Electrophoretic Mobility Shift Assay Studies Research Articles

Synthesis, Characterization and Binding Studies of Polymeric Nanoparticles using Gemcitabine Hydrochloride

Background: Gemcitabine is a clinically valuable drug delivered intravenously. In order to explore other routes of administration for more efficacious drug delivery, its redevelopment for application through oral route with the help of nanotechnology is an ongoing thrust area. Nanotech-nology helps the drug enter into tissues at the molecular level, with increased drug localisation and cellular uptake, larger surface area with modifiable biologic properties, mediate molecular interac-tions and identify molecular changes. Objective: The objective of the study was to use Eudragit RS100 to prepare polymeric nanoparticles of gemcitabine (GEM) in order to improve its half-life, reduce dosage and increase the stability of the drug. Methods: GEM polymeric nanoparticles were prepared by nanoprecipitation technique. They were characterized for particle size, zeta potential (ZP), drug content, entrapment efficiency (EE) and in-vitro drug release. Further, they were also evaluated using TEM, DSC and FTIR spectroscopy. Mechanistic insights of the synthesized nanoparticles were explored using a protein binding study, electrophoretic mobility shift assay (EMSA) and plasma protein binding study. Docking study was carried out to check the binding of the drug and polymer with DNA and protein. Results: The synthesized GEM polymeric nanoparticles showed particle size in the range of 200-450 nm. Due to physical stability issues, optimized polymeric nanoparticles of GEM were lyophi-lized and exhibited a zeta potential of +11.9 mV, drug content 96.74% w/v and EE of 68-75% w/v. In-vitro drug release study demonstrated sustained release. Protein binding study with bovine serum albumin (BSA) revealed protein binding of GEM-loaded polymeric nanoparticles comparable with the marketed formulation (Oncogem 200, Cipla Ltd.). In addition to this, human plasma protein binding studies showed negligible interaction of GEM with plasma proteins with both formulations. EMSA displayed binding with CT-DNA. Conclusion: Lyophilized GEM nanoparticles were found to be stable and the mechanistic studies found them comparable to that of marketed formulation.

Structural insights into inhibitor regulation of the DNA repair protein DNA-PKcs

The DNA-dependent protein kinase catalytic subunit (DNA-PKcs) has a central role in non-homologous end joining, one of the two main pathways that detect and repair DNA double-strand breaks (DSBs) in humans1,2. DNA-PKcs is of great importance in repairing pathological DSBs, making DNA-PKcs inhibitors attractive therapeutic agents for cancer in combination with DSB-inducing radiotherapy and chemotherapy3. Many of the selective inhibitors of DNA-PKcs that have been developed exhibit potential as treatment for various cancers4. Here we report cryo-electron microscopy (cryo-EM) structures of human DNA-PKcs natively purified from HeLa cell nuclear extracts, in complex with adenosine-5′-(γ-thio)-triphosphate (ATPγS) and four inhibitors (wortmannin, NU7441, AZD7648 and M3814), including drug candidates undergoing clinical trials. The structures reveal molecular details of ATP binding at the active site before catalysis and provide insights into the modes of action and specificities of the competitive inhibitors. Of note, binding of the ligands causes movement of the PIKK regulatory domain (PRD), revealing a connection between the p-loop and PRD conformations. Electrophoretic mobility shift assay and cryo-EM studies on the DNA-dependent protein kinase holoenzyme further show that ligand binding does not have a negative allosteric or inhibitory effect on assembly of the holoenzyme complex and that inhibitors function through direct competition with ATP. Overall, the structures described in this study should greatly assist future efforts in rational drug design targeting DNA-PKcs, demonstrating the potential of cryo-EM in structure-guided drug development for large and challenging targets.

Transcription Factor RUNX1 Regulates Factor FXIIIA Subunit (F13A1) Expression in Megakaryocytic Cells and Platelet F13A1 Expression is Downregulated in RUNX1 Haplodeficiency

