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A. Danilkovich

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Jeffrey Townsend

Yale University

Darya P Vanichkina

The University of Sydney

Dr. Devendra Dusane

The Ohio State University

Christina Richards

University of South Florida

Maja Vasiljevic

University of Belgrade

Md. Iqbal Kabir Jahid

Jessore University of Science & Technology

Awanti Sambarey

University of Michigan

surekha Satpute

Savitribai Phule Pune University

North Carolina State University

María Del Carmen Garcia

Instituto Universitario Hospital Italiano

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Papers by A. Danilkovich

[Genes coding for RNA polymerase in bacteria. III. The use of modified Sanger's method for sequencing the C-terminal region of rpoB gene, N-terminal region of rpoC gene and intercistron region of RNA polymerase in Pseudomonas putida]

Bioorganicheskaia khimiia, 1988

The Sanger method was modified and the primary structure of the SalI-C fragment of the Pseudomona... more

[Classification of self-organizing peptides]

Bioorganicheskaia khimiia

Amino acid sequences of known natural and synthetic self-assembling peptides were searched and an... more Amino acid sequences of known natural and synthetic self-assembling peptides were searched and analyzed for their characteristic patterns. The attempted formal numerical description of the repeating motifs, which have been revealed, resulted in building of general classification system embracing core-sequences of the peptides capable of nanostructure formation. Advantages and potency of the proposed rational classification were demonstrated via its comparison with the output from the earlier system described by the others.

Galanin-1 receptor up-regulation mediates the excess colonic fluid production caused by infection with enteric pathogens

Nature medicine, 2000

Galanin is widely distributed in enteric nerve terminals lining the gastrointestinal tract. We pr... more Galanin is widely distributed in enteric nerve terminals lining the gastrointestinal tract. We previously showed that pathogenic Escherichia coli, but not normal commensal organisms, increase galanin-1 receptor expression by epithelial cells lining the colon (i.e., colonocytes). When present, galanin-1 receptor activation by ligand causes colonocyte Cl- secretion. We herein demonstrate that disparate pathogens including Salmonella typhimurium and Shigella flexerii also increase colonocyte galanin-1 receptor expression, whose activation is responsible for a principal component of the increased colonic fluid secretion observed. Although eliminating the GAL1R gene by homologous recombination does not alter basal colonic fluid secretion, removal of one or both alleles completely attenuates the increase in fluid secretion due to infection with enteric pathogens. Galanin-1 receptor up-regulation therefore represents a novel mechanism accounting for the increased colonic fluid secretion ob...

Azoxymethane-induced fulminant hepatic failure in C57BL/6J mice: characterization of a new animal model

The American journal of physiology, 1999

Without transplantation, approximately 50-90% of all patients with fulminant hepatic failure (FHF... more Without transplantation, approximately 50-90% of all patients with fulminant hepatic failure (FHF) die. This poor outcome is due in part to the absence of an appropriate animal model, which would allow for a greater understanding of the pathophysiology of this syndrome. Given the reports of liver injury in humans and livestock fed cycad palm nuts on the island of Guam, we hypothesized that the active ingredient azoxymethane (AOM) could cause FHF. We therefore evaluated AOM in C57BL/6J mice. Histologically, we observed microvesicular steatosis 2 h, sinusoidal dilatation 4 h, and centrilobular necrosis 20 h after AOM administration, and transmission electron microscopy showed that this agent causes mitochondrial injury. FHF was associated with all four stages of encephalopathy, as well as by a prodromal period of decreased eating and drinking lasting approximately 15 h before the development of stage I encephalopathy (i.e., loss of scatter reflex). Late encephalopathy was associated w...

