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1.
Physiol Genomics ; 48(1): 1-11, 2016 Jan.
Article in English | MEDLINE | ID: mdl-26487704

ABSTRACT

Lower muscle strength in midlife predicts disability and mortality in later life. Blood-borne factors, including growth differentiation factor 11 (GDF11), have been linked to muscle regeneration in animal models. We aimed to identify gene transcripts associated with muscle strength in adults. Meta-analysis of whole blood gene expression (overall 17,534 unique genes measured by microarray) and hand-grip strength in four independent cohorts (n = 7,781, ages: 20-104 yr, weighted mean = 56), adjusted for age, sex, height, weight, and leukocyte subtypes. Separate analyses were performed in subsets (older/younger than 60, men/women). Expression levels of 221 genes were associated with strength after adjustment for cofactors and for multiple statistical testing, including ALAS2 (rate-limiting enzyme in heme synthesis), PRF1 (perforin, a cytotoxic protein associated with inflammation), IGF1R, and IGF2BP2 (both insulin like growth factor related). We identified statistical enrichment for hemoglobin biosynthesis, innate immune activation, and the stress response. Ten genes were associated only in younger individuals, four in men only and one in women only. For example, PIK3R2 (a negative regulator of PI3K/AKT growth pathway) was negatively associated with muscle strength in younger (<60 yr) individuals but not older (≥ 60 yr). We also show that 115 genes (52%) have not previously been linked to muscle in NCBI PubMed abstracts. This first large-scale transcriptome study of muscle strength in human adults confirmed associations with known pathways and provides new evidence for over half of the genes identified. There may be age- and sex-specific gene expression signatures in blood for muscle strength.


Subject(s)
Aging/physiology , Heart/physiology , Muscle Strength/genetics , RNA, Messenger/genetics , Adult , Age Factors , Aged , Aged, 80 and over , Cohort Studies , Female , Gene Ontology , Humans , Knee/physiology , Male , Middle Aged , RNA, Messenger/metabolism , Reproducibility of Results , Sex Characteristics , Young Adult
2.
Mol Psychiatry ; 19(11): 1179-85, 2014 Nov.
Article in English | MEDLINE | ID: mdl-24393808

ABSTRACT

RNA-sequencing (RNA-seq) is a powerful technique to investigate the complexity of gene expression in the human brain. We used RNA-seq to survey the brain transcriptome in high-quality postmortem dorsolateral prefrontal cortex from 11 individuals diagnosed with bipolar disorder (BD) and from 11 age- and gender-matched controls. Deep sequencing was performed, with over 350 million reads per specimen. At a false discovery rate of <5%, we detected five differentially expressed (DE) genes and 12 DE transcripts, most of which have not been previously implicated in BD. Among these, Prominin 1/CD133 and ATP-binding cassette-sub-family G-member2 (ABCG2) have important roles in neuroplasticity. We also show for the first time differential expression of long noncoding RNAs (lncRNAs) in BD. DE transcripts include those of serine/arginine-rich splicing factor 5 (SRSF5) and regulatory factor X4 (RFX4), which along with lncRNAs have a role in mammalian circadian rhythms. The DE genes were significantly enriched for several Gene Ontology categories. Of these, genes involved with GTPase binding were also enriched for BD-associated SNPs from previous genome-wide association studies, suggesting that differential expression of these genes is not simply a consequence of BD or its treatment. Many of these findings were replicated by microarray in an independent sample of 60 cases and controls. These results highlight common pathways for inherited and non-inherited influences on disease risk that may constitute good targets for novel therapies.


Subject(s)
Bipolar Disorder/metabolism , Circadian Rhythm/physiology , GTP Phosphohydrolases/metabolism , Neuronal Plasticity/physiology , Prefrontal Cortex/metabolism , Transcriptome , Adult , Aged , Bipolar Disorder/genetics , Circadian Rhythm/genetics , Female , GTP Phosphohydrolases/genetics , Genome-Wide Association Study , Humans , Male , Meta-Analysis as Topic , Microarray Analysis , Middle Aged , Neuronal Plasticity/genetics , Polymerase Chain Reaction , Principal Component Analysis , Sequence Analysis, RNA/methods , Young Adult
3.
Brain Behav Immun ; 27(1): 63-70, 2013 Jan.
Article in English | MEDLINE | ID: mdl-23022913

