanism by which intracellular materials are delivered into lysosome for degradation that is, microautophagy, chaperone-mediated autophagy (CMA), and macroautophagy. In microautophagy cytoplasm material is sequestered through direct invagination to the lysosomal membrane. Whereas in CMA proteins flagged with pentapeptide motif (KFERQ) were selectively degraded through direct translocation into lysosome. Macroautophagy involves the formation of subcellular double-membrane-bound structures called autophagosomes that contain degradable contents of cytoplasm materials and deliver them into lysosomes for breakdown by lysosomal enzymes. The molecular mechanism of autophagy involves several conserved Atg (autophagy-related) proteins. Systems produce modified complexes Atg8-PE and Atg5-Atg12-Atg16 as autophagy regulators. Autophagy is activated in response to diverse stress and physiological conditions. For example, food deprivation, hyperthermia, and hypoxia are mediated by factors like insulin/IGF-1, m-TOR signaling, FOXO transcription factors, and chaperones. The perturbance in autophagy may lead to several types of cancers, myopathies, and neuromuscular disorders. Several autophagy inducers and inhibitors like 3-methyladenine (3-MA), bafilomycin A1, LY294002 (LY), and Velcade have been used to treat disease is an intense field of study. Mallikarjun Badadani Copyright © 2012 Mallikarjun Badadani. All rights reserved. An Integrative Network Biology Approach to Evaluate the Role of Endoplasmic Reticulum Stress Response in Obese Type 2 Diabetes Tue, 22 May 2012 13:33:59 +0000 Extracellular/intracellular stimuli can influence eukaryotic cell function through organelles that regulate critical signaling pathways. The endoplasmic reticulum (ER), for example, impacts cellular processes including protein synthesis, folding and secretion; amino acid transport; apoptosis; cell proliferation; lipid synthesis across major cell types in response to stimuli such as accumulation of misfolded proteins and glucose deprivation. Dysregulated signaling pathways underlying the ER-mediated processes mentioned above have been linked to disease conditions such as diabetes, obesity, and Alzheimer's disease. Our current understanding, however, lacks a detailed network view that integrates organelle-mediated pathway dysregulation with cellular processes and disease pathogenesis. In this report, we introduce an integrative network biology approach that combines ER-stress response pathways with basic cellular processes using data from peer-reviewed literature. As an example, we apply our systems biology approach to study the role of ER stress in pancreatic β cells under obese diabetic conditions, generate testable hypotheses, and provide novel insights into β-cell pathogenesis. Anup Mammen Oommen, Usha Narayanan, and M. R. Jagannath Copyright © 2012 Anup Mammen Oommen et al. All rights reserved. Apoptosis: Reprogramming and the Fate of Mature Cells Tue, 17 Apr 2012 11:01:27 +0000 Apoptosis is essential for embryogenesis, organ metamorphosis, and tissue homeostasis. In embryonic stem cells, self-renewal is balanced with proliferative potential, inhibition of differentiation, and prevention of senescence and apoptosis. Growing evidence supports the role of apoptosis in self-renewal, differentiation of pluripotent stem cells, and dedifferentiation (reprogramming) of somatic cells. In this paper we discuss the multiple roles of apoptosis in embryonic stem cells (ESCs) and reprogramming of differentiated cells to pluripotency. The role of caspases and p53 as key effectors in controlling the generation of iPSC is emphasized. Remarkably, the complication of apoptosis arising during reprogramming may provide insights into technical improvements for derivation of iPSC from senescent cells as a tool for modeling aging-related diseases. Hoi-Hung Cheung, Xiaozhuo Liu, and Owen M. Rennert Copyright © 2012 Hoi-Hung Cheung et al. All rights reserved. Co-localization of the PDGF β-Receptor and Actin during PDGF Stimulation in Mouse Fibroblasts Mon, 19 Mar 2012 14:14:57 +0000 The subcellular localization of the PDGF β-receptor was investigated in relation with PDGF-induced actin and membrane dynamics in mouse C3H10T1/2 fibroblasts. Serum-starved cells exhibit a nonhomogenous distribution of PDGF β-receptors. However, the observed pattern does not resemble the localization of PDGF-induced actin structures. Interestingly, the PDGF β-receptor showed a changed