Plasma Factor XIII, a transglutaminase, is a complex of two A (gene F13A1) chains with catalytic activity and two B chains (gene F13B). FXIII induces clot stabilization and retraction via cross-linking of fibrin monomers and other proteins. Factor XIII deficiency in plasma causes a major bleeding disorder with impaired clot retraction. FXIIIA is synthesized in megakaryocytes, and is abundant in platelets. It is expressed on activated platelets and cross-links proteins on platelet surface. Little is known regarding the regulation of F13A1 in megakaryocytes and platelets. RUNX1 is a major hematopoietic transcription factor and regulates expression of numerous genes in megakaryocytes and platelets. Patients with RUNX1 haplodeficiency (RHD) with heterozygous mutations have thrombocytopenia, platelet dysfunction with impaired responses to activation, and predisposition to myeloid malignancies. Platelet expression profiling using Affymetrix microarrays of a patient (P1) with a heterozygous RUNX1 mutation (c.969-323G>T) revealed decreased F13A expression, which encodes for subunit A of FXIII: fold-change 0.30; p=0.006; patient profiled twice 10 months apart and compared to 6 healthy subjects. These findings were confirmed by qPCR With RT-PCR platelet F13A mRNA expression was decreased to ~ 20% of mean expression in 4 subjects. Platelet F13A protein expression was decreased by ~50% as assessed by corrected total cellular fluorescence imaging. Platelet F13A mRNA expression was also decreased (to less than 20% of expression in 5 controls) in two siblings (P2 and P3 ages 8 and 3 years) from an unrelated family with a heterozygous RUNX1 mutation 508+1G>A). Plasma FXIII was normal in the patient P1. We studied the regulation of F13A by RUNX1 in human erythroleukemia (HEL) cells treated with phorbol myristate acetate (PMA) to induce megakaryocytic transformation. In silico analyses of the 5' upstream region of F13A showed 7 RUNX1 consensus sites within 545bp from ATG. Chromatin immunoprecipitation studies performed using HEL cells and RUNX1 antibody showed that that RUNX1 binds in the region encompassing site 4 and sites 5-7. In parallel, electrophoretic mobility shift assay (EMSA) studies showed binding of nuclear protein to labeled DNA probes with sites 1, 4, 5, 6, and 7. RUNX1 antibody produced a "supershift" with addition suggesting RUNX1 binding. Site-directed mutagenesis of the RUNX1 binding sites in F13A1 promoter decreased promoter activity in luciferase reporter studies in HEL cells, providing evidence that the binding sites are functional. Further, overexpression of RUNX1 in HEL cells increased F13A1 promoter activity and protein while siRNA RUNX1 knockdown reduced F13A1 protein. We assessed clot retraction over 90 min at 37oC in the patient P1 and his daughter (also with RUNX1 mutation) in citrated whole blood following addition of tissue factor (1 pM) and CaCl2 (1 mM), and in washed platelets resuspended in platelet poor plasma from a healthy subject supplemented with added fibrinogen (0.5 mg/mL) and stimulated with 0.5 U/mL thrombin in the presence of CaCl2. These preliminary studies suggested that clot retraction was slower in the patient P1 compared to the controls, particularly in studies with platelet suspensions. Conclusions: Overall, these studies provide the first evidence that hematopoietic transcription factor RUNX1 regulates expression of F13A1 in megakaryocytic cells and that platelet expression of F13A1 is decreased in platelets from patients with RUNX1 haplodeficiency. The decreased expression of F13A1 in RHD may contribute to the platelet dysfunction in RHD. These findings are particularly interesting because they reflect regulation of a coagulation protein (FXIIIA) by hematopoietic transcription factor RUNX1. Disclosures Lambert: Dova: Consultancy, Membership on an entity's Board of Directors or advisory committees; Principia: Consultancy, Membership on an entity's Board of Directors or advisory committees; Novartis: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Shionogi: Consultancy; Educational Concepts in Medicine: Consultancy; Octapharma: Consultancy, Research Funding; Bayer: Consultancy; Platelet Disorder Support Association (PDSA): Consultancy; 22qSociety: Consultancy; ITP Australia: Consultancy; CdLS Foundation: Consultancy; RDMD ITP study: Consultancy; Sysmex: Research Funding; AstraZeneca: Research Funding; Argenix: Consultancy; ClinGen: Honoraria.

Computational and structural studies of MeCP2 and associated mutants

Rett Syndrome is a rare genetic disorder exclusively seen in girls. Approximately 95% of RTT cases is caused by mutations in the MeCP2 gene which codes for Methyl-CpG-binding protein 2 (MeCP2). In this review, first, a brief introductory review of Rett Syndrome, MeCP2 protein structure and function, mutation types and frequencies, and phenotype–genotype relationships were provided. After that, the current knowledge on the wild-type and mutant MeCP2 protein structure and dynamics as well as its binding to DNA is reviewed. The review particularly focuses on computational (such as molecular dynamics) and experimental (such as electrophoretic mobility shift assays) studies on the MeCP2 binding to different types of DNA as well as the computational and experimental (such as circular dichroism) studies on the stability changes upon mutations. In the end, a brief opinion on future outlook for further computational studies is provided.

