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PubMed | Indian Veterinary Research Institute, Nippon Institute for Biological Science, Council of Scientific and Industrial Research Center for Cellular and Molecular Biology, Tamil Nadu Veterinary and Animal Sciences University and 7 more.
Type: Journal Article | Journal: Proceedings of the National Academy of Sciences of the United States of America | Year: 2015

The phylum Apicomplexa includes serious pathogens of humans and animals. Understanding the distribution and population structure of these protozoan parasites is of fundamental importance to explain disease epidemiology and develop sustainable controls. Predicting the likely efficacy and longevity of subunit vaccines in field populations relies on knowledge of relevant preexisting antigenic diversity, population structure, the likelihood of coinfection by genetically distinct strains, and the efficiency of cross-fertilization. All four of these factors have been investigated for Plasmodium species parasites, revealing both clonal and panmictic population structures with exceptional polymorphism associated with immunoprotective antigens such as apical membrane antigen 1 (AMA1). For the coccidian Toxoplasma gondii only genomic diversity and population structure have been defined in depth so far; for the closely related Eimeria species, all four variables are currently unknown. Using Eimeria tenella, a major cause of the enteric disease coccidiosis, which exerts a profound effect on chicken productivity and welfare, we determined population structure, genotype distribution, and likelihood of cross-fertilization during coinfection and also investigated the extent of naturally occurring antigenic diversity for the E. tenella AMA1 homolog. Using genome-wide Sequenom SNP-based haplotyping, targeted sequencing, and single-cell genotyping, we show that in this coccidian the functionality of EtAMA1 appears to outweigh immune evasion. This result is in direct contrast to the situation in Plasmodium and most likely is underpinned by the biology of the direct and acute coccidian life cycle in the definitive host.


Singh S.K.,Council of Scientific and Industrial Research Center for Cellular and Molecular Biology | Kotakonda A.,Council of Scientific and Industrial Research Center for Cellular and Molecular Biology | Kapardar R.K.,Council of Scientific and Industrial Research Center for Cellular and Molecular Biology | Kankipati H.K.,Council of Scientific and Industrial Research Center for Cellular and Molecular Biology | And 6 more authors.
Frontiers in Microbiology | Year: 2015

Ocean iron fertilization is an approach to increase CO2 sequestration. The Indo-German iron fertilization experiment "LOHAFEX" was carried out in the Southern Ocean surrounding Antarctica in 2009 to monitor changes in bacterial community structure following iron fertilization-induced phytoplankton bloom of the seawater from different depths. 16S rRNA gene libraries were constructed using metagenomic DNA from seawater prior to and after iron fertilization and the clones were sequenced for identification of the major bacterial groups present and for phylogenetic analyses. A total of 4439 clones of 16S rRNA genes from ten 16S rRNA gene libraries were sequenced. More than 97.35% of the sequences represented four bacterial lineages i.e. Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and Firmicutes and confirmed their role in scavenging of phytoplankton blooms induced following iron fertilization. The present study demonstrates the response of Firmicutes due to Iron fertilization which was not observed in previous southern ocean Iron fertilization studies. In addition, this study identifies three unique phylogenetic clusters LOHAFEX Cluster 1 (affiliated to Bacteroidetes), 2, and 3 (affiliated to Firmicutes) which were not detected in any of the earlier studies on iron fertilization. The relative abundance of these clusters in response to iron fertilization was different. The increase in abundance of LOHAFEX Cluster 2 and Papillibacter sp. another dominant Firmicutes may imply a role in phytoplankton degradation. Disappearance of LOHAFEX Cluster 3 and other bacterial genera after iron fertilization may imply conditions not conducive for their survival. It is hypothesized that heterotrophic bacterial abundance in the Southern Ocean would depend on their ability to utilize algal exudates, decaying algal biomass and other nutrients thus resulting in a dynamic bacterial succession of distinct genera. © 2015 Singh, Kotakonda, Kapardar, Kankipati, Sreenivasa Rao, Sankaranarayanan, Vetaikorumagan, Gundlapally, Nagappa and Shivaji.