Pathogenic Escherichia coli increase Cl- secretion from intestinal epithelia by upregulating galanin-1 receptor expression

The Journal of clinical investigation, 1999

Galanin is widely distributed in enteric nerve terminals lining the human gastrointestinal (GI) t... more Galanin is widely distributed in enteric nerve terminals lining the human gastrointestinal (GI) tract. We have shown previously that galanin-1 receptors (Gal1-R) are expressed by epithelial cells lining the human GI tract, and upon activation cause Cl- secretion. Because expression of this receptor is transcriptionally regulated by nuclear factor-kappa B (NF-kappa B), which is activated by enteric pathogens as a part of the host epithelial response to infection, we investigated whether such bacterial pathogens could directly increase Gal1-R expression in the T84-cell model system. Pathogenic Escherichia coli, but not nonpathogenic E. coli, activate a p50/p65 NF-kappa B complex that binds to oligonucleotides corresponding to a recognition site located within the 5' flanking region of the human GAL1R gene. Pathogenic E. coli, but not normal commensal organisms, increase Gal1-R mRNA synthesis and [(125)I]galanin binding sites. Whereas galanin increases short-circuit current (Isc) a...

[Genes coding for RNA polymerase in bacteria. III. The use of modified Sanger's method for sequencing the C-terminal region of rpoB gene, N-terminal region of rpoC gene and intercistron region of RNA polymerase in Pseudomonas putida]

by Tatyana Azhikina and A. Danilkovich

Bioorganicheskaia khimiia, 1988

The Sanger method was modified and the primary structure of the SalI-C fragment of the Pseudomona... more

Distinctive H-(RLDL)4-OH peptide complexes potentiate nanostructure self-assembling in water

Doklady Biochemistry and Biophysics, 2012

Characterization of gastrin-releasing peptide receptors aberrantly expressed by non-antral gastric adenocarcinomas

Peptides, 1999

Epithelial cells lining the GI tract except in the gastric antrum do not normally express gastrin... more Epithelial cells lining the GI tract except in the gastric antrum do not normally express gastrin-releasing peptide receptors (GRP-R). Because GRP-R activation causes the proliferation of many GI cancer cell lines, aberrant expression has been presumed to negatively influence patient survival. We therefore determined the incidence and quality of GRP-R aberrantly expressed by non-antral gastric adenocarcinomas, and evaluated the impact of receptor expression on patient survival. We studied RNA isolated from 20 consecutive non-antral gastric adenocarcinomas, and determined that 8 (40%) aberrantly expressed GRP-R. Of these, 6 (75%) were found to be mutated. Pharmacologically, the effect of these mutations ranged from rendering the GRP-R non-functional to constitutively active. Contrary to expectations, however, survival of patients whose tumor expressed functional GRP-R (18.5 Ϯ 9.8 months) was not statistically different from those that did not (8.3 Ϯ 1.8 months; p ϭ 0.24). Thus our data indicate that mutated isoforms of GRP-R are commonly expressed by non-antral gastric adenocarcinomas. However, expression of functional GRP-R does not alter patient survival, suggesting that this receptor may not be clinically important to the growth of gastric cancers.

A Nucleoprotein Complex containing CCAAT/Enhancer-binding Protein beta Interacts with an Insulin Response Sequence in the Insulin-like Growth Factor-binding Protein-1 Gene and Contributes to Insulin-regulated Gene Expression

Journal of Biological Chemistry, 2001

Highly related insulin response sequences (IRSs) mediate effects of insulin on the expression of ... more Highly related insulin response sequences (IRSs) mediate effects of insulin on the expression of multiple genes in the liver, including insulin-like growth factor binding protein-1 (IGFBP-1) and phosphoenolpyruvate carboxykinase (PEPCK). Gel shift studies reveal that oligonucleotide probes containing an IRS from the IG-FBP-1 or PEPCK gene form a similar complex with hepatic nuclear proteins. Unlabeled competitors containing the IGFBP-1 or PEPCK IRS or a binding site for C/EBP proteins inhibit the formation of this complex. Antibody against C/EBP␤ (but not other C/EBP proteins) supershifts this complex, and Western blotting of affinity purified proteins confirms that C/EBP␤ is present in this complex. Studies with affinity purified and recombinant protein indicate that C/EBP␤ does not interact directly with the IRS, but that other factors are required. Gel shift assays and reporter gene studies with constructs containing point mutations within the IRS reveal that the ability to interact with factors required for the formation of this complex correlates well with the ability of insulin to regulate promoter activity via this IRS (r ‫؍‬ 0.849, p < 0.01). Replacing the IRS in reporter gene constructs with a C/EBP-binding site (but not an HNF-3/forkhead site or cAMP response element) maintains the effect of insulin on promoter activity. Together, these findings indicate that a nucleoprotein complex containing C/EBP␤ interacts with IRSs from the IGFBP-1 and PEPCK genes in a sequence-specific fashion and may contribute to the ability of insulin to regulate gene expression.