ABSTRACT

PURPOSE: Neuroinflammatory mechanisms are associated with fatigue in neurodegenerative conditions such as Parkinson's. The symptoms in Parkinson's including fatigue are thought to be related to α-synuclein overexpression. This study investigated genomic correlates of fatigue experienced by men with prostate cancer receiving external beam radiation therapy (EBRT). PATIENTS AND METHODS: Sixteen men with non-metastatic prostate cancer who were scheduled to receive EBRT were enrolled. Fatigue scores and blood were obtained at baseline (prior to EBRT, D0); one hour following initiation of EBRT (D1), day 7 (D7), day 14 (D14), midpoint (days 19-21, D21), completion (days 38-42, D42), and four weeks post-EBRT (days 68-72, D72). Gene expression profiling using microarray analysis was performed from peripheral blood and confirmatory qPCR and protein (ELISA) analyses verified the microarray results. Correlations between fatigue and gene/protein expressions were determined using a mixed model approach. RESULTS: Microarray data showed significant, differential expression of 463 probesets following EBRT. SNCA had a 2.95-fold change at D21 from baseline. SNCA expression was confirmed by qPCR (p<0.001) and ELISA (p<0.001) over time during EBRT. Fatigue scores were significantly correlated with SNCA gene expression on D14 (r=0.55, p<0.05) and plasma α-synuclein concentrations on D42 of EBRT (r=0.54, p=0.04). CONCLUSION: Fatigue experienced during EBRT may be mediated by α-synuclein overexpression. Alpha-synuclein may serve as a useful biomarker to understand the mechanisms and pathways related to the development of fatigue in this population.


Subject(s)
Fatigue/metabolism , Prostatic Neoplasms/radiotherapy , RNA, Messenger/analysis , Up-Regulation , alpha-Synuclein/metabolism , Adult , Aged , Aged, 80 and over , Case-Control Studies , Enzyme-Linked Immunosorbent Assay , Fatigue/etiology , Gene Expression Profiling , Humans , Inflammation/metabolism , Male , Middle Aged , Prostatic Neoplasms/complications , Real-Time Polymerase Chain Reaction , Time Factors
4.
Hum Mol Genet ; 19(12): 2468-86, 2010 Jun 15.
Article in English | MEDLINE | ID: mdl-20360305

ABSTRACT

Retinal pigment epithelium (RPE) is a polarized cell layer critical for photoreceptor function and survival. The unique physiology and relationship to the photoreceptors make the RPE a critical determinant of human vision. Therefore, we performed a global expression profiling of native and cultured human fetal and adult RPE and determined a set of highly expressed 'signature' genes by comparing the observed RPE gene profiles to the Novartis expression database (SymAtlas: http://wombat.gnf.org/index.html) of 78 tissues. Using stringent selection criteria of at least 10-fold higher expression in three distinct preparations, we identified 154 RPE signature genes, which were validated by qRT-PCR analysis in RPE and in an independent set of 11 tissues. Several of the highly expressed signature genes encode proteins involved in visual cycle, melanogenesis and cell adhesion and Gene ontology analysis enabled the assignment of RPE signature genes to epithelial channels and transporters (ClCN4, BEST1, SLCA20) or matrix remodeling (TIMP3, COL8A2). Fifteen RPE signature genes were associated with known ophthalmic diseases, and 25 others were mapped to regions of disease loci. An evaluation of the RPE signature genes in a recently completed AMD genomewide association (GWA) data set revealed that TIMP3, GRAMD3, PITPNA and CHRNA3 signature genes may have potential roles in AMD pathogenesis and deserve further examination. We propose that RPE signature genes are excellent candidates for retinal diseases and for physiological investigations (e.g. dopachrome tautomerase in melanogenesis). The RPE signature gene set should allow the validation of RPE-like cells derived from human embryonic or induced pluripotent stem cells for cell-based therapies of degenerative retinal diseases.


Subject(s)
Gene Expression Profiling , Gene Expression , Macular Degeneration/genetics , Retinal Pigment Epithelium/metabolism , Adult , Amino Acid Sequence , Cells, Cultured , Genome-Wide Association Study , Humans , Intramolecular Oxidoreductases/genetics , Molecular Sequence Data , Oligonucleotide Array Sequence Analysis , Retinal Pigment Epithelium/cytology , Retinal Pigment Epithelium/embryology
5.
Prostate ; 71(6): 649-58, 2011 May.
Article in English | MEDLINE | ID: mdl-20949546

