Role of the Cytoplasmic Polyadenylation Element Binding Proteins in Neuron: A Dissertation

Genome regulation is an extremely complex phenomenon. There are various mechanisms in place to ensure smooth performance of the organism. Post-transcriptional regulation of gene expression is one such mechanism. Many proteins bind to mRNAs and regulate their translation. In this thesis, I have focused on the Cytoplasmic Polyadenylation Element Binding family of proteins (CPEB1-4); a group of sequence specific RNA binding proteins important for cell cycle progression, senescence, neuronal function and plasticity. CPEB protein binds mRNAs containing a short Cytoplasmic Polyadenylation Element (CPE) in 3’ untranslated Region (UTR) and regulates the polyadenylation of these mRNAs and thereby controls translation. In Chapter II, I have presented my work on the regulation of mitochondrial function by CPEB. CPEB knockout mice have brain specific defects in mitochondrial function owing to a reduction in Electron transport chain complex I component protein NDUFV2. CPEB controls the translation of this NDUFV2 mRNA and thus affects mitochondrial function. A consequence of this reduced bioenergetics is reduced growth and branching of neurons, again emphasizing the importance of this pathway. Chapter III focuses on the role of CPEB4 in neuronal survival and protection against apoptosis. CPEB4 shuttles between nucleus and cytoplasm and becomes nuclear in response to stimulation with ionotropic glutamate receptors, focal ischemia in vivo and when cultured neurons are deprived of oxygen and glucose; nuclear CPEB4 affords protection against apoptosis in ischemia model. The underlying cause for nuclear translocation is reduction in Endoplasmic Reticulum calcium levels. These studies give an insight into the function and dynamics of these two RNA binding proteins and provide a better understanding of cellular biology

Coexistence of para and ferromagnetic phases of Fe3+ in undoped CdZnTe (Zn r-v 4%) crystals

The signatures of the coexistence of para and ferromagnetic phases for the Fe3+ charge state of iron have been identified in the low temperature electron spin resonance (ESR) spectra in undoped CdZnTe (Zn ~ 4%) crystals and independently verified by superconducting quantum interference device (SQUID)and AC susceptibility measurements. In the paramagnetic phase the inverse of AC susceptibility follows the Curie-Weiss law. In the ferromagnetic phase the thermal evolution of magnetization follows the well-known Bloch T3/2 law. This is further supported by the appearance of hysteresis in the SQUID measurements at 2 Kbelow Tc which is expected to lie in between 2 and 2.5 K

Correction: Hydrophobic Core Variations Provide a Structural Framework for Tyrosine Kinase Evolution and Functional Specialization.

[This corrects the article DOI: 10.1371/journal.pgen.1005885.]

Specificity factors in cytoplasmic polyadenylation

Poly(A) tail elongation after export of an messenger RNA (mRNA) to the cytoplasm is called cytoplasmic polyadenylation. It was first discovered in oocytes and embryos, where it has roles in meiosis and development. In recent years, however, has been implicated in many other processes, including synaptic plasticity and mitosis. This review aims to introduce cytoplasmic polyadenylation with an emphasis on the factors and elements mediating this process for different mRNAs and in different animal species. We will discuss the RNA sequence elements mediating cytoplasmic polyadenylation in the 3′ untranslated regions of mRNAs, including the CPE, MBE, TCS, eCPE, and C-CPE. In addition to describing the role of general polyadenylation factors, we discuss the specific RNA binding protein families associated with cytoplasmic polyadenylation elements, including CPEB (CPEB1, CPEB2, CPEB3, and CPEB4), Pumilio (PUM2), Musashi (MSI1, MSI2), zygote arrest (ZAR2), ELAV like proteins (ELAVL1, HuR), poly(C) binding proteins (PCBP2, αCP2, hnRNP-E2), and Bicaudal C (BICC1). Some emerging themes in cytoplasmic polyadenylation will be highlighted. To facilitate understanding for those working in different organisms and fields, particularly those who are analyzing high throughput data, HUGO gene nomenclature for the human orthologs is used throughout. Where human orthologs have not been clearly identified, reference is made to protein families identified in man

AlignHUSH: Alignment of HMMs using structure and hydrophobicity information

Abstract Background Sensitive remote homology detection and accurate alignments especially in the midnight zone of sequence similarity are needed for better function annotation and structural modeling of proteins. An algorithm, AlignHUSH for HMM-HMM alignment has been developed which is capable of recognizing distantly related domain families The method uses structural information, in the form of predicted secondary structure probabilities, and hydrophobicity of amino acids to align HMMs of two sets of aligned sequences. The effect of using adjoining column(s) information has also been investigated and is found to increase the sensitivity of HMM-HMM alignments and remote homology detection. Results We have assessed the performance of AlignHUSH using known evolutionary relationships available in SCOP. AlignHUSH performs better than the best HMM-HMM alignment methods and is observed to be even more sensitive at higher error rates. Accuracy of the alignments obtained using AlignHUSH has been assessed using the structure-based alignments available in BaliBASE. The alignment length and the alignment quality are found to be appropriate for homology modeling and function annotation. The alignment accuracy is found to be comparable to existing methods for profile-profile alignments. Conclusions A new method to align HMMs has been developed and is shown to have better sensitivity at error rates of 10% and above when compared to other available programs. The proposed method could effectively aid obtaining clues to functions of proteins of yet unknown function. A web-server incorporating the AlignHUSH method is available at http://crick.mbu.iisc.ernet.in/~alignhush/</p