Protein Kinase B/Akt Mediates Effects of Insulin on Hepatic Insulin-like Growth Factor-binding Protein-1 Gene Expression through a Conserved Insulin Response Sequence

Journal of Biological Chemistry, 1998

Insulin regulates the expression of multiple hepatic genes through a conserved insulin response s... more Insulin regulates the expression of multiple hepatic genes through a conserved insulin response sequence (IRS) (CAAAAC/TAA) by an as yet undetermined mechanism. Protein kinase B/Akt (PKB/Akt), a member of the PKA/PKC serine/threonine kinase family, functions downstream from phosphatidylinositol 3-kinase (PI3K) in mediating effects of insulin on glucose transport and glycogen synthesis. We asked whether PKB/Akt mediates sequence-specific effects of insulin on hepatic gene expression using the model of the insulin-like growth factor binding protein-1 (IGFBP-1) promoter. Insulin lowers IGFBP-1 mRNA levels, inhibits IGFBP-1 promoter activity, and activates PKB/Akt in HepG2 hepatoma cells through a PI3K-dependent, rapamycin-insensitive mechanism. Constitutively active PI3K and PKB/ Akt are each sufficient to mediate effects of insulin on the IGFBP-1 promoter in a nonadditive fashion. Dominant negative K179 PKB/Akt disrupts the ability of insulin and PI3K to activate PKB/Akt and to inhibit promoter activity. The IGFBP-1 promoter contains two IRSs each of which is sufficient to mediate sequencespecific effects of insulin, PI3K, and PKB/Akt on promoter activity. Highly related IRSs from the phosphoenolpyruvate carboxykinase and apolipoprotein CIII genes also are effective in this setting. These results indicate that PKB/Akt functions downstream from PI3K in mediating sequence-specific effects of insulin on the expression of IGFBP-1 and perhaps multiple hepatic genes through a conserved IRS.

Methods of the theory of liquids as an efficient approach to the analysis of polar peptide complexes

by A. Danilkovich and D. Tikhonov

Doklady Physical Chemistry, 2013

Galanin Causes Cl- Secretion in the Human Colon: Potential Significance of Inflammation-Associated NF-kappaB Activation on Galanin-1 Receptor Expression and Function

Annals of the New York Academy of Sciences, 1998

Galanin is widely distributed in enteric nerves and nerve terminals throughout the gastrointestin... more Galanin is widely distributed in enteric nerves and nerve terminals throughout the gastrointestinal (GI) tract. Within the GI tract galanin is best known for its ability to alter smooth muscle contractility and regulate intestinal motility. However, recent studies also indicate that galanin can modulate epithelial ion transport. We previously showed that epithelial cells lining the human GI tract, including those of colonic origin, express Gal1 galanin receptors (Gal1-R). We herein demonstrate that epithelial cells lining the human colon only express Gal1-R receptors and do not express other galanin receptor subtypes. We previously showed that Gal1-R expression was transcriptionally regulated by the transcription factor NF-B. Consistent with this transcription factor being activated in a number of inflammatory conditions, we show increased colonic Gal1-R expression in patients with colitis due to a variety of causes. To further evaluate the physiology of Gal1-R activation, we studied this receptor expressed by the human colon epithelial cell line T84. Gal1-R activation resulted in a dose-dependent increase in Clsecretion; whereas infection of T84 cells with pathogens known to activate NF-B augmented Gal1-R expression and Clsecretion. Thus, galanin acts as a secretagogue in epithelial cells lining the human colon, with alterations in Gal1-R expression possibly playing an important role in the diarrhea associated with various inflammatory processes affecting the GI tract.

