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1

From residue matching patterns to protein folding topographies: General model and bovine  

E-print Network

From residue matching patterns to protein folding topographies: General model and bovine pancreatic-grained model for protein-folding dynamics is introduced based on a discretized representation of torsional, pattern recognition, and general characteristics of protein folding kinetics. Topology here implies

Berry, R. Stephen

2

Protein Crystal Bovine Insulin  

NASA Technical Reports Server (NTRS)

The comparison of protein crystal, Bovine Insulin space-grown (left) and earth-grown (right). Facilitates the incorporation of glucose into cells. In diabetics, there is either a decrease in or complete lack of insulin, thereby leading to several harmful complications. Principal Investigator is Larry DeLucas.

1991-01-01

3

Exploring the interaction of a micelle entrapped biologically important proton transfer probe with the model transport protein bovine serum albumin.  

PubMed

This article describes the interaction of a micelle entrapped pharmaceutically important isoindole fused imidazole derivative, namely, 1-(2-hydroxy-5-methyl-phenyl)-3,5-dioxo-1H-imidazo-[3,4-b] isoindole (ADII), with the model transport protein bovine serum albumin (BSA). Different spectroscopic techniques such as steady state absorption, emission, circular dichroism, dynamic light scattering, etc., have been employed to explore preferential interaction of this drug template with micelles and protein BSA. Binding of ADII with BSA is found to be enormously modified when it is released from the micellar environment. The binding constant of the ADII-BSA complex is reduced when the probe is released from anionic SDS micelle, whereas the binding is observed to be strengthened in cationic CTAB micellar medium due to the formation of a 1:2 complex (ADII-BSA). Time-resolved studies also support our steady state findings that the released drug from the micellar environment is found to be strongly bound with the protein BSA. Circular dichroism (CD) and dynamic light scattering (DLS) study reveals that the secondary structure of BSA gets some stabilization in SDS medium after binding of drug template to protein. The probable binding location of the probe within the protein cavity (hydrophilic subdomain IA) has been explored from an AutoDock-based blind docking simulation study. PMID:25068392

Ray, Debarati; Kundu, Ashis; Pramanik, Animesh; Guchhait, Nikhil

2015-02-12

4

Detection of bovine milk proteins in soymilk by Western blotting.  

PubMed

A Western blotting method for the detection of whey milk proteins in commercial soymilks was applied to assess the food safety. Soy proteins and milk proteins were separated by SDS-PAGE in PhastSystem equipment. After the electrophoretic separation, immunodetection with anti-bovine alpha-lactalbumin and anti-bovine beta-lactoglobulin antisera was performed. Adulteration with bovine protein in percentages of 0.1% in soy protein can be detected. Western blotting of bovine alpha-lactalbumin and bovine beta-lactoglobulin was applied to detect adulteration by bovine milk proteins in different soymilks: powdered soymilk and soy infant formulas. PMID:9874352

Molina, E; Amigo, L; Ramos, M

1998-12-01

5

Original article Effects of bovine colostrum acid protein on bone  

E-print Network

that bovine milk and its basic proteins, and bovine colostrums (BC) and their extracts have positive effects- : BCAP [/] ; : ( 0.04 g·d-1 ) BCAP ; BCAP (0.04~0.40 g·d-1 ) / / / / Résumé ­ Effets de la basiques, le colostrum bovin et ses extraits, ont un effet positif sur la croissance osseuse de l'Homme ou

Boyer, Edmond

6

Inelastic neutron scattering analysis of low-frequency motions in proteins: Harmonic and damped harmonic models of bovine pancreatic tryspin inhibitor  

NASA Astrophysics Data System (ADS)