ABSTRACT

BACKGROUND: Class 3 semaphorins are secreted proteins that act as guidance cues for migrating cells via their transmembrane receptors plexins and neuropilins. Semaphorins have a role in cancer affecting tumor progression both directly, and indirectly by affecting angiogenesis. METHODS: The expression of semaphorins and their receptors in prostate cancer cell lines and tissue was determined by RT-PCR, Western blotting and immunohistochemistry. The effect of Sema3E on prostate cancer cell lines was determined by adhesion assays and transwell migration assays. RESULTS: Semaphorins and their receptors, plexins and neuropilins, are widely co-expressed in prostate cancer cell lines and tissue with a significant overexpression of Sema3E in tumor tissue. Sema3E affected integrin-mediated adhesion to fibronectin of prostate cancer cells, and inhibited their motility. Expression of Sema3C was upregulated and Sema3A and Sema3E were down regulated in prostate cells by hypoxia, consistent with an additional role for Sema3A and 3E as anti-angiogenic factors in prostate cancer. CONCLUSIONS: Semaphorin 3E is aberrantly expressed in prostate cancer and affects adhesion and motility of prostate cancer cells, indicating a role for the Sema3E/PlexinD1 signaling pathway in prostate cancer and identifying a new possible target for therapy.


Subject(s)
Cell Adhesion Molecules/biosynthesis , Nerve Tissue Proteins/biosynthesis , Neuropilins/biosynthesis , Prostatic Neoplasms/metabolism , Semaphorins/biosynthesis , Cell Adhesion/physiology , Cell Adhesion Molecules/genetics , Cell Adhesion Molecules/metabolism , Cell Line, Tumor , Cell Movement/physiology , Humans , Immunohistochemistry , Male , Nerve Tissue Proteins/genetics , Nerve Tissue Proteins/metabolism , Neuropilins/genetics , Neuropilins/metabolism , Prostatic Neoplasms/genetics , Prostatic Neoplasms/pathology , RNA, Neoplasm/chemistry , RNA, Neoplasm/genetics , Reverse Transcriptase Polymerase Chain Reaction , Semaphorins/genetics , Semaphorins/metabolism , Signal Transduction
6.
Allergy ; 66(10): 1304-11, 2011 Oct.
Article in English | MEDLINE | ID: mdl-21605126

ABSTRACT

BACKGROUND: Leukotriene B(4) (LTB(4)) and cysteinyl leukotrienes (cysLTs) are important immune mediators, often found concomitantly at sites of inflammation. Although some of the leukotriene-mediated actions are distinctive (e.g., bronchial constriction for cysLTs), many activities such as leukocyte recruitment to tissues and amplification of inflammatory responses are shared by both classes of leukotrienes. OBJECTIVE: We used human monocytes to characterize leukotriene-specific signaling, gene expression signatures, and functions and to identify interactions between LTB(4)- and cysLTs-induced pathways. METHODS: Responsiveness to leukotrienes was assessed using oligonucleotide microarrays, real-time PCR, calcium mobilization, kinase activation, and chemotaxis assays. RESULTS: Human monocytes were found to express mRNA for high- and low-affinity LTB(4) receptors, BLT(1) and BLT(2), but signal predominantly through BLT(1) in response to LTB(4) stimulation as shown using selective agonists, inhibitors, and gene knock down experiments. LTB(4) acting through BLT(1) coupled to G-protein α inhibitory subunit activated calcium signaling, p44/42 mitogen-activated protein kinase, gene expression, and chemotaxis. Twenty-seven genes, including immediate early genes (IEG), transcription factors, cytokines, and membrane receptors were significantly up-regulated by LTB(4). LTB(4) and LTD(4) had similar effects on signaling, gene expression, and chemotaxis indicating redundant cell activation pathways but costimulation with both lipid mediators was additive for many monocyte functions. CONCLUSION: Leukotriene B(4) and LTD(4) display both redundant and cooperative effects on intracellular signaling, gene expression, and chemotaxis in human monocytes. These findings suggest that therapies targeting either leukotriene alone may be less effective than approaches directed at both.


Subject(s)
Leukotriene B4/metabolism , Leukotriene D4/metabolism , Monocytes/metabolism , Signal Transduction , Calcium/metabolism , Chemotaxis , GTP-Binding Protein alpha Subunits, Gi-Go/metabolism , Gene Expression Regulation , Humans , Mitogen-Activated Protein Kinases/metabolism , Receptors, Leukotriene B4/metabolism
7.
Science ; 151(3708): 330-1, 1966 Jan 21.
Article in English | MEDLINE | ID: mdl-5903339

ABSTRACT

Added thyrocalcitonin greatly diminished parathyroid-hormone-induced resorption of bone in tissue culture. The results indicate that bone is primary site of action of thyrocalcitonin.