Hydrogel Synthesis and Analysis of its Electrical and Mechanical Properties

Hydrogels are an up-and-coming material having numerous potential applications with a multitude of properties. They are known for their self-healing, high toughness, electrical conductivity, and much more. Hydrogels in the market currently only cater to one application or focus on one feature rather than a combination of them. This study aims to produce a hydrogel from a pre-established synthesis containing polydopamine-polypyrrole nanoparticles and alter it to improve the electrical conductivity, mechanical strength, and swelling capabilities. The analysis revealed that the hydrogel that only contained polypyrrole nanoparticles produced the best conductivity value of 0.070309 S/m, contradicting previous literature which suggests that the addition of polydopamine would improve conductivity. For the mechanical analysis, the highest amount of force is able to be sustained by a sample containing 82.1 mg of the polydopamine-polypyrrole nanoparticles, which had a maximum force withstanding at approximately 15 N. All samples exhibited a high amount of swelling ability, with the hydrogel encompassing exhibiting the greatest water absorption capacity at 830% of its initial mass The success in water absorption displays that these hydrogels could be reused and would remove the need for single-use products. Overall, the findings demonstrate that by varying compositions of nanoparticles added in the hydrogel synthesis, it is possible to adapt them to have desired features. The multifunctional product exhibits promising properties for wound dressing and shows potential for improving biocompatibility. Along with this, the analysis emphasizes the versatility and potential of hydrogels as a general-use material with a range of characteristics

A dataintegration approach to predict host-pathogen protein-protein interactions: application to recognize protein interactions between human and a malarial parasite

Lack of large-scale efforts aimed at recognizing interactions between host and pathogens limits our understanding of many diseases. We present a simple and generally applicable bioinformatics approach for the analysis of possible interactions between the proteins of a parasite, Plasmodium falciparum, and human host. In the first step, the physically compatible interactions between the parasite and human proteins are recognized using homology detection. This dataset of putative in vitro interactions is combined with large-scale datasets of expression and sub-cellular localization. This integrated approach reduces drastically the number of false positives and hence can be used for generating testable hypotheses. We could recognize known interactions previously suggested in the literature. We also propose new predictions which involve interactions of some of the parasite proteins of yet unknown function. The method described is generally applicable to any host-pathogen pair and can thus be of general value to studies of host-pathogen protein-protein interactions

Prediction of protein-protein interactions between Helicobacter pylori and a human host

A lack of information on protein-protein interactions at the host-pathogen interface is impeding the understanding of the pathogenesis process. A recently developed, homology search-based method to predict protein-protein interactions is applied to the gastric pathogen, Helicobacter pylori to predict the interactions between proteins of H. pylori and human proteins in vitro. Many of the predicted interactions could potentially occur between the pathogen and its human host during pathogenesis as we focused mainly on the H. pylori proteins that have a transmembrane region or are encoded in the pathogenic island and those which are known to be secreted into the human host. By applying the homology search approach to protein-protein interaction databases DIP and iPfam, we could predict in vitro interactions for a total of 623 H. pylori proteins with 6559 human proteins. The predicted interactions include 549 hypothetical proteins of as yet unknown function encoded in the H. pylori genome and 13 experimentally verified secreted proteins. We have recognized 833 interactions involving the extracellular domains of transmembrane proteins of H. pylori. Structural analysis of some of the examples reveals that the interaction predicted by us is consistent with the structural compatibility of binding partners. Examples of interactions with discernible biological relevance are discussed

Co-Conserved MAPK Features Couple D-Domain Docking Groove to Distal Allosteric Sites via the C-Terminal Flanking Tail

<div><p>Mitogen activated protein kinases (MAPKs) form a closely related family of kinases that control critical pathways associated with cell growth and survival. Although MAPKs have been extensively characterized at the biochemical, cellular, and structural level, an integrated evolutionary understanding of how MAPKs differ from other closely related protein kinases is currently lacking. Here, we perform statistical sequence comparisons of MAPKs and related protein kinases to identify sequence and structural features associated with MAPK functional divergence. We show, for the first time, that virtually all MAPK-distinguishing sequence features, including an unappreciated short insert segment in the β4-β5 loop, physically couple distal functional sites in the kinase domain to the D-domain peptide docking groove via the C-terminal flanking tail (C-tail). The coupling mediated by MAPK-specific residues confers an allosteric regulatory mechanism unique to MAPKs. In particular, the regulatory αC-helix conformation is controlled by a MAPK-conserved salt bridge interaction between an arginine in the αC-helix and an acidic residue in the C-tail. The salt-bridge interaction is modulated in unique ways in individual sub-families to achieve regulatory specificity. Our study is consistent with a model in which the C-tail co-evolved with the D-domain docking site to allosterically control MAPK activity. Our study provides testable mechanistic hypotheses for biochemical characterization of MAPK-conserved residues and new avenues for the design of allosteric MAPK inhibitors.</p></div