Functional characterization of host toxic EcdB transcription factor protein of echinocandin B biosynthetic gene cluster.

The ecdB is a transcription factor, located in the echinocandin B biosynthetic gene cluster of Emericella rugulosa NRRL11440. Here, we validated the ecdB mRNA sequence for functional expression and to explore the role of EcdB protein in the echinocandin B regulation. The sequence alignment study revealed that the ecdB coding sequence was found 75bp shorter than the reference mRNA sequence. This coding sequence encodes for EcdB protein and comprises three conserved domains; DNA binding domain (DBD), coiled-coil domain, and signature middle homology region. The full-length and DBD (truncated) DNA sequences were expressed in Escherichia coli BL21(DE3) under different tested conditions. The expression of EcdB protein was found to be toxic, which curbs the cell growth. In contrast to truncated protein (GST:EcdB1-54), the full-length (GST:EcdB) protein was expressed at very low titer and not detectable in SDS-PAGE under the varying isopropyl β-d-1-thiogalactopyranoside (IPTG), temperature, and media conditions. However, GST:EcdB1-54 was successfully purified under standard conditions (0.5mM IPTG at 0.5OD) with 33kDa expected size. The functionality of GST:EcdB1-54 was attained by electrophoretic mobility shift assay study as a clear band shifting showed with ecdA promoter. Taken together, we conclude that EcdB interacts with the ecdA promoter that reflected to require for echinocandin B regulation.

LcpRVH2 - regulating the expression of latex-clearing proteins in Gordonia polyisoprenivorans VH2.

Gordonia polyisoprenivorans VH2 harbours two latex clearing proteins, which are responsible for the cleavage of poly(cis-1,4-isoprene) into oligoisoprenes, thereby allowing growth in presence of, e.g. natural rubber. A gene coding for a putative regulator of the TetR-family (lcpRVH2) is located 131 bp upstream of lcp1VH2. We heterologously expressed lcpRVH2 in Escherichia coli, and purified and characterized the protein with respect to its ability to bind to the operator region of lcp1VH2. LcpRVH2 forms a dimer in its native state. The size of the dimer was determined to be 52.7 kDa by size exclusion chromatography, whereas the calculated size of a monomer was 24.1 kDa. Electrophoretic mobility shift assays (EMSAs) with the purified protein revealed a shift upon binding to the intergenic region between lcpRVH2 and lcp1VH2. Within this region, an inverted repeat was identified in silico, probably being the binding site of LcpRVH2. This binding sequence was confirmed by a DNase I footprinting assay. A shift also occurred in EMSAs with this 44 bp sequence only. Interestingly, no regulator was detected upstream of the second lcp (lcp2VH2). Therefore, we performed EMSA studies with LcpRVH2 and the putative operator region upstream of lcp2VH2, and discovered by DNase I footprinting another binding sequence upstream of lcp2VH2. Hence, we concluded that LcpRVH2 binds the operator region of both lcps and, most likely, regulates their expression in G. polyisoprenivorans VH2.

Genetic variations in the DNA replication origins of human papillomavirus family correlate with their oncogenic potential

Human papillomaviruses (HPVs) encompass a large family of viruses that range from benign to highly carcinogenic. The crucial differences between benign and carcinogenic types of HPV remain unknown, except that the two HPV types differ in the frequency of DNA replication. We have systematically analyzed the mechanism of HPV DNA replication initiation in low-risk and high-risk HPVs. Our results demonstrate that HPV-encoded E2 initiator protein and its four binding sites in the replication origin play pivotal roles in determining the destiny of the HPV-infected cell. We have identified strain-specific single nucleotide variations in E2 binding sites found only in the high-risk HPVs. We have demonstrated that these variations result in attenuated formation of the E2-DNA complex. E2 binding to these sites is linked to the activation of the DNA replication origin as well as initiation of DNA replication. Both electrophoretic mobility shift assay and atomic force microscopy studies demonstrated that binding of E2 from either low- or high-risk HPVs with variant binding sequences lacked multimeric E2-DNA complex formation in vitro. These results provided a molecular basis of differential DNA replication in the two types of HPVs and pointed to a correlation with the development of cancer.