Subject(s)
Bone Resorption/drug effects , Calcitonin/pharmacology , Parathyroid Hormone/pharmacology , Animals , Chick Embryo , Culture Techniques , Mice
8.
Science ; 154(3751): 885-6, 1966 Nov 18.
Article in English | MEDLINE | ID: mdl-4304559

ABSTRACT

Analysis of thyrocalcitonin, by density-gradient ultracentrifugation at high speed, showed that its molecular weight (5000 to 6000) is considerably less than was heretofore recognized.


Subject(s)
Calcitonin/analysis , Adrenocorticotropic Hormone/analysis , Animals , Cattle , Centrifugation, Density Gradient , Hypocalcemia/chemically induced , Molecular Weight , Rats , Swine
9.
Science ; 251(4997): 1061-3, 1991 Mar 01.
Article in English | MEDLINE | ID: mdl-17802091

ABSTRACT

Earthquake-induced liquefaction features in Holocene sediments provide evidence of strong prehistoric shaking, magnitude m(b) 6.2 to 6.7, in the Wabash Valley bordering Indiana and Illinois. The source of the one or more earthquakes responsible was almost certainly in or near the Wabash Valley. The largest event is interpreted to have occurred between 7500 and 1500 years ago on the basis of archeological, pedological, and stratigraphic relations.

10.
Mol Cell Biol ; 8(9): 3943-6, 1988 Sep.
Article in English | MEDLINE | ID: mdl-2851732

ABSTRACT

When monkey cells were treated with mitomycin C 24 h before transfection with UV-irradiated pZ189 (a simian virus 40-based shuttle vector), there was a twofold increase in the frequency of mutations in the supF gene of the vector. These results suggest the existence of an enhancible mutagenesis pathway in mammalian cells. However, DNA sequence analysis of the SupF- mutants suggested no dramatic changes in the mechanisms of mutagenesis due to mitomycin C treatment of the cells.


Subject(s)
Genetic Vectors , Mitomycins/pharmacology , Mutation , Simian virus 40/genetics , Transfection/drug effects , Animals , Base Composition , Base Sequence , Cell Line , Chlorocebus aethiops , Genes , Genetic Vectors/radiation effects , Kidney , Mitomycin , Molecular Sequence Data , RNA, Transfer/drug effects , RNA, Transfer/genetics , Transfection/radiation effects , Ultraviolet Rays
11.
Mol Cell Biol ; 6(10): 3349-56, 1986 Oct.
Article in English | MEDLINE | ID: mdl-3540589

ABSTRACT

We used a simian virus 40-based shuttle vector plasmid, pZ189, to determine the role of pyrimidine cyclobutane dimers in UV light-induced mutagenesis in monkey cells. The vector DNA was UV irradiated and then introduced into monkey cells by transfection. After replication, vector DNA was recovered from the cells and tested for mutations in its supF suppressor tRNA marker gene by transformation of Escherichia coli carrying a nonsense mutation in the beta-galactosidase gene. When the irradiated vector was treated with E. coli photolyase prior to transfection, pyrimidine cyclobutane dimers were removed selectively. Removal of approximately 90% of the pyrimidine cyclobutane dimers increased the biological activity of the vector by 75% and reduced its mutation frequency by 80%. Sequence analysis of 72 mutants recovered indicated that there were significantly fewer tandem double-base changes and G X C----A X T transitions (particularly at CC sites) after photoreactivation of the DNA. UV-induced photoproducts remained (although at greatly reduced levels) at all pyr-pyr sites after photoreactivation, but there was a relative increase in photoproducts at CC and TC sites and a relative decrease at TT and CT sites, presumably due to a persistence of (6-4) photoproducts at some CC and TC sites. These observations are consistent with the fact that mutations were found after photoreactivation at many sites at which only cyclobutane dimers would be expected to occur. From these results we conclude that UV-induced pyrimidine cyclobutane dimers are mutagenic in DNA replicated in monkey cells.