Inelastic neutron scattering spectra are calculated from harmonic and damped harmonic models of the internal dynamics of a small protein, the bovine pancreatic trypsin inhibitor (BPTI). Numerical Fourier transformation of the intermediate scattering function Fvibinc (q, t) is used to calculate the inelastic scattering. This permits the inclusion of multiphonon scattering and frictional damping effects. Although for a typical experimental configuration, the multiphonon contribution does not significantly alter the form of the scattering at frequencies below about 30 cm-1, it does have a significant effect on the scattering intensity at higher frequencies. Frictional damping is introduced into the harmonic model by assuming that each mode acts as an independent damped Langevin oscillator. With this model and the assumption that the lowest frequency modes are overdamped while the higher frequency modes are underdamped, improved agreement with the experimental BPTI powder results is obtained. The measured scattering from BPTI in solution shows increased intensity at frequencies below 50 cm-1 relative to the powder results. The solution scattering profile can be reproduced approximately by the addition of overdamped Langevin oscillator normal modes to the dynamic model in best agreement with the powder data. Several other aspects of neutron scattering from proteins are examined. Anisotropy in the harmonic resolution broadened scattering is demonstrated. Spectra calculated assuming classical equations of motion are shown to agree with those calculated with the full quantum-mechanical dynamical model. Translational diffusion broadening is found to be small compared to the instrumental resolution broadening for the range of scattering wave vectors of interest. The contribution of the coherent scattering to the measured intensity is calculated for the case of a partially hydrated protein. Under typical experimental conditions, the measured cross sections are dominated by the incoherent scattering and the self part of the coherent scattering, a result that justifies the comparison of experimental data with calculated incoherent scattering spectra.

Smith, Jeremy; Cusack, Stephen; Tidor, Bruce; Karplus, Martin

1990-09-01

7

Protein metabolism and strength performance after bovine colostrum supplementation  

Microsoft Academic Search

Summary. This study was designed to determine the responses of muscle protein, serum amino acids, and strength performance to bovine colostrum supplementation in physically active men. The rest (R) group (n=6) and the exercise (E) group (n=6) carried out twice a 2-week experiment randomly assigned in a double-blind fashion with either placebo (PLA; consuming daily 20?g maltodextrin) or bovine colostrum

A. Mero; T. Nyknen; O. Keinnen; J. Knuutinen; K. Lahti; M. Alen; S. Rasi; J. Leppluoto

2005-01-01

8

Chemical alteration by tooth bleaching of human salivary proteins that infiltrated subsurface enamel lesions--experimental study with bovine lesion model systems.  

PubMed

Salivary macromolecules infiltrate white and brown spot enamel lesions and adsorb onto hydroxyapatite. Calcium-binding salivary proteins such as statherin hinder remineralization of these lesions. We assessed whether bleaching agents can remove salivary components that have infiltrated and bound to experimental subsurface lesions in bovine enamel prepared by immersing specimens in acid and then human saliva. Transversal microradiography showed that such demineralized lesions mimicked incipient carious lesions. Bound proteins to the experimental and untreated control specimens were eluted in a stepwise manner with phosphatebuffered saline, 0.4 M phosphate buffer, and 1 M HCl. SDS-PAGE of dialyzed extracts showed that specific salivary proteins bound to the lesions, while virtually no protein bands were detected if the specimens were bleached. Western blotting showed that even statherin, which was more firmly bound than other proteins, was removed. In-office bleaching agent may be useful in treating enamel lesions for removing proteins bound to these lesions. PMID:25273046

Iizuka, Junko; Mukai, Yoshiharu; Taniguchi, Motoe; Mikuni-Takagaki, Yuko; Ten Cate, Jacob Martien; Teranaka, Toshio

2014-01-01

9

Characterization of a Deswapped Triple Mutant Bovine Odorant Binding Protein  

PubMed Central

The stability and functionality of GCC-bOBP, a monomeric triple mutant of bovine odorant binding protein, was investigated, in the presence of denaturant and in acidic pH conditions, by both protein and 1-aminoanthracene ligand fluorescence measurements, and compared to that of both bovine and porcine wild type homologues. Complete reversibility of unfolding was observed, though refolding was characterized by hysteresis. Molecular dynamics simulations, performed to detect possible structural changes of the monomeric scaffold related to the presence of the ligand, pointed out the stability of the ?-barrel lipocalin scaffold. PMID:21731442

Polverini, Eugenia; Lardi, Paolo; Mazzini, Alberto; Sorbi, Robert T.; Virna, Conti; Ramoni, Roberto; Favilla, Roberto

2011-01-01

10

Bovine immunoglobulin protein isolates for the nutritional management of enteropathy.  