Puri D.,Council of Scientific and Industrial Research Center for Cellular and Molecular Biology | Puri D.,Max Planck Institute of Immunobiology and Epigenetics | Gala H.,Council of Scientific and Industrial Research Center for Cellular and Molecular Biology | Gala H.,Institute for Stem Cell Biology and Regenerative Medicine | And 3 more authors.
FEBS Journal | Year: 2015

Emerging evidence aided by genome-wide analysis of chromatin and transcriptional states has shed light on the mechanisms by which stem cells achieve cellular memory. The epigenetic and transcriptional plasticity governing stem cell behavior is highlighted by the identification of 'poised' genes, which permit cells to maintain readiness to undertake alternate developmental fates. This review focuses on two crucial mechanisms of gene poising: bivalent chromatin marks and RNA polymerase II stalling. We provide the context for these mechanisms by exploring the current consensus on the regulation of chromatin states, especially in quiescent adult stem cells, where poised genes are critical for recapitulating developmental choices, leading to regenerative function. Epigenetic and transcriptional plasticity governs stem cell behavior. The discovery of 'poised' genes suggests mechanisms that permit cells to maintain readiness for alternate developmental fates. This review focuses on two key mechanisms of gene poising: bivalent chromatin marks and RNA Polymerase II stalling, in the context of stem cell memory. © 2014 FEBS.


Cheedipudi S.,Institute for Stem Cell Biology and Regenerative Medicine | Cheedipudi S.,Council of Scientific and Industrial Research Center for Cellular and Molecular Biology | Cheedipudi S.,Max Planck Institute for Heart and Lung Research | Gala H.P.,Institute for Stem Cell Biology and Regenerative Medicine | And 5 more authors.
Genomics Data | Year: 2015

Quiescent stem cells contribute to tissue homeostasis and repair in adult mammals. We identified a tumor suppressor PRDM2, as an epigenetic regulator induced in quiescent muscle stem cells as well as in cultured quiescent myoblasts. To delineate the functions of PRDM2 in muscle cells, we compared the gene expression profiles of control and PRDM2 knockdown myoblasts in growing, differentiating and quiescent conditions (GEO accession number: GSE 58676). To identify the direct targets of PRDM2 and the promoters co-associated with H3K9me2 (mark catalyzed by PRDM2), ChIP-Chip analysis was performed (GSE58748). In this report we discuss in detail the methodology used to identify PRDM2 regulated genes and classify them into potential direct and indirect targets. © 2015 Elsevier Inc.


PubMed | Manipal University India, Council of Scientific and Industrial Research Center for Cellular and Molecular Biology, University of Southern Denmark, Max Planck Institute for Heart and Lung Research and 2 more.
Type: Journal Article | Journal: Nucleic acids research | Year: 2015

Adult stem cell quiescence is critical to ensure regeneration while minimizing tumorigenesis. Epigenetic regulation contributes to cell cycle control and differentiation, but few regulators of the chromatin state in quiescent cells are known. Here we report that the tumor suppressor PRDM2/RIZ, an H3K9 methyltransferase, is enriched in quiescent muscle stem cells in vivo and controls reversible quiescence in cultured myoblasts. We find that PRDM2 associates with >4400 promoters in G0 myoblasts, 55% of which are also marked with H3K9me2 and enriched for myogenic, cell cycle and developmental regulators. Knockdown of PRDM2 alters histone methylation at key promoters such as Myogenin and CyclinA2 (CCNA2), and subverts the quiescence program via global de-repression of myogenesis, and hyper-repression of the cell cycle. Further, PRDM2 acts upstream of the repressive PRC2 complex in G0. We identify a novel G0-specific bivalent chromatin domain in the CCNA2 locus. PRDM2 protein interacts with the PRC2 protein EZH2 and regulates its association with the bivalent domain in the CCNA2 gene. Our results suggest that induction of PRDM2 in G0 ensures that two antagonistic programs-myogenesis and the cell cycle-while stalled, are poised for reactivation. Together, these results indicate that epigenetic regulation by PRDM2 preserves key functions of the quiescent state, with implications for stem cell self-renewal.