[Genes coding for RNA-polymerase in bacteria. II. Conservative sites in the central region of the beta-subunit of Pseudomonas putida RNA-polymerase]

by Tatyana Azhikina and A. Danilkovich

Bioorganicheskaia khimiia, 1988

SalI--L fragment of the P. putida rpoBC operon has been sequenced and conservative regions of the... more

[Genes coding for RNA polymerase in bacteria. III. The use of modified Sanger's method for sequencing the C-terminal region of rpoB gene, N-terminal region of rpoC gene and intercistron region of RNA polymerase in Pseudomonas putida]

Bioorganicheskaia khimiia, 1988

The Sanger method was modified and the primary structure of the SalI-C fragment of the Pseudomona... more

[Classification of self-organizing peptides]

Bioorganicheskaia khimiia

Amino acid sequences of known natural and synthetic self-assembling peptides were searched and an... more Amino acid sequences of known natural and synthetic self-assembling peptides were searched and analyzed for their characteristic patterns. The attempted formal numerical description of the repeating motifs, which have been revealed, resulted in building of general classification system embracing core-sequences of the peptides capable of nanostructure formation. Advantages and potency of the proposed rational classification were demonstrated via its comparison with the output from the earlier system described by the others.

Galanin-1 receptor up-regulation mediates the excess colonic fluid production caused by infection with enteric pathogens

Nature medicine, 2000

Galanin is widely distributed in enteric nerve terminals lining the gastrointestinal tract. We pr... more Galanin is widely distributed in enteric nerve terminals lining the gastrointestinal tract. We previously showed that pathogenic Escherichia coli, but not normal commensal organisms, increase galanin-1 receptor expression by epithelial cells lining the colon (i.e., colonocytes). When present, galanin-1 receptor activation by ligand causes colonocyte Cl- secretion. We herein demonstrate that disparate pathogens including Salmonella typhimurium and Shigella flexerii also increase colonocyte galanin-1 receptor expression, whose activation is responsible for a principal component of the increased colonic fluid secretion observed. Although eliminating the GAL1R gene by homologous recombination does not alter basal colonic fluid secretion, removal of one or both alleles completely attenuates the increase in fluid secretion due to infection with enteric pathogens. Galanin-1 receptor up-regulation therefore represents a novel mechanism accounting for the increased colonic fluid secretion ob...

Azoxymethane-induced fulminant hepatic failure in C57BL/6J mice: characterization of a new animal model

The American journal of physiology, 1999

Without transplantation, approximately 50-90% of all patients with fulminant hepatic failure (FHF... more Without transplantation, approximately 50-90% of all patients with fulminant hepatic failure (FHF) die. This poor outcome is due in part to the absence of an appropriate animal model, which would allow for a greater understanding of the pathophysiology of this syndrome. Given the reports of liver injury in humans and livestock fed cycad palm nuts on the island of Guam, we hypothesized that the active ingredient azoxymethane (AOM) could cause FHF. We therefore evaluated AOM in C57BL/6J mice. Histologically, we observed microvesicular steatosis 2 h, sinusoidal dilatation 4 h, and centrilobular necrosis 20 h after AOM administration, and transmission electron microscopy showed that this agent causes mitochondrial injury. FHF was associated with all four stages of encephalopathy, as well as by a prodromal period of decreased eating and drinking lasting approximately 15 h before the development of stage I encephalopathy (i.e., loss of scatter reflex). Late encephalopathy was associated w...

Pathogenic Escherichia coli increase Cl- secretion from intestinal epithelia by upregulating galanin-1 receptor expression

The Journal of clinical investigation, 1999

Galanin is widely distributed in enteric nerve terminals lining the human gastrointestinal (GI) t... more Galanin is widely distributed in enteric nerve terminals lining the human gastrointestinal (GI) tract. We have shown previously that galanin-1 receptors (Gal1-R) are expressed by epithelial cells lining the human GI tract, and upon activation cause Cl- secretion. Because expression of this receptor is transcriptionally regulated by nuclear factor-kappa B (NF-kappa B), which is activated by enteric pathogens as a part of the host epithelial response to infection, we investigated whether such bacterial pathogens could directly increase Gal1-R expression in the T84-cell model system. Pathogenic Escherichia coli, but not nonpathogenic E. coli, activate a p50/p65 NF-kappa B complex that binds to oligonucleotides corresponding to a recognition site located within the 5' flanking region of the human GAL1R gene. Pathogenic E. coli, but not normal commensal organisms, increase Gal1-R mRNA synthesis and [(125)I]galanin binding sites. Whereas galanin increases short-circuit current (Isc) a...