PubMed

The gastrointestinal tract is responsible for a multitude of digestive and immune functions which depend upon the balanced interaction of the intestinal microbiota, diet, gut barrier function, and mucosal immune response. Disruptions in one or more of these factors can lead to intestinal disorders or enteropathies which are characterized by intestinal inflammation, increased gut permeability, and reduced capacity to absorb nutrients. Enteropathy is frequently associated with human immunodeficiency virus (HIV) infection, inflammatory bowel disease, autoimmune enteropathy, radiation enteritis, and irritable bowel syndrome (IBS), where pathologic changes in the intestinal tract lead to abdominal discomfort, bloating, abnormal bowel function (e.g., diarrhea, urgency, constipation and malabsorption). Unfortunately, effective therapies for the management of enteropathy and restoring intestinal health are still not available. An accumulating body of preclinical studies has demonstrated that oral administration of plasma- or serum-derived protein concentrates containing high levels of immunoglobulins can improve weight, normalize gut barrier function, and reduce the severity of enteropathy in animal models. Recent studies in humans, using serum-derived bovine immunoglobulin/protein isolate, demonstrate that such protein preparations are safe and improve symptoms, nutritional status, and various biomarkers associated with enteropathy. Benefits have been shown in patients with HIV infection or diarrhea-predominant IBS. This review summarizes preclinical and clinical studies with plasma/serum protein concentrates and describes the effects on host nutrition, intestinal function, and markers of intestinal inflammation. It supports the concept that immunoglobulin-containing protein preparations may offer a new strategy for restoring functional homeostasis in the intestinal tract of patients with enteropathy. PMID:25206275

Petschow, Bryon W; Blikslager, Anthony T; Weaver, Eric M; Campbell, Joy M; Polo, Javier; Shaw, Audrey L; Burnett, Bruce P; Klein, Gerald L; Rhoads, J Marc

2014-09-01

11

Bovine immunoglobulin protein isolates for the nutritional management of enteropathy  

PubMed Central

The gastrointestinal tract is responsible for a multitude of digestive and immune functions which depend upon the balanced interaction of the intestinal microbiota, diet, gut barrier function, and mucosal immune response. Disruptions in one or more of these factors can lead to intestinal disorders or enteropathies which are characterized by intestinal inflammation, increased gut permeability, and reduced capacity to absorb nutrients. Enteropathy is frequently associated with human immunodeficiency virus (HIV) infection, inflammatory bowel disease, autoimmune enteropathy, radiation enteritis, and irritable bowel syndrome (IBS), where pathologic changes in the intestinal tract lead to abdominal discomfort, bloating, abnormal bowel function (e.g., diarrhea, urgency, constipation and malabsorption). Unfortunately, effective therapies for the management of enteropathy and restoring intestinal health are still not available. An accumulating body of preclinical studies has demonstrated that oral administration of plasma- or serum-derived protein concentrates containing high levels of immunoglobulins can improve weight, normalize gut barrier function, and reduce the severity of enteropathy in animal models. Recent studies in humans, using serum-derived bovine immunoglobulin/protein isolate, demonstrate that such protein preparations are safe and improve symptoms, nutritional status, and various biomarkers associated with enteropathy. Benefits have been shown in patients with HIV infection or diarrhea-predominant IBS. This review summarizes preclinical and clinical studies with plasma/serum protein concentrates and describes the effects on host nutrition, intestinal function, and markers of intestinal inflammation. It supports the concept that immunoglobulin-containing protein preparations may offer a new strategy for restoring functional homeostasis in the intestinal tract of patients with enteropathy. PMID:25206275

Petschow, Bryon W; Blikslager, Anthony T; Weaver, Eric M; Campbell, Joy M; Polo, Javier; Shaw, Audrey L; Burnett, Bruce P; Klein, Gerald L; Rhoads, J Marc

2014-01-01

12

Artificial transmembrane oncoproteins smaller than the2 bovine papillomavirus E5 protein redefine sequence requirements3  

E-print Network

KTS 1 1 Artificial transmembrane oncoproteins smaller than the2 bovine papillomavirus E5 protein; bovine papillomavirus21 Word count: Abtract = 190; Text = 8,63722 * Corresponding author: Tel: 203.asm.orgDownloadedfrom #12;KTS 2 ABSTRACT24 The bovine papillomavirus E5 protein (BPV E5) is a 44-amino acid homodimeric25