PubMed | Sathya Kidney Center & Super Speciality Hospital, Council of Scientific and Industrial Research Center for Cellular and Molecular Biology, Sridevi Maternity & Nursing Home and Universitaetsmedizin Mainz
Type: Journal Article | Journal: Orthopaedic journal of sports medicine | Year: 2015

Articular cartilage (AC) injuries and malformations are commonly noticed because of trauma or age-related degeneration. Many methods have been adopted for replacing or repairing the damaged tissue. Currently available AC repair methods, in several cases, fail to yield good-quality long-lasting results, perhaps because the reconstructed tissue lacks the cellular and matrix properties seen in hyaline cartilage (HC).To reconstruct HC tissue from 2-dimensional (2D) and 3-dimensional (3D) cultures of AC-derived human chondrocytes that would specifically exhibit the cellular and biochemical properties of the deep layer of HC.Descriptive laboratory study.Two-dimensional cultures of human AC-derived chondrocytes were established in classical medium (CM) and newly defined medium (NDM) and maintained for a period of 6 weeks. These cells were suspended in 2 mm-thick collagen I gels, placed in 24-well culture inserts, and further cultured up to 30 days. Properties of chondrocytes, grown in 2D cultures and the reconstructed 3D cartilage tissue, were studied by optical and scanning electron microscopic techniques, immunohistochemistry, and cartilage-specific gene expression profiling by reverse transcription polymerase chain reaction and were compared with those of the deep layer of native human AC.Two-dimensional chondrocyte cultures grown in NDM, in comparison with those grown in CM, showed more chondrocyte-specific gene activity and matrix properties. The NDM-grown chondrocytes in 3D cultures also showed better reproduction of deep layer properties of HC, as confirmed by microscopic and gene expression analysis. The method used in this study can yield cartilage tissue up to approximately 1.6 cm in diameter and 2 mm in thickness that satisfies the very low cell density and matrix composition properties present in the deep layer of normal HC.This study presents a novel and reproducible method for long-term culture of AC-derived chondrocytes and reconstruction of cartilage tissue with properties similar to the deep layer of HC in vitro.The HC tissue obtained by the method described can be used to develop an implantable product for the replacement of damaged or malformed AC, especially in younger patients where the lesions are caused by trauma or mechanical stress.


Nanduri V.,Council of Scientific and Industrial Research Center for Cellular and Molecular Biology | Tattikota S.M.,Council of Scientific and Industrial Research Center for Cellular and Molecular Biology | Tattikota S.M.,Universitaetsmedizin Mainz | Avinash Raj T.,Council of Scientific and Industrial Research Center for Cellular and Molecular Biology | And 3 more authors.
Orthopaedic Journal of Sports Medicine | Year: 2014