Photoactive platinum(II) complexes of nonsteroidal anti-inflammatory drug naproxen: Interaction with biological targets, antioxidant activity and cytotoxicity

The effect on the therapeutic efficacy of Pt(II) complexes on combining non-steroidal anti-inflammatory drugs (NSAIDs) is an attractive strategy to circumvent chronic inflammation mediated by cancer and metastasis. Two square-planar platinum(II) complexes: [Pt(dach)(nap)Cl] (1) and [Pt(dach)(nap)2] (2), where dach = (1R,2R)-dichloro(cyclohexane-1,2-diamine) and NSAID drug naproxen (nap), have been designed for studying their biological activity. The naproxen bound to the Pt(II) centre get released upon photoirradiation with low-power UV-A light as confirmed by the significant enhancement in emission intensities of the complexes. The compounds were evaluated for their photophysical properties, photostability, reactivity with 5′-guanosine monophophosphate (5′-GMP), interactions with CT-DNA and BSA, antioxidant activity and reactive oxygen species mediated photo-induced DNA damage properties. ESI-MS studies demonstrated the formation of bis-adduct with 5′-GMP and the formation of PtII-DNA crosslinks by gel electrophoretic mobility shift assay and ITC studies. The interaction of the complexes 1 and 2 with the CT-DNA exhibits potential binding affinity (Kb ∼ 104 M−1, Kapp∼ 105 M−1), implying intercalation to CT-DNA through planar naphthyl ring of the complexes. Both the complexes also exhibit strong binding affinity towards BSA (KBSA∼ 105 M−1). The complexes exhibit efficient DNA damage activity on irradiation at 365 nm via formation of singlet oxygen (1O2) and hydroxyl radical (•OH) under physiological conditions. Both the complexes were cytotoxic in dark and exhibit significant enhancement of cytotoxicity upon photo-exposure against HeLa and HepG2 cancer cells giving IC50 values ranging from 8 to 12 μM for 1 and 2. The cellular internalization data showed cytosolic and nuclear localization of the complexes in the HeLa cells.

Cellulase from Trichoderma harzianum interacts with roots and triggers induced systemic resistance to foliar disease in maize.

Trichoderma harzianum is well known to exhibit induced systemic resistance (ISR) to Curvularia leaf spot. We previously reported that a C6 zinc finger protein (Thc6) is responsible for a major contribution to the ISR to the leaf disease, but the types of effectors and the signals mediated by Thc6 from Trichoderma are unclear. In this work, we demonstrated that two hydrolases, Thph1 and Thph2, from T. harzianum were regulated by Thc6. Furthermore, an electrophoretic mobility shift assay (EMSA) study revealed that Thc6 regulated mRNA expression by binding to GGCTAA and GGCTAAA in the promoters of the Thph1 and Thph2 genes, respectively. Moreover, the Thph1 and Thph2 proteins triggered the transient production of reactive oxygen species (ROS) and elevated the free cytosolic calcium levels in maize leaf. Furthermore, the genes related to the jasmonate/ethylene signaling pathway were up-regulated in the wild-type maize strain. However, the ΔThph1- or ΔThph2-deletion mutants could not activate the immune defense-related genes in maize to protect against leaf disease. Therefore, we conclude that functional Thph1 and Thph2 may be required in T. harzianum to activate ISR in maize.

Binding Specificities of the Telomere Phage ϕKO2 Prophage Repressor CB and Lytic Repressor Cro.

Temperate bacteriophages possess a genetic switch which regulates the lytic and lysogenic cycle. The genomes of the temperate telomere phages N15, PY54, and ϕKO2 harbor a primary immunity region (immB) comprising genes for the prophage repressor (cI or cB), the lytic repressor (cro) and a putative antiterminator (q). The roles of these products are thought to be similar to those of the lambda proteins CI (CI prophage repressor), Cro (Cro repressor), and Q (antiterminator Q), respectively. Moreover, the gene order and the location of several operator sites in the prototype telomere phage N15 and in ϕKO2 are reminiscent of lambda-like phages. We determined binding sites of the ϕKO2 prophage repressor CB and lytic repressor Cro on the ϕKO2 genome in detail by electrophoretic mobility shift assay (EMSA) studies. Unexpectedly, ϕKO2 CB and Cro revealed different binding specificities. CB was bound to three OR operators in the intergenic region between cB and cro, two OL operators between cB and the replication gene repA and even to operators of N15. Cro bound exclusively to the 16 bp operator site OR3 upstream of the ϕKO2 prophage repressor gene. The ϕKO2 genes cB and cro are regulated by several strong promoters overlapping with the OR operators. The data suggest that Cro represses cB transcription but not its own synthesis, as already reported for PY54 Cro. Thus, not only PY54, but also phage ϕKO2 possesses a genetic switch that diverges significantly from the switch of lambda-like phages.