Gerstein, Mark

13

Bovine viral diarrhea viruses differentially alter the expression of the protein kinases and related proteins affecting the development of infection and anti-viral mechanisms in bovine monocytes  

Microsoft Academic Search

Using a proteomics approach, we evaluated the effect of cytopathic (cp), and non-cytopathic (ncp) bovine viral diarrhea viruses (BVDV) on the expression of protein kinases and related proteins in bovine monocytes. Proteins were isolated from membrane and cytosolic fractions with the differential detergent fractionation (DDF) method and identified with 2D-LC ESI MS2. Of approximately 10,000 proteins identified, 378 proteins had

George V. Pinchuk; Sang-Ryul Lee; Bindu Nanduri; Kelly L. Honsinger; John V. Stokes; Lesya M. Pinchuk

2008-01-01

14

Rapid thermal equilibration of differentially heated protein and water in bovine corneal stroma  

NASA Astrophysics Data System (ADS)

We measure and simulate the thermal response of bovine corneal stroma to a picosecond IR heating pulse. A thermal diffusion model is developed for this tissue based on the spatial distribution and properties of protein and water constituents in the stroma. In this idealized model, differentially heated protein and water constituents thermally equilibrate with a thermalization time of 515 ps. Using transient absorption spectroscopy for picosecond protein thermometry, a significantly faster thermalization time of 165 ps is measured. The implications of this faster than expected thermalization for the energy-partition model of short-pulse mid-IR tissue ablation are discussed.

Marcus, George Alexander; Schwettman, H. Alan

2011-10-01

15

TRANSLATION OF BOVINE LEUKEMIA VIRUS GENOME INFORMATION IN HETEROLOGOUS PROTEIN SYNTHESIZING SYSTEMS  

E-print Network

TRANSLATION OF BOVINE LEUKEMIA VIRUS GENOME INFORMATION IN HETEROLOGOUS PROTEIN SYNTHESIZING, probablement situé du côté 3' du génome viral. Introduction. Bovine leukemia is a lymphoproliferative disease whose etiological agent is a retrovirus called Bovine Leukemia Virus (BLV). The cha- racteristics

Paris-Sud XI, Université de

16

Structural and functional characteristics of bovine milk protein glycosylation.  

PubMed

Most secreted and cell membrane proteins in mammals are glycosylated. Many of these glycoproteins are also prevalent in milk and play key roles in the biomodulatory properties of milk and ultimately in determining milk's nutritional quality. Although a significant amount of information exists on the types and roles of free oligosaccharides in milk, very little is known about the glycans associated with milk glycoproteins, in particular, the biological properties that are linked to their presence. The main glycoproteins found in bovine milk are lactoferrin, the immunoglobulins, glycomacropeptide, a glycopeptide derived from ?-casein, and the glycoproteins of the milk fat globule membrane. Here, we review the glycoproteins present in bovine milk, the information currently available on their glycosylation and the biological significance of their oligosaccharide chains. PMID:24398766

O'Riordan, Noelle; Kane, Marian; Joshi, Lokesh; Hickey, Rita M

2014-03-01

17

A Bovine Babesiosis model with dispersion.  

PubMed

Bovine Babesiosis (BB) is a tick borne parasitic disease with worldwide over 1.3 billion bovines at potential risk of being infected. The disease, also called tick fever, causes significant mortality from infection by the protozoa upon exposure to infected ticks. An important factor in the spread of the disease is the dispersion or migration of cattle as well as ticks. In this paper, we study the effect of this factor. We introduce a number, [Formula: see text], a "proliferation index," which plays the same role as the basic reproduction number [Formula: see text] with respect to the stability/instability of the disease-free equilibrium, and observe that [Formula: see text] decreases as the dispersion coefficients increase. We prove, mathematically, that if [Formula: see text] then the tick fever will remain endemic. We also consider the case where the birth rate of ticks undergoes seasonal oscillations. Based on data from Colombia, South Africa, and Brazil, we use the model to determine the effectiveness of several intervention schemes to control the progression of BB. PMID:24257900

Friedman, Avner; Yakubu, Abdul-Aziz

2014-01-01

18

Epitope mapping of bovine viral diarrhea virus nonstructural protein 3.  