subcellular distribution in relation to the formation of PDGF-BB-induced actin structures. Upon PDGF exposure, PDGF β-receptors were found to accumulate in dorsal circular ruffles. The presence of both macropinosomes and clathrin in the induced circular ruffles suggests that the accumulation of PDGF β-receptors in circular ruffles results in the efficient internalization of PDGF β-receptors. Maarten J. A. Moes, Yeping Zhou, and Johannes Boonstra Copyright © 2012 Maarten J. A. Moes et al. All rights reserved. Molecular Mechanisms of Cytotoxicity and Apoptosis Induced by Inorganic Fluoride Wed, 07 Mar 2012 12:18:06 +0000 Fluoride (F) is ubiquitous natural substance and widespread industrial pollutant. Although low fluoride concentrations are beneficial for normal tooth and bone development, acute or chronic exposure to high fluoride doses results in adverse health effects. The molecular mechanisms underlying fluoride toxicity are different by nature. Fluoride is able to stimulate G-proteins with subsequent activation of downstream signal transduction pathways such as PKA-, PKC-, PI3-kinase-, Ca2+-, and MAPK-dependent systems. G-protein-independent routes include tyrosine phosphorylation and protein phosphatase inhibition. Along with other toxic effects, fluoride was shown to induce oxidative stress leading to excessive generation of ROS, lipid peroxidation, decrease in the GSH/GSSH ratio, and alterations in activities of antioxidant enzymes, as well as to inhibit glycolysis thus causing the depletion of cellular ATP and disturbances in cellular metabolism. Fluoride triggers the disruption of mitochondria outer membrane and release of cytochrome c into cytosol, what activates caspases-9 and -3 (intrinsic) apoptotic pathway. Extrinsic (death receptor) Fas/FasL-caspase-8 and -3 pathway was also described to be implicated in fluoride-induced apoptosis. Fluoride decreases the ratio of antiapoptotic/proapoptotic Bcl-2 family proteins and upregulates the expression of p53 protein. Finally, fluoride changes the expression profile of apoptosis-related genes and causes endoplasmic reticulum stress leading to inhibition of protein synthesis. Natalia Ivanovna Agalakova and Gennadii Petrovich Gusev Copyright © 2012 Natalia Ivanovna Agalakova and Gennadii Petrovich Gusev. All rights reserved. Morphological Changes of Mammalian Nucleoli during Spermatogenesis and Their Possible Role in the Chromatoid Body Assembling Tue, 06 Mar 2012 08:28:44 +0000 Chromatoid body (CB) is a typical cytoplasmic organelle of germ cells, and it seems to be involved in RNA/protein accumulation for later germ-cell differentiation. Despite most of the events in mammals spermatogenesis had been widely described in the past decades and the increase in the studies related to the CB molecular composition and physiology, the origins and functions of this important structure of male germ cells are still unclear. The aims of this study were to describe the nucleolar cycle and also to find some relationship between the nucleolar organization and the CB assembling during the spermatogenesis in mammals. Cytochemical and cytogenetics analysis showed nucleolar fragmentation in post-pachytene spermatocytes and nucleolar reorganization in post-meiotic spermatids. Significant difference in the number and in the size of nucleoli between spermatogonia and round spermatids, as well as differences in the nucleolar position within the nucleus were also observed. Ultrastructural analysis showed the CB assembling in the cytoplasm of primary spermatocytes and the nucleolar fragmentation occurring at the same time. In conclusion our results suggest that the CB may play important roles during the spermatogenesis process in mammals and that its origin may be related to the nucleolar cycle during the meiotic cell cycle. Rita Luiza Peruquetti, Sebastião Roberto Taboga, and Maria Tercília Vilela de Azeredo-Oliveira Copyright © 2012 Rita Luiza Peruquetti et al. All rights reserved. Meiotic Chromosome Interactions: Nonhomologous Centromere (Un)Coupling and Homologous Synapsis Sun, 04 Mar 2012 08:12:51 +0000 The fundamental function of meiosis, segregation of the maternal and paternal chromosomes, is facilitated by reciprocal recombination and intimate juxtaposition (synapsis) between the homologous chromosomes in meiotic prophase. Homolog synapsis, mediated by the synaptonemal complex (SC), is preceded by a stage of pairing between the centromeres of nonhomologous chromosomes. This