BI-03 * DLX HOMEOBOX GENES REGULATE NEURONAL VS OLIGODENDROGLIAL CELL FATE DECISIONS: POTENTIAL RELEVANCE TO PEDIATRIC GLIONEURONAL TUMORS AND HIGH GRADE GLIOMAS

BACKGROUND: Pediatric high grade gliomas (pHGG) are localized to different neuroanatomic compartments with significant differences in their gene expression profiles. In Histone H3.3 G34V/R mutants, DLX2 homeobox gene expression is increased with a corresponding decrease in myelin transcription factor (MYT1) expression. DLX genes are necessary for tangential migration and differentiation of inhibitory interneurons during CNS development. Neural progenitors derived from DLX1/DLX2 double knockout (DKO) mice transplanted into a wild-type forebrain differentiate into oligodendrocytes, providing support for the DLX homeobox genes in neuronal-glial cell fate decisions. METHODS: Chromatin immunoprecipitation (ChIP) assays using a DLX2 antibody were followed by qPCR. ChIP-reChIP assays were performed using antibodies that recognize specific histone modifications. Electrophoretic mobility shift assays (EMSA) were performed using recombinant DLX2 protein and oligonucleotide probes from ChIP-specified promoter regions. Reporter gene assays provided functional assessment of protein-DNA interactions in vitro. Target gene expression was assessed comparing wild-type (WT) and DLX1/DLX2 DKO tissues. RESULTS: Homeodomain binding sites were localized to the promoters of Olig2, Myt1, Nkx2.2 and others in silico. ChIP assays confirmed promoter occupancy by DLX2. ChIPseq experiments are underway. EMSA studies demonstrated specific DLX2-promoter complexes. Luciferase assays showed repression of Olig2 and Nkx2.2 reporter gene expression, consistent with co-occupancy of H3K27me3 in WT and increased target gene expression in DLX1/DLX2 DKO embryonic tissues. We also demonstrated DLX2 expression in a cohort of gangliogliomas. CONCLUSIONS: Our results support a role for DLX transcription factors in controlling neural progenitor specification by activating GABAergic and inhibiting oligodendroglial cell fates through transcriptional repression of a suite of genes required for oligodendrocyte differentiation. Understanding how pHGG and glioneuronal tumors co-opt these neurodevelopmental programs will lead to novel pharmacologic approaches that promote glioma differentiation.

A heroin addiction severity-associated intronic single nucleotide polymorphism modulates alternative pre-mRNA splicing of the μ opioid receptor gene OPRM1 via hnRNPH interactions.

Single nucleotide polymorphisms (SNPs) in the OPRM1 gene have been associated with vulnerability to opioid dependence. The current study identifies an association of an intronic SNP (rs9479757) with the severity of heroin addiction among Han-Chinese male heroin addicts. Individual SNP analysis and haplotype-based analysis with additional SNPs in the OPRM1 locus showed that mild heroin addiction was associated with the AG genotype, whereas severe heroin addiction was associated with the GG genotype. In vitro studies such as electrophoretic mobility shift assay, minigene, siRNA, and antisense morpholino oligonucleotide studies have identified heterogeneous nuclear ribonucleoprotein H (hnRNPH) as the major binding partner for the G-containing SNP site. The G-to-A transition weakens hnRNPH binding and facilitates exon 2 skipping, leading to altered expressions of OPRM1 splice-variant mRNAs and hMOR-1 proteins. Similar changes in splicing and hMOR-1 proteins were observed in human postmortem prefrontal cortex with the AG genotype of this SNP when compared with the GG genotype. Interestingly, the altered splicing led to an increase in hMOR-1 protein levels despite decreased hMOR-1 mRNA levels, which is likely contributed by a concurrent increase in single transmembrane domain variants that have a chaperone-like function on MOR-1 protein stability. Our studies delineate the role of this SNP as a modifier of OPRM1 alternative splicing via hnRNPH interactions, and suggest a functional link between an SNP-containing splicing modifier and the severity of heroin addiction.

TRANSCRIPTIONAL REGULATION OF OLIGODENDROGLIAL CELL FATE BY DLX HOMEOBOX GENES: POTENTIAL RELEVANCE TO HISTONE H3.3 MUTATIONS IN PEDIATRIC HIGH GRADE GLIOMA