PubMed

Six consecutive overlapped coding regions (F1-F6) of whole NS3 molecule of bovine viral diarrhea virus (BVDV) were cloned into pMAL-c2X plasmid vector and expressed in Escherichia coli cells (BL21 strain). The recombinant proteins were then purified by amylose resin to determine the most immunogenic domain(s) of the NS3 molecule. Evaluation of the recombinant proteins was carried out by indirect ELISAs using several bovine sera (previously characterized by virus neutralization test, a commercial ELISA kit, and a newly developed NS3-ELISA) and 6 monoclonal antibodies. The experiments showed that the most immunogenic domain of the NS3 protein was the fourth designed fragment (F4), a 122 amino-acid (AA) region of about 13.5 kDa (nucleotide 1003-1368; residue 335-456). Purified recombinant F4 was also evaluated as single ELISA antigen (F4-ELISA) for the detection of anti-BVDV antibodies in sera of infected cattle. Although this small recombinant fragment of NS3 protein was almost completely soluble and expressed more efficient respect to whole NS3 molecule, it did not show enough sensitivity and specificity to be a proper substitute for NS3 as ELISA antigen to detect specific antibodies against BVDV. However, statistical analyses showed a medium correlation between the results of the developed F4-ELISA and virus neutralization test (kappa coefficient=0.63, P<0.001), with the relative sensitivity and specificity of 78.05% and 84.91%, respectively, suggesting the potential use of this fragment as an ELISA antigen along with other antigens or monoclonal antibody(s) in a competitive ELISA. PMID:25205011

Mahmoodi, Pezhman; Shapouri, Masoud Reza Seyfi Abad; Ghorbanpour, Masoud; Ekhtelat, Maryam; Hajikolaei, Mohammad Rahim Haji; Lotfi, Mohsen; Boroujeni, Mahdi Pourmahdi; Daghari, Maryam

2014-10-15

19

Control of domain swapping in bovine odorant-binding protein.  

PubMed

As revealed by the X-ray structure, bovine odorant-binding protein (OBPb) is a domain swapped dimer [Tegoni, Ramoni, Bignetti, Spinelli and Cambillau (1996) Nat. Struct. Biol. 3, 863-867; Bianchet, Bains, Petosi, Pevsner, Snyder, Monaco and Amzel (1996) Nat. Struct. Biol. 3, 934-939]. This contrasts with all known mammalian OBPs, which are monomers, and in particular with porcine OBP (OBPp), sharing 42.3% identity with OBPb. By the mechanism of domain swapping, monomers are proposed to evolve into dimers and oligomers, as observed in human prion. Comparison of bovine and porcine OBP sequences pointed at OBPp glycine 121, in the hinge linking the beta-barrel to the alpha-helix. The absence of this residue in OBPb might explain why the normal lipocalin beta-turn is not formed. In order to decipher the domain swapping determinants we have produced a mutant of OBPb in which a glycine residue was inserted after position 121, and a mutant of OBPp in which glycine 121 was deleted. The latter mutation did not result in dimerization, while OBPb-121Gly+ became monomeric, suggesting that domain swapping was reversed. Careful structural analysis revealed that besides the presence of a glycine in the hinge, the dimer interface formed by the C-termini and by the presence of the lipocalins conserved disulphide bridge may also control domain swapping. PMID:11931632

Ramoni, Roberto; Vincent, Florence; Ashcroft, Alison E; Accornero, Paolo; Grolli, Stefano; Valencia, Christel; Tegoni, Mariella; Cambillau, Christian

2002-08-01

20

Control of domain swapping in bovine odorant-binding protein.  