Subject(s)
Mutation , Pyrimidine Dimers/radiation effects , Suppression, Genetic/radiation effects , Ultraviolet Rays , Animals , Base Sequence , Cell Line , Chlorocebus aethiops , Escherichia coli/genetics , Genes, Bacterial/radiation effects , Genetic Vectors , Kidney , Plasmids
12.
Cancer Res ; 60(15): 4289-98, 2000 Aug 01.
Article in English | MEDLINE | ID: mdl-10945644

ABSTRACT

Infection with high-risk human papillomaviruses (HPVs) represents a major risk factor for the development of cervical cancer. The HPV-16 E6 and E7 proteins are highly expressed in differentiating keratinocytes, where they inactivate the p53 and retinoblastoma (pRb) proteins, two important transcriptional regulators. We have used cDNA expression arrays to identify global alterations in gene expression induced by E6 and E7 in differentiating cultures of human cervical keratinocytes. We show that E6 and E7 decrease expression of TGF-beta2 mRNA and alter expression of multiple TGF-beta-responsive genes involved in cell cycle regulation, apoptosis, and tissue remodeling. E6 and E7 inhibited expression of TGF-beta2 RNA 7-fold (relative effectiveness, E6/ E7 > E6 > E7 > control) and decreased secretion of biologically active TGF-beta2 by 70-80% (reduced from 70 to 10 pg/10(6) cells/24 h). Downregulation occurred through p53- and pRb-dependent pathways. In contrast, E6 and E7 did not alter expression of TGF-beta1 and TGF-beta3. Down-regulation of TGF-beta2 was biologically relevant because the addition of recombinant cytokine (10-200 pg/ml) to E6/E7-expressing cells restored expression of TGF-P-responsive genes, inhibited growth of keratinocytes, and decreased immortalization by E6 and E7. These results suggest that TGF-32- and TGF-3-responsive genes are important targets for the HPV-16 E6 and E7 oncoproteins in differentiating cervical keratinocytes.


Subject(s)
Cervix Uteri/virology , Keratinocytes/virology , Oncogene Proteins, Viral/physiology , Papillomaviridae , Repressor Proteins , Transforming Growth Factor beta/antagonists & inhibitors , Blotting, Northern , Cell Differentiation/physiology , Cell Division/physiology , Cell Transformation, Viral , Cells, Cultured , Cervix Uteri/cytology , Cervix Uteri/metabolism , Down-Regulation/physiology , Female , Gene Silencing , Genes, Retinoblastoma , Genes, p53 , Humans , Keratinocytes/cytology , Keratinocytes/metabolism , Oncogene Proteins, Viral/genetics , Oncogene Proteins, Viral/metabolism , Papillomaviridae/genetics , Papillomavirus E7 Proteins , Retroviridae/genetics , Reverse Transcriptase Polymerase Chain Reaction , Transforming Growth Factor beta/biosynthesis , Transforming Growth Factor beta/metabolism , Tumor Suppressor Protein p53/genetics , Tumor Suppressor Protein p53/metabolism
13.
J Mol Biol ; 267(2): 446-63, 1997 Mar 28.
Article in English | MEDLINE | ID: mdl-9096237

ABSTRACT

The three-dimensional fold of a protein is described by the organization of its secondary structure elements in 3D space, i.e. its "topology". We find that the protein topology can be recognized from the ID sequence of secondary structure states of the residues alone. Automated recognition is facilitated by use of hidden Markov models (HMMs) to represent topology families of proteins. Such models can be trained on the experimentally observed secondary structure sequences of family members using well established algorithms. Here, we model various topology groups in the alpha class of proteins and identify, from a large database, those proteins having the topology described by each model. The correct topology family for protein secondary structure sequences could be recognized 12 out of 14 times. When the observed secondary structure sequences are replaced with predicted sequences recognition is still achievable 8 out of 14 times. The success rate for observed sequences indicates that our approach will become increasingly useful as the accuracy of secondary prediction algorithms is improved. Our study indicates that the HMMs are useful for protein topology recognition even when no detectable primary amino acid sequence similarity is present. To illustrate the potential utility of our method, protein topology recognition is attempted on leptin, the obese gene product, and the human interleukin-6 sequence, for which fold predictions have been previously published.