Background: Articular cartilage (AC) injuries and malformations are commonly noticed because of trauma or age-related degeneration. Many methods have been adopted for replacing or repairing the damaged tissue. Currently available AC repair methods, in several cases, fail to yield good-quality long-lasting results, perhaps because the reconstructed tissue lacks the cellular and matrix properties seen in hyaline cartilage (HC). Purpose: To reconstruct HC tissue from 2-dimensional (2D) and 3-dimensional (3D) cultures of AC-derived human chondrocytes that would specifically exhibit the cellular and biochemical properties of the deep layer of HC. Study Design: Descriptive laboratory study. Methods: Two-dimensional cultures of human AC–derived chondrocytes were established in classical medium (CM) and newly defined medium (NDM) and maintained for a period of 6 weeks. These cells were suspended in 2 mm–thick collagen I gels, placed in 24-well culture inserts, and further cultured up to 30 days. Properties of chondrocytes, grown in 2D cultures and the reconstructed 3D cartilage tissue, were studied by optical and scanning electron microscopic techniques, immunohistochemistry, and cartilage-specific gene expression profiling by reverse transcription polymerase chain reaction and were compared with those of the deep layer of native human AC. Results: Two-dimensional chondrocyte cultures grown in NDM, in comparison with those grown in CM, showed more chondrocyte-specific gene activity and matrix properties. The NDM-grown chondrocytes in 3D cultures also showed better reproduction of deep layer properties of HC, as confirmed by microscopic and gene expression analysis. The method used in this study can yield cartilage tissue up to approximately 1.6 cm in diameter and 2 mm in thickness that satisfies the very low cell density and matrix composition properties present in the deep layer of normal HC. Conclusion: This study presents a novel and reproducible method for long-term culture of AC-derived chondrocytes and reconstruction of cartilage tissue with properties similar to the deep layer of HC in vitro. Clinical Relevance: The HC tissue obtained by the method described can be used to develop an implantable product for the replacement of damaged or malformed AC, especially in younger patients where the lesions are caused by trauma or mechanical stress. © The Author(s) 2014.


Singh V.P.,Council of Scientific and Industrial Research Center for Cellular and Molecular Biology | Gurunathan C.,Council of Scientific and Industrial Research Center for Cellular and Molecular Biology | Singh S.,Council of Scientific and Industrial Research Center for Cellular and Molecular Biology | Singh B.,Council of Scientific and Industrial Research Center for Cellular and Molecular Biology | And 4 more authors.
Diabetologia | Year: 2014

Aim/hypothesis: Type 2 diabetes is a complex disease characterised by hyperglycaemia, hyperinsulinaemia, dyslipidaemia and insulin resistance accompanied by inflammation. Previously, we showed that mice lacking the Wdr13 gene had increased islet mass due to enhanced beta cell proliferation. We hypothesised that introgression of a Wdr13-null mutation, a beta cell-proliferative phenotype, into Leprdb/db mice, a beta cell-destructive phenotype, might rescue the diabetic phenotype of the latter.Methods: Wdr13-deficient mice were crossed with Leprdb/db mice to generate mice with the double mutation. We measured various serum metabolic variables of Wdr13+/0Leprdb/db and Wdr13−/0Leprdb/db mice. Further, we analysed the histopathology and gene expression of peroxisome proliferator-activated receptor (PPAR)γ and, activator protein (AP)1 targets in various metabolic tissues.Results: Leprdb/db mice with the Wdr13 deletion had a massively increased islet mass, hyperinsulinaemia and adipocyte hypertrophy. The increase in beta cell mass in Wdr13−/0Leprdb/db mice was due to an increase in beta cell proliferation. Hypertrophy of adipocytes may be the result of increase in transcription of Pparg and its target genes, leading in turn to increased expression of several lipogenic genes. We also observed a significant decrease in the expression of AP1 and nuclear factor κ light chain enhancer of activated B cells (NFκB) target genes involved in inflammation.Conclusions/interpretation: This study provides evidence that loss of WD repeat domain 13 (WDR13) protein in the Leprdb/db mouse model of diabetes is beneficial. Based on these findings, we suggest that WDR13 may be a potential drug target for ameliorating hyperglycaemia and inflammation in diabetic conditions. © 2014, Springer-Verlag Berlin Heidelberg.