BACKGROUND: The discovery of variant histone H3.3 somatic driver mutations in pediatric high grade gliomas (pHGG) has provided important insights into their pathogenesis. The K27M and G34V/R mutants are usually localized to different neuroanatomic compartments (deep midline/brainstem or superficial/cortical, respectively) and have significant differences in their gene expression profiles. For example, there is a marked increase in the expression of the homeobox gene DLX2 and a corresponding decrease in the expression of the myelin transcription factor, MYT1. When neural progenitors that are mutant for both DLX1 and DLX2 are transplanted into a wild-type background in the developing mouse forebrain, they differentiate into cells of the oligodendrocyte lineage, supporting a role for the DLX homeobox genes in neuronal-glial cell fate decisions. METHODS: Bioinformatics approaches were used to identify homeodomain consensus TAAT/ATTA tetranucleotide DNA binding motifs in regulatory regions of genes required for oligodendrocyte differentiation, Modified chromatin immunoprecipitation (ChIP) assays using a DLX2 antibody were followed by qPCR. ChIP-reChIP assays were performed using antibodies that recognize specific histone modifications at active or repressed regulatory regions of chromatin. Electrophoretic mobility shift assays (EMSA) were performed using recombinant DLX2 protein and oligonucleotide probes from ChIP-specified promoter regions. Reporter gene assays provided functional assessment of protein-DNA interactions in vitro. Target gene expression was assessed comparing wild-type (WT) and DLX1/DLX2 mutant forebrain and retina. RESULTS: Homeodomain binding sites were localized to the promoters of several genes, including Olig2, Myt1 and Nkx2.2 in silico. ChIP assays confirmed promoter occupancy by DLX2 in several regions of these gene promoters. ChIPseq experiments are in progress. EMSA studies demonstrated specific DLX2: promoter complexes. Of interest, luciferase assays showed repression of Olig2 and Nkx2.2 reporter gene expression, consistent with co-occupancy of H3K27me3 in WT and increased target gene expression in the DLX1/DLX2 double KO embryonic tissues. CONCLUSIONS: DLX homeobox genes are necessary for tangential migration and differentiation of inhibitory interneurons in the developing CNS. Collectively, our results support a role for these transcription factors in controlling neural progenitor specification by activating GABAergic and inhibiting oligodendroglial cell fates through transcriptional repression of a suite of genes required for oligodendrocyte differentiation. Understanding how pHGG co-opt these neurodevelopmental programs will lead to novel pharmacologic approaches that promote glioma differentiation. SECONDARY CATEGORY: Pediatrics.

Temperature- and nitrogen source-dependent regulation of GlnR target genes in Listeria monocytogenes.

The ubiquitous pathogen Listeria monocytogenes lives either saprophytically in the environment or within cells in a vertebrate host, thus adapting its lifestyle to its ecological niche. Growth experiments at 24 and 37 °C (environmental and host temperature) with ammonium or glutamine as nitrogen sources revealed that ammonium is the preferred nitrogen source of L. monocytogenes. Reduced growth on glutamine is more obvious at 24 °C. Global transcriptional microarray analyses showed that the most striking difference in temperature-dependent transcription was observed for central nitrogen metabolism genes, glnR (glutamine synthetase repressor GlnR), glnA (glutamine synthetase GlnA), amtB (ammonium transporter AmtB), glnK (PII regulatory protein GlnK), and gdh (glutamate dehydrogenase) when cells were grown on glutamine. When grown on ammonium, both at 24 and 37 °C, the transcriptional level of these genes resembles that of cells grown with glutamine at 37 °C. Electrophoretic mobility shift assay studies and qPCR analyses in the wild-type L. monocytogenes and the deletion mutant L. monocytogenes ∆glnR revealed that the transcriptional regulator GlnR is directly involved in temperature- and nitrogen source-dependent regulation of the respective genes. Glutamine, a metabolite known to influence GlnR activity, seems unlikely to be the (sole) intracellular signal mediating this temperature-and nitrogen source-dependent metabolic adaptation.

Thermodynamic characterization of the interaction between the antimicrobial peptide LL‐37 and DNA oligonucleotides (978.3)

LL‐37 is a small peptide of innate immunity that sequesters extracellular DNA and transports it across the cell membrane. Recent discoveries have implicated LL‐37‐mediated pathways as potential inciting mechanisms for the onset of anti‐DNA autoimmunity. We have used electrophoretic mobility shift assays (EMSA), isothermal titration calorimetry (ITC), and western blotting to examine the details of complex formation between LL‐37 and 24‐bp DNA fragments with CpG, GpC, and poly(AT) sequences. ITC studies indicate that LL‐37 binding to CpG DNA fits a two‐site model, with association binding constants (Ka1 and Ka2) on the order of 108‐109 M‐1 and peptide:DNA ratios of 15‐25. Quantitative EMSA studies allow the construction of binding curves and demonstrate the formation of large peptide‐DNA complexes that form over a narrow concentration range. Parallel western blotting experiments detect LL‐37 self‐complexes that increase in size with increasing LL‐37 concentration and that decrease in size in the presence of DNA. LL‐37 appears to display higher affinity for poly(A/T) DNA than for CpG DNA in the EMSA assay. These data are consistent with a model in which LL‐37 self‐associations serve to tether DNA with high affinity into large complexes containing 20 LL‐37 molecules per 24 bp DNA fragment. This research was supported by the Mary Baldwin College Summer Undergraduate Research Fellows Program.