Subject(s)
Markov Chains , Protein Conformation , Protein Structure, Secondary , Proteins/chemistry , Algorithms , Amino Acid Sequence , Computer Simulation , Cytochromes/chemistry , Cytokines/chemistry , Databases, Factual , Globins/chemistry , Interleukin-6/chemistry , Leptin , Models, Molecular , Protein Folding , Proteins/classification , Sequence Alignment
14.
Protein Sci ; 6(12): 2538-47, 1997 Dec.
Article in English | MEDLINE | ID: mdl-9416603

ABSTRACT

Linkers that connect repeating secondary structures fall into conformational classes based on distance and main-chain torsion clustering. A data set of 300 unique protein chains with low pairwise sequence identity was clustered into only a few groups representing the preferred motifs. The linkers of two to eight residues for the nonredundant data set are designated H-Ln-H, H-Ln-E, E-Ln-H, E-Ln-E, where n is the length, H stands for alpha-helices, and E for beta-strands. Most of the clusters identified here corroborate earlier findings. However, 19 new clusters are identified in this paper, with many of them having seven and eight residue linkers. In our first analysis, the secondary structures flanking the linkers are both interacting and noninteracting and there is no precise angle of orientation between them. A second analysis was performed on a set of proteins with restricted orientations for the flanking elements, namely, mainly alpha class of proteins with orthogonal architecture. Two definite clusters are identified, one corresponding to linkers of orthogonal helices and the other to linkers of antiparallel helices. Loops forming binding sites or involved in catalytic activity are important determinants of the function of proteins. Although the structural conservation of the residues around the catalytic triad of serine proteases has been studied widely, there has not been a systematic analysis of the conformation of the loops that contain them. Residues of the catalytic triad reside in the linkers of beta-strands, with varying lengths of more than eight residues. Here, we analyze the structural conservation of such linkers by superposition, and observe a conserved structural feature of the linkers incorporating each of the three residues of the catalytic triad.


Subject(s)
Protein Structure, Secondary , Proteins/chemistry , Amino Acid Sequence , Binding Sites , Catalysis , Molecular Sequence Data , Protein Conformation , Sequence Alignment , Serine Endopeptidases/chemistry , Serine Endopeptidases/metabolism
15.
Protein Sci ; 6(7): 1467-81, 1997 Jul.
Article in English | MEDLINE | ID: mdl-9232648

ABSTRACT

Statistical potentials based on pairwise interactions between C alpha atoms are commonly used in protein threading/fold-recognition attempts. Inclusion of higher order interaction is a possible means of improving the specificity of these potentials. Delaunay tessellation of the C alpha-atom representation of protein structure has been suggested as a means of defining multi-body interactions. A large number of parameters are required to define all four-body interactions of 20 amino acid types (20(4) = 160,000). Assuming that residue order within a four-body contact is irrelevant reduces this to a manageable 8,855 parameters, using a nonredundant dataset of 608 protein structures. Three lines of evidence support the significance and utility of the four-body potential for sequence-structure matching. First, compared to the four-body model, all lower-order interaction models (three-body, two-body, one-body) are found statistically inadequate to explain the frequency distribution of residue contacts. Second, coherent patterns of interaction are seen in a graphic presentation of the four-body potential. Many patterns have plausible biophysical explanations and are consistent across sets of residues sharing certain properties (e.g., size, hydrophobicity, or charge). Third, the utility of the multi-body potential is tested on a test set of 12 same-length pairs of proteins of known structure for two protocols: Sequence-recognizes-structure, where a query sequence is threaded (without gap) through the native and a non-native structure; and structure-recognizes-sequence, where a query structure is threaded by its native and another non-native sequence. Using cross-validated training, protein sequences correctly recognized their native structure in all 24 cases. Conversely, structures recognized the native sequence in 23 of 24 cases. Further, the score differences between correct and decoy structures increased significantly using the three- or four-body potential compared to potentials of lower order.


Subject(s)
Protein Conformation , Sequence Alignment/methods , Statistics as Topic/methods , Models, Chemical , Protein Folding , Thermodynamics
16.
Protein Sci ; 5(1): 106-13, 1996 Jan.
Article in English | MEDLINE | ID: mdl-8771202

ABSTRACT

Most recent protein secondary structure prediction methods use sequence alignments to improve the prediction quality. We investigate the relationship between the location of secondary structural elements, gaps, and variable residue positions in multiple sequence alignments. We further investigate how these relationships compare with those found in structurally aligned protein families. We show how such associations may be used to improve the quality of prediction of the secondary structure elements, using the Quadratic-Logistic method with profiles. Furthermore, we analyze the extent to which the number of homologous sequences influences the quality of prediction. The analysis of variable residue positions shows that surprisingly, helical regions exhibit greater variability than do coil regions, which are generally thought to be the most common secondary structure elements in loops. However, the correlation between variability and the presence of helices does not significantly improve prediction quality. Gaps are a distinct signal for coil regions. Increasing the coil propensity for those residues occurring in gap regions enhances the overall prediction quality. Prediction accuracy increases initially with the number of homologues, but changes negligibly as the number of homologues exceeds about 14. The alignment quality affects the prediction more than other factors, hence a careful selection and alignment of even a small number of homologues can lead to significant improvements in prediction accuracy.