Sultan A.,Council of Scientific and Industrial Research Center for Cellular and Molecular Biology | Raman B.,Council of Scientific and Industrial Research Center for Cellular and Molecular Biology | Rao C.M.,Council of Scientific and Industrial Research Center for Cellular and Molecular Biology | Tangirala R.,Council of Scientific and Industrial Research Center for Cellular and Molecular Biology
Journal of Biological Chemistry | Year: 2013

Fibril formation of β2-microglobulin and associated inflammation occur in patients on long term dialysis.Weshow that the plasma protein haptoglobin prevents the fatty acid-promoted de novo fibril formation of β2-microglobulin even at substoichiometric concentration. The fibrils are cytotoxic, and haptoglobin abolishes the cytotoxicity by preventing fibril formation. Haptoglobin does not alleviate the cytotoxicity of preformed fibrils. Fibrillarβ2-microglobulin is resistant to lysosomal degradation. However, the species ofβ2-microglobulin populated in the presence of haptoglobin is susceptible to degradation. We observed that haptoglobin interacts with oligomeric prefibrillar species of β2-microglobulin but not with monomeric or fibrillarβ 2-microglobulin that may underlie the molecular mechanism. 1,1'- Bis(4-anilino)naphthalene-5,5'-disulfonic acid cross-linking to haptoglobin significantly compromises its chaperone activity, suggesting the involvement of hydrophobic surfaces. Haptoglobin is an acute phase protein whose level increases severalfold during inflammation, where local acidosis can occur. Our data show that haptoglobin prevents fibril formation of β2- microglobulin under conditions of physiological acidosis (betweenpH 5.5 and 6.5) but with relatively decreased efficiency. However, compromise in its chaperone activity under these conditions is more than compensated by its increased level of expression under inflammation. Erythrolysis is known to release hemoglobin into the plasma. Haptoglobin forms a 1:1 (mol/mol) complex with hemoglobin. This complex, like haptoglobin, interacts with the prefibrillar species ofβ2-microglobulin, preventing its fibril formation and the associated cytotoxicity and resistance to intracellular degradation. Thus, our study demonstrates that haptoglobin is a potential extracellular chaperone forβ2-microglobulin even in moderately acidic conditions relevant during inflammation, with promising therapeutic implications in β2-microglobulin amyloid-related diseases. © 2013 by The American Society for Biochemistry and Molecular Biology, Inc.


PubMed | Council of Scientific and Industrial Research Center for Cellular and Molecular Biology
Type: Journal Article | Journal: Diabetologia | Year: 2015

Type 2 diabetes is a complex disease characterised by hyperglycaemia, hyperinsulinaemia, dyslipidaemia and insulin resistance accompanied by inflammation. Previously, we showed that mice lacking the Wdr13 gene had increased islet mass due to enhanced beta cell proliferation. We hypothesised that introgression of a Wdr13-null mutation, a beta cell-proliferative phenotype, into Lepr(db/db) mice, a beta cell-destructive phenotype, might rescue the diabetic phenotype of the latter.Wdr13-deficient mice were crossed with Lepr(db/db) mice to generate mice with the double mutation. We measured various serum metabolic variables of Wdr13(+/0)Lepr(db/db) and Wdr13(-/0) Lepr(db/db) mice. Further, we analysed the histopathology and gene expression of peroxisome proliferator-activated receptor (PPAR) and, activator protein (AP)1 targets in various metabolic tissues.Lepr(db/db) mice with the Wdr13 deletion had a massively increased islet mass, hyperinsulinaemia and adipocyte hypertrophy. The increase in beta cell mass in Wdr13(-/0)Lepr(db/db) mice was due to an increase in beta cell proliferation. Hypertrophy of adipocytes may be the result of increase in transcription of Pparg and its target genes, leading in turn to increased expression of several lipogenic genes. We also observed a significant decrease in the expression of AP1 and nuclear factor light chain enhancer of activated B cells (NFB) target genes involved in inflammation.This study provides evidence that loss of WD repeat domain 13 (WDR13) protein in the Lepr (db/db) mouse model of diabetes is beneficial. Based on these findings, we suggest that WDR13 may be a potential drug target for ameliorating hyperglycaemia and inflammation in diabetic conditions.

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