Immune activities comparison of polysaccharide and polysaccharide-protein complex from Lycium barbarum L.

Lycium barbarum L., known as wolfberry, is an important Chinese herbal medicine. In the research, we purified water-soluble polysaccharide-protein complex (LBPF4) and polysaccharide (LBPF4-OL) from the fruiting bodies of L. barbarum L. The monosaccharide and amino acid composition of LBPF4 and LBPF4-OL was elucidated with fractional acid hydrolization, GC/MC and NMR techniques. LBPF4-OL molecular weight was 181kDa, as determined by high-performance gel-permeation chromatography (HPGPC). In vitro assay, we found that LBPF4 induced splenocyte proliferations depended on both B cells and T cells, but LBPF4-OL induced splenocyte proliferations mainly depended on B cells. ELISA results showed that both LBPF4 and LBPF4-OL significantly induced TNF-α, IL-1β and NO production on macrophage. We also found that both LBPF4 and LBPF4-OL can enhance macrophage phagocytosis. Furthermore, electrophoretic mobility shift assay (EMSA) studies suggest that LBPF4 100μg/ml treatment can more effectively increase NF-κB activity than LBPF4-OL. Taken together, our results demonstrate that LBPF4 can enhance T, B cells and macrophages functions, but LBPF4-OL can only enhance B cells and macrophage functions. This is partly due to LBPF4 being able to more significantly enhance lymphocytes NF-κB activity.

Active site–inactivated factor VIIa inhibits nuclear factor kappa B activation in intestinal ischemia and reperfusion

BackgroundIntestinal ischemia and reperfusion (I/R) injury is a pivotal mechanism in critical illness and in the development of multiple organ dysfunction syndrome, in which the nuclear factor kappa B (NF-κB) activation plays a central role. Intestinal I/R injury initiates the extrinsic tissue factor or factor VIIa–dependent pathway of coagulation, also of importance in multiple organ dysfunction syndrome. Our aim was to analyze NF-κB activation in I/R injury in the rat intestine and in two main “shock” organs, that is, the liver and lungs. Pretreatment with active site–inactivated factor VII (FVIIai), an inhibitor of the extrinsic pathway, was evaluated. Materials and methodsNF-κB activation was analyzed using enzyme-linked immunosorbent assay (ELISA) and electrophoretic mobility shift assay (EMSA) studies of nuclear extracts from the intestine, liver, and lungs in rats subjected to intestinal I/R injury. FVIIai was given 90min before the induction of intestinal ischemia. ResultsI/R induced NF-κB p65 activation in all three organs, especially in the liver. Pretreatment with FVIIai counteracted NF-κB activation in all three tissues studied. A commercially available ELISA for (human) NF-κB p65 and EMSA gave parallel results. ConclusionsI/R injury in the rat intestine induces a pronounced activation of NF-κB p50 or p65 in the small intestine and in the liver and lungs. The NF-κB activation is especially pronounced in the liver and plays a central role in the regulation of transcription of cytokines, adhesion molecules, and chemokines. ELISA for (human) NF-κB p65 and “gold standard” EMSA gave parallel results. Pretreatment with FVIIai completely counteracted NF-κB activation in the intestine and liver, although not in the lungs.

Translocation of Heme Oxygenase-1 to Mitochondria Is a Novel Cytoprotective Mechanism against Non-steroidal Anti-inflammatory Drug-induced Mitochondrial Oxidative Stress, Apoptosis, and Gastric Mucosal Injury