Subject(s)
Protein Structure, Secondary , Sequence Homology, Amino Acid , Amino Acid Sequence , Animals , Humans , Molecular Sequence Data , Mutagenesis, Insertional , Sequence Deletion
17.
Endocr Relat Cancer ; 11(4): 897-911, 2004 Dec.
Article in English | MEDLINE | ID: mdl-15613462

ABSTRACT

Pheochromocytomas in von Hippel-Lindau (VHL) syndrome produce exclusively norepinephrine, whereas those in multiple endocrine neoplasia type 2 (MEN 2) produce epinephrine. This study examined the pathways activated in VHL-associated pheochromocytomas by comparing gene expression profiles in VHL and MEN 2 tumors in relationship to profiles in sporadic norepinephrine- and epinephrine-producing tumors. Larger and more distinct differences in gene expression among hereditary than sporadic tumors indicated the importance of the underlying mutation to gene expression profiles. Many of the genes over-expressed in VHL compared with MEN 2 tumors were clearly linked to the hypoxia-driven angiogenic pathways that are activated in VHL-associated tumorigenesis. Such genes included those for the glucose transporter, vascular endothelial growth factor (VEGF), placental growth factor, angiopoietin 2, tie-1, VEGF receptor 2 and its coreceptor, neuropilin-1. Other up-regulated genes, such as connective tissue growth factor, cysteine-rich 61, matrix metalloproteinase 1, vascular endothelial cadherin, tenascin C, stanniocalcin 1, and cyclooxygenases 1 and 2 are known to be involved in VEGF-regulated angiogenesis. Shared differences in expression of subsets of genes in norepinephrine- versus epinephrine-producing hereditary and sporadic pheochromocytomas indicated other differences in gene expression that may underlie the biochemical phenotype. Over-expression of the hypoxia-inducible transcription factor, HIF-2alpha, in norepinephrine-predominant sporadic and VHL tumors compared with epinephrine-producing tumors indicates that expression of this gene depends on the noradrenergic biochemical phenotype. The findings fit with the known expression of HIF-2alpha in norepinephrine-producing cells of the sympathetic nervous system and might explain both the development and noradrenergic biochemical phenotype of pheochromocytomas in VHL syndrome.


Subject(s)
Adrenal Gland Neoplasms/genetics , Pheochromocytoma/genetics , von Hippel-Lindau Disease/genetics , Adolescent , Adrenal Gland Neoplasms/complications , Adult , Basic Helix-Loop-Helix Transcription Factors/biosynthesis , Child , Epinephrine , Female , Gene Expression Profiling , Humans , Hypoxia , Male , Middle Aged , Multiple Endocrine Neoplasia Type 2a/complications , Multiple Endocrine Neoplasia Type 2a/genetics , Norepinephrine , Oligonucleotide Array Sequence Analysis , Pheochromocytoma/complications , von Hippel-Lindau Disease/complications
18.
Endocrinology ; 99(2): 371-8, 1976 Aug.
Article in English | MEDLINE | ID: mdl-954638

ABSTRACT

Lactating rats were compared with nonlactating controls, with regard to the intake and absorption of calcium, serum calcium level, and te protective effect of thyroacalcitonin (TC) against hypercalcemia and hyperphosphatemia. While consuming a commercial diet, intact, nonfasted lactating rats maintained a serum calcium level of approximately 9 mg/100 ml, which was 1 mg/100 ml lower than that of nonlactating controls. The level rose to that of the controls within one day after removal of the litters from the mother. Compared with nonlactating rats, lactating rats had a three-fold higher calcium intake and a six-fold higher rate of net absorption of calcium. After intragastric calcium (10 mg/100 g body wt) the increase in serum calcium was small (1 mg/100 ml) 2 h later in both groups of sham-operated rats but was markedly increased in thyroparathyroidectomized groups, with the lactating rats showing a significantly greater increase than the nonlactating rats. The injection of a small dose of porcine thyrocalcitonin completely counteracted this hypercalcemia in lactating rats, but did not have any effect on nonlactating controls. Protection by the thyroid gland against hyperphosphatemia after intragastric calcium also was significant in both lactating and nonlactating rats. The results show that TC is much more effective in lactating than in nonlactating rats, suggesting that TC may be of particular importance in lactation by restricting elevations of serum calcium and phosphorus levels after eating, thereby aiding in conservation of these ions.