pairing, named nonhomologous centromere coupling (NCC), depends upon the meiotic cohesin Rec8 and the SC protein Zip1. Nonhomologously coupled centromeres (NCCs), if remain tethered, must interfere with complete homolog synapsis (SC formation). Recent experiments demonstrate the existence of a mechanism that regulates NCC. Importantly, this is part of a regulatory network which couples dissolution of the NCCs with SC formation between the homologous chromosomes, thereby ensuring appropriate meiotic chromosome interactions. This paper reviews this network and presents speculations relating to the initiation of SC formation at centromere. Amit Bardhan Copyright © 2012 Amit Bardhan. All rights reserved. The Modification of Xa-ATIII-Heparin Dynamics by Protamine Sulfate Thu, 01 Mar 2012 10:58:25 +0000 Heparin promotes the formation of 1∘ FXaα-ATIII and FXaβ-ATIII complexes from the free enzymes and antithrombin III. It further stimulates the transformations of the 1∘ complexes into the corresponding 3∘ complexes. Additionally, it stimulates the degradation of the 1∘ FXaα-ATIII and FXaβ-ATIII complexes into free FXaα, FXaβ and ATIIIM. Protamine sulfate (PS) stimulates the transformation of FXaα into FXaβ and hence to FXaγ. It also stimulates the transformation of the 1∘-, 2∘-, and 3∘- FXα-ATIII complexes into their corresponding β-complexes. It further promotes the degradation of the 1∘ FXaα- and FXaβ-ATIII complexes into their corresponding 3∘- FXaα- and FXaβ-ATIII complexes, with the concommittant release of FXaγ. The addition of PS to FXa/ATIII/H mixtures results in a reduction in free FXa, ATIII, and 1∘ Xa-ATIII complex formation, together with the concommittant increase in 3∘-FXa- ATIII complex formation and release of FXaγ. The likeliest explanation of these results resides in the removal of the effective free heparin as a consequence of the generation of a stable heparin/PS salt upon the addition of the PS to the FXa/ATIII/H mixtures, thereby effectively lowering clotting times. Martin H. Coggin and Arthur S. Brecher Copyright © 2012 Martin H. Coggin and Arthur S. Brecher. All rights reserved. Nitric Oxide Synthase Inhibitors Modulate Nerve-Growth-Factor Mediated Activation of Akt Thu, 01 Mar 2012 10:29:30 +0000 Nitric oxide (NO) modulates nerve-growth-factor- (NGF-) mediated signaling and gene expression. In the present paper, the role of NO in NGF-mediated Akt activation in PC12 and IMR32 cells was investigated. Cells were treated with NGF (50 ng/mL) in the presence or absence of NO synthase (NOS) inhibitors and Akt phosphorylation assessed by western blot analysis. In both cell lines, Akt was phosphorylated within 15 min of NGF treatment. In PC12 cells, this level of phosphorylation was sustained for 60 min, while in IMR32 cells, the activation decreased after 30 min of NGF treatment. The nonselective NOS inhibitor Nω-nitro-L-arginine methylester (L-NAME; 20 mM) had no effect on NGF-mediated Akt phosphorylation in PC12 cells but in combination with NGF, the iNOS selective inhibitor s-methylisothiourea (S-MIU; 2.0 mM) maintained Akt phosphorylation up to 2 h. In IMR32 cells, both L-NAME and S-MIU prolonged the activation of Akt. Pretreatment with 50 μM U0126, a MAP kinase pathway inhibitor, also increased the activation of Akt in both cell lines. These data suggest that NO modulates the duration of phosphorylation of Akt in response to NGF and that this effect may, in part, be mediated by the effects of NO on the Ras-MAP kinase pathway. Cheryl L. Cragg, Janet C. MacKinnon, and Bettina E. Kalisch Copyright © 2012 Cheryl L. Cragg et al. All rights reserved. Focus on ADF/Cofilin: Beyond Actin Cytoskeletal Regulation Sun, 19 Feb 2012 11:51:29 +0000 Actin depolymerizing factor (ADF)/cofilin, an actin-binding protein ubiquitously expressed in a variety of organisms, is required for regulation of actin dynamics. The activity of ADF/cofilin is dependent on serine 3 phosphorylation by LIM kinase (LIMK), which is regulated by the Rho small GTPase signaling pathway. ADF/cofilin is strongly associated with several important cell biological functions, including cell cycle, morphological maintenance, and locomotion. These functions affect several biological events, including embryogenesis, oncology, nephropathy, and neurodegenerations. Here, we focus on the biochemical and pathophysiological role of ADF/cofilin in mammals. Cheng-Han Tsai and Yi-Jang Lee Copyright © 2012 Cheng-Han Tsai and Yi-Jang Lee. All rights reserved.