[Genes coding for RNA polymerase in bacteria. III. The use of modified Sanger's method for sequencing the C-terminal region of rpoB gene, N-terminal region of rpoC gene and intercistron region of RNA polymerase in Pseudomonas putida]

by Tatyana Azhikina and A. Danilkovich

Bioorganicheskaia khimiia, 1988

The Sanger method was modified and the primary structure of the SalI-C fragment of the Pseudomona... more

Distinctive H-(RLDL)4-OH peptide complexes potentiate nanostructure self-assembling in water

Doklady Biochemistry and Biophysics, 2012

Characterization of gastrin-releasing peptide receptors aberrantly expressed by non-antral gastric adenocarcinomas

Peptides, 1999

Epithelial cells lining the GI tract except in the gastric antrum do not normally express gastrin... more Epithelial cells lining the GI tract except in the gastric antrum do not normally express gastrin-releasing peptide receptors (GRP-R). Because GRP-R activation causes the proliferation of many GI cancer cell lines, aberrant expression has been presumed to negatively influence patient survival. We therefore determined the incidence and quality of GRP-R aberrantly expressed by non-antral gastric adenocarcinomas, and evaluated the impact of receptor expression on patient survival. We studied RNA isolated from 20 consecutive non-antral gastric adenocarcinomas, and determined that 8 (40%) aberrantly expressed GRP-R. Of these, 6 (75%) were found to be mutated. Pharmacologically, the effect of these mutations ranged from rendering the GRP-R non-functional to constitutively active. Contrary to expectations, however, survival of patients whose tumor expressed functional GRP-R (18.5 Ϯ 9.8 months) was not statistically different from those that did not (8.3 Ϯ 1.8 months; p ϭ 0.24). Thus our data indicate that mutated isoforms of GRP-R are commonly expressed by non-antral gastric adenocarcinomas. However, expression of functional GRP-R does not alter patient survival, suggesting that this receptor may not be clinically important to the growth of gastric cancers.

A Nucleoprotein Complex containing CCAAT/Enhancer-binding Protein beta Interacts with an Insulin Response Sequence in the Insulin-like Growth Factor-binding Protein-1 Gene and Contributes to Insulin-regulated Gene Expression

Journal of Biological Chemistry, 2001

Highly related insulin response sequences (IRSs) mediate effects of insulin on the expression of ... more Highly related insulin response sequences (IRSs) mediate effects of insulin on the expression of multiple genes in the liver, including insulin-like growth factor binding protein-1 (IGFBP-1) and phosphoenolpyruvate carboxykinase (PEPCK). Gel shift studies reveal that oligonucleotide probes containing an IRS from the IG-FBP-1 or PEPCK gene form a similar complex with hepatic nuclear proteins. Unlabeled competitors containing the IGFBP-1 or PEPCK IRS or a binding site for C/EBP proteins inhibit the formation of this complex. Antibody against C/EBP␤ (but not other C/EBP proteins) supershifts this complex, and Western blotting of affinity purified proteins confirms that C/EBP␤ is present in this complex. Studies with affinity purified and recombinant protein indicate that C/EBP␤ does not interact directly with the IRS, but that other factors are required. Gel shift assays and reporter gene studies with constructs containing point mutations within the IRS reveal that the ability to interact with factors required for the formation of this complex correlates well with the ability of insulin to regulate promoter activity via this IRS (r ‫؍‬ 0.849, p < 0.01). Replacing the IRS in reporter gene constructs with a C/EBP-binding site (but not an HNF-3/forkhead site or cAMP response element) maintains the effect of insulin on promoter activity. Together, these findings indicate that a nucleoprotein complex containing C/EBP␤ interacts with IRSs from the IGFBP-1 and PEPCK genes in a sequence-specific fashion and may contribute to the ability of insulin to regulate gene expression.