Subject(s)
Calcitonin/metabolism , Calcium/metabolism , Lactation , Animals , Calcium/blood , Female , Phosphorus/blood , Pregnancy , Rats , Thyroidectomy
19.
Endocrinology ; 128(5): 2259-65, 1991 May.
Article in English | MEDLINE | ID: mdl-2019250

ABSTRACT

We have confirmed the serum calcium-raising effect of adrenalectomy in young male rats 5-6 h after parathyroidectomy that was first observed by others many years ago. (The phenomenon has also been reported in cats, dogs, and mice.) In addition, we have shown that adrenalectomy raises the serum ionized calcium as well as total calcium and that the effect occurs in young female as well as in young male rats. Furthermore, we have found that the serum calcium-raising effect of adrenalectomy occurs if the adrenalectomy is performed several days before parathyroidectomy or 6 h after parathyroidectomy, as well as at the same time as the parathyroidectomy. When the rats were adrenalectomized 7-9 days before parathyroidectomy and given small daily life-maintaining doses of corticosterone or cortisone acetate, this glucocorticoid treatment did not reverse the adrenalectomy effect. This led us to think at first that the effect of adrenalectomy must be due to the loss of an unknown adrenal factor rather than to loss of glucocorticoid. Additional experiments, however, in which corticosterone or hydrocortisone was administered by continuous release pellets, demonstrated conclusively that a small continuous supply of corticosterone (within the physiological range as determined by immunoassay of plasma) was sufficient to reverse the adrenalectomy effect. The results with hydrocortisone were similar at even lower doses than of corticosterone. Somewhat higher doses of corticosterone or hydrocortisone reduced the serum calcium even below the parathyroidectomy level. In a preliminary investigation of the specificity of the glucocorticoid effect we found that aldosterone, dehydroepiandrosterone, or estradiol had no effect on serum calcium under similar conditions. We conclude that the fall in serum calcium after parathyroidectomy in rats is due in part to the hypocalcemic effect of endogenous corticosterone. Thus, the loss of corticosterone after adrenalectomy explains the serum calcium-raising effect of adrenalectomy in parathyroidectomized rats. These results also suggest that glucocorticoids at physiological levels have a significant effect on calcium metabolism in general.


Subject(s)
Adrenalectomy , Corticosterone/blood , Hypocalcemia/metabolism , Parathyroidectomy , Animals , Calcium/blood , Corticosterone/pharmacology , Female , Ions , Male , Osmolar Concentration , Rats , Rats, Inbred Strains , Reference Values , Steroids/pharmacology , Time Factors
20.
Endocrinology ; 100(4): 1014-21, 1977 Apr.
Article in English | MEDLINE | ID: mdl-837869

ABSTRACT

Gastrin secretion was studied in 16 young anesthetized pigs weighing 14-26 kg. Test substances were infused (0.1 ml/min x 10-20 min) directly into the gastric antrum via a catheter in the right gastroepiploic artery. Samples were collected from a catheter in the right gastroepiploic vein and plasma gastrin was measured by radiommunoassay. The following results were observed: 1) basal gastrin in antral venous blood was 10-5 times that in peripheral blood (620+/-222 pg/ml vs. 41+/-10 pg/ml, 2) native bovine parathyroid hormone (PTH) and synthetic human 1-34 PTH (0.02-4U/min) produced rapid (within 10-30 min) and pronounced (approximately 10-fold) increases in gastrin release with no increase in plasma calcium and, in several animals, in the face of a falling plasma calcium concentration, 3) neither acute thyroidectomy nor infusion of porcine thyrocalcitonin (TCT), 0.5-2.5 U/min) consistently altered basal gastrin secretion (N=3-6), and 4) infusion of TCT (0.5 U/min)along with PTH (2U/min) significantly suppressed the 10-11-fold increase in gastrin release observed when PTH subsequently was infused alone in each pig (N=6). The results demonstrate that PTH can stimulate gastrin secretion in the pig and that TCT can suppress this effect.


Subject(s)
Calcitonin/pharmacology , Gastrins/metabolism , Parathyroid Hormone/pharmacology , Animals , Calcium/blood , Female , Gastrins/blood , Male , Peptide Fragments/pharmacology , Swine , Thyroidectomy
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