The mechanism of action of heme oxygenase-1 (HO-1) in mitochondrial oxidative stress (MOS)-mediated apoptotic tissue injury was investigated. MOS-mediated gastric mucosal apoptosis and injury were introduced in rat by indomethacin, a non-steroidal anti-inflammatory drug. Here, we report that HO-1 was not only induced but also translocated to mitochondria during gastric mucosal injury to favor repair mechanisms. Furthermore, mitochondrial translocation of HO-1 resulted in the prevention of MOS and mitochondrial pathology as evident from the restoration of the complex I-driven mitochondrial respiratory control ratio and transmembrane potential. Mitochondrial translocation of HO-1 also resulted in time-dependent inhibition of apoptosis. We searched for the plausible mechanisms responsible for HO-1 induction and mitochondrial localization. Free heme, the substrate for HO-1, was increased inside mitochondria during gastric injury, and mitochondrial entry of HO-1 decreased intramitochondrial free heme content, suggesting that a purpose of mitochondrial translocation of HO-1 is to detoxify accumulated heme. Heme may activate nuclear translocation of NF-E2-related factor 2 to induce HO-1 through reactive oxygen species generation. Electrophoretic mobility shift assay and chromatin immunoprecipitation studies indicated nuclear translocation of NF-E2-related factor 2 and its binding to HO-1 promoter to induce HO-1 expression during gastric injury. Inhibition of HO-1 by zinc protoporphyrin aggravated the mucosal injury and delayed healing. Zinc protoporphyrin further reduced the respiratory control ratio and transmembrane potential and enhanced MOS and apoptosis. In contrast, induction of HO-1 by cobalt protoporphyrin reduced MOS, corrected mitochondrial dysfunctions, and prevented apoptosis and gastric injury. Thus, induction and mitochondrial localization of HO-1 are a novel cytoprotective mechanism against MOS-mediated apoptotic tissue injury.

Runx2 contributes to murine Col10a1 gene regulation through direct interaction with its cis-enhancer

We have recently shown that a 150-bp Col10a1 distal promoter (−4296 to −4147 bp) is sufficient to direct hypertrophic chondrocyte-specific reporter (LacZ) expression in vivo. More recently, through detailed sequence analysis we identified two putative tandem-repeat Runx2 binding sites within the 3′-end of this 150-bp region (TGTGGG-TGTGGC, −4187 to −4176 bp). Candidate electrophoretic mobility shift assay (EMSA), chromatin immunoprecipitation, and transfection studies demonstrate that these putative Runx2 sites bind Runx2 and mediate upregulated Col10a1/reporter activity in vitro. Transgenic studies using the 5′-sequence without Runx2 sites were not able to drive the cell-specific LacZ reporter activity, suggesting the in vivo requirement of the Runx2 sites located in the 3′-end in mediating Col10a1/reporter expression. Indeed, mutating the Runx2 sites in the context of the 150-bp promoter abolishes its capacity to drive hypertrophic chondrocyte-specific reporter expression in transgenic mice. We have also generated multiple transgenic mouse lines using only the 3′-sequence containing the Runx2 sites to drive the LacZ gene. Interestingly, no hypertrophic chondrocyte-specific blue staining was observed in these transgenic mice. Together, our data support that Runx2 directly interacts with murine Col10a1 cis-enhancer. This interaction is required but not sufficient for cell-specific Col10a1 promoter activity in vivo. Additional cooperative/repressive elements within the 5′- or 3′-sequences of this 150-bp promoter are needed to work with Runx2 together to mediate cell-specific Col10a1 expression. Further delineation of these elements/factors has the potential to identify novel therapeutic targets for multiple skeletal disorders, including osteoarthritis, that show abnormal Col10a1 expression and altered chondrocyte maturation. © 2011 American Society for Bone and Mineral Research

Prolactin regulatory element-binding protein involved in cAMP-mediated suppression of adiponectin gene.

Adiponectin (ApN) has several protective effects against diabetes and atherosclerosis. However, the detailed mechanisms of the regulation of the ApN gene have not yet been clarified. Prolactin regulatory element–binding (PREB) protein has been identified as a factor that regulates insulin gene expression in the pancreas. PREB is located not only in the pancreas but also in adipose tissue; however, its role in adipose tissue is not known. To analyse the effects of PREB on ApN gene transcription, we employed a reporter gene assay and electrophoretic mobility shift assay (EMSA). In the cells expressing or knocking down the PREB, ApN expression was determined. PREB was located mainly in the nuclei of adipose tissue and its cell line, 3T3-L1 cells. The nuclear extract contained ApN promoter-binding activity that was super-shifted by PREB antiserum in EMSA studies. In the 3T3-L1 cells, the co-expression of PREB and the ApN promoter inhibited the activity of the latter. The addition of cAMP to the cells increased PREB expression in a dose-dependent manner. A deletional analysis of the ApN promoter showed that the PREB-responsive cis-element in the ApN promoter mediated the transcriptional effect of PREB, whereas a mutant of this motif in the ApN promoter abrogated the effect of PREB, as well as that of cAMP. Furthermore, cells expressing or knocking down PREB exhibited decreased and increased ApN expression, respectively. These results demonstrate that PREB may contribute to the regulation of ApN gene transcription, in response to cAMP activation in adipocytes.