Protein Kinase B/Akt Mediates Effects of Insulin on Hepatic Insulin-like Growth Factor-binding Protein-1 Gene Expression through a Conserved Insulin Response Sequence

Journal of Biological Chemistry, 1998

Insulin regulates the expression of multiple hepatic genes through a conserved insulin response s... more Insulin regulates the expression of multiple hepatic genes through a conserved insulin response sequence (IRS) (CAAAAC/TAA) by an as yet undetermined mechanism. Protein kinase B/Akt (PKB/Akt), a member of the PKA/PKC serine/threonine kinase family, functions downstream from phosphatidylinositol 3-kinase (PI3K) in mediating effects of insulin on glucose transport and glycogen synthesis. We asked whether PKB/Akt mediates sequence-specific effects of insulin on hepatic gene expression using the model of the insulin-like growth factor binding protein-1 (IGFBP-1) promoter. Insulin lowers IGFBP-1 mRNA levels, inhibits IGFBP-1 promoter activity, and activates PKB/Akt in HepG2 hepatoma cells through a PI3K-dependent, rapamycin-insensitive mechanism. Constitutively active PI3K and PKB/ Akt are each sufficient to mediate effects of insulin on the IGFBP-1 promoter in a nonadditive fashion. Dominant negative K179 PKB/Akt disrupts the ability of insulin and PI3K to activate PKB/Akt and to inhibit promoter activity. The IGFBP-1 promoter contains two IRSs each of which is sufficient to mediate sequencespecific effects of insulin, PI3K, and PKB/Akt on promoter activity. Highly related IRSs from the phosphoenolpyruvate carboxykinase and apolipoprotein CIII genes also are effective in this setting. These results indicate that PKB/Akt functions downstream from PI3K in mediating sequence-specific effects of insulin on the expression of IGFBP-1 and perhaps multiple hepatic genes through a conserved IRS.

Methods of the theory of liquids as an efficient approach to the analysis of polar peptide complexes

by A. Danilkovich and D. Tikhonov

Doklady Physical Chemistry, 2013

Galanin Causes Cl- Secretion in the Human Colon: Potential Significance of Inflammation-Associated NF-kappaB Activation on Galanin-1 Receptor Expression and Function

Annals of the New York Academy of Sciences, 1998

Galanin is widely distributed in enteric nerves and nerve terminals throughout the gastrointestin... more Galanin is widely distributed in enteric nerves and nerve terminals throughout the gastrointestinal (GI) tract. Within the GI tract galanin is best known for its ability to alter smooth muscle contractility and regulate intestinal motility. However, recent studies also indicate that galanin can modulate epithelial ion transport. We previously showed that epithelial cells lining the human GI tract, including those of colonic origin, express Gal1 galanin receptors (Gal1-R). We herein demonstrate that epithelial cells lining the human colon only express Gal1-R receptors and do not express other galanin receptor subtypes. We previously showed that Gal1-R expression was transcriptionally regulated by the transcription factor NF-B. Consistent with this transcription factor being activated in a number of inflammatory conditions, we show increased colonic Gal1-R expression in patients with colitis due to a variety of causes. To further evaluate the physiology of Gal1-R activation, we studied this receptor expressed by the human colon epithelial cell line T84. Gal1-R activation resulted in a dose-dependent increase in Clsecretion; whereas infection of T84 cells with pathogens known to activate NF-B augmented Gal1-R expression and Clsecretion. Thus, galanin acts as a secretagogue in epithelial cells lining the human colon, with alterations in Gal1-R expression possibly playing an important role in the diarrhea associated with various inflammatory processes affecting the GI tract.

[Genes coding for RNA-polymerase in bacteria. II. Conservative sites in the central region of the beta-subunit of Pseudomonas putida RNA-polymerase]

by Tatyana Azhikina and A. Danilkovich

Bioorganicheskaia khimiia, 1988

SalI--L fragment of the P. putida rpoBC operon has been sequenced and conservative regions of the... more