PubMed Central

As revealed by the X-ray structure, bovine odorant-binding protein (OBPb) is a domain swapped dimer [Tegoni, Ramoni, Bignetti, Spinelli and Cambillau (1996) Nat. Struct. Biol. 3, 863-867; Bianchet, Bains, Petosi, Pevsner, Snyder, Monaco and Amzel (1996) Nat. Struct. Biol. 3, 934-939]. This contrasts with all known mammalian OBPs, which are monomers, and in particular with porcine OBP (OBPp), sharing 42.3% identity with OBPb. By the mechanism of domain swapping, monomers are proposed to evolve into dimers and oligomers, as observed in human prion. Comparison of bovine and porcine OBP sequences pointed at OBPp glycine 121, in the hinge linking the beta-barrel to the alpha-helix. The absence of this residue in OBPb might explain why the normal lipocalin beta-turn is not formed. In order to decipher the domain swapping determinants we have produced a mutant of OBPb in which a glycine residue was inserted after position 121, and a mutant of OBPp in which glycine 121 was deleted. The latter mutation did not result in dimerization, while OBPb-121Gly+ became monomeric, suggesting that domain swapping was reversed. Careful structural analysis revealed that besides the presence of a glycine in the hinge, the dimer interface formed by the C-termini and by the presence of the lipocalins conserved disulphide bridge may also control domain swapping. PMID:11931632

Ramoni, Roberto; Vincent, Florence; Ashcroft, Alison E; Accornero, Paolo; Grolli, Stefano; Valencia, Christel; Tegoni, Mariella; Cambillau, Christian

2002-01-01

21

Detection of G proteins in purified bovine brain myelin.  

PubMed

Following a previous report on detection of muscarinic receptors in myelin with the implied presence of G proteins, we now demonstrate by more direct means the presence of such proteins and their quantification. Using [35S]guanosine 5'-O-(3-thiotriphosphate) ([35S]GTP gamma S) as the binding ligand, purified myelin from bovine brain was found to contain approximately half the binding activity of whole white matter (138 +/- 9 vs. 271 +/- 18 pmol/mg of protein). Scatchard analysis of saturation binding data revealed two slopes, a result suggesting at least two binding populations. This binding was inhibited by GTP and its analog but not by 5'-adenylylimidodiphosphate [App(NH)p], GMP, or UTP. Following sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE) of myelin proteins and blotting on nitrocellulose, [alpha-32P]GTP bound to three bands in the 21-27-kDa range in a manner inhibited by GTP and GTP gamma S but not App(NH)p. ADP-ribosylation of myelin with [32P]NAD+ and cholera toxin labeled a protein of 43 kDa, whereas reaction with pertussis toxin labeled two components of 40 kDa. Cholate extract of myelin subjected to chromatography on a column of phenyl-Sepharose gave at least three major peaks of [35S]GTP gamma S binding activity. SDS-PAGE and immunoblot analyses of peak I indicated the presence of Go alpha, Gi alpha, and Gs alpha. Further fractionation of peak II by diethyl-aminoethyl-Sephacel chromatography gave one [35S]GTP gamma S binding peak with the low-molecular-mass (21-27 kDa) proteins and a second showing two major protein bands of 36 and 40 kDa on SDS-PAGE.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:1904910

Larocca, J N; Golly, F; Ledeen, R W

1991-07-01

22

Identification of highly active flocculant proteins in bovine blood  

Technology Transfer Automated Retrieval System (TEKTRAN)

Bovine blood is an excellent flocculating agent, faster acting and as effective on a mass basis as polyacrylamide, the most widely utilized polymeric flocculant. To determine the molecular basis of flocculation activity, whole bovine blood (BB) and BB plasma were fractionated by size exclusion chro...

23

NMR structure of the bovine prion protein Francisco Lo pez Garcia, Ralph Zahn, Roland Riek, and Kurt Wu thrich*  

E-print Network

NMR structure of the bovine prion protein Francisco Lo´ pez Garci´a, Ralph Zahn, Roland Riek structures of the recombinant 217-residue polypeptide chain of the mature bovine prion protein, bPrP(23 there are characteristic local differences relative to the confor- mations of the murine and Syrian hamster prion proteins

Riek, Roland

24

Gene expression and cDNA cloning identified a major basic protein constituent of bovine seminal plasma as bovine monocyte-chemoattractant protein-1 (MCP-1).  

PubMed

P6 is one of the major basic proteins of bovine seminal plasma. Using cell-free translation of poly(A)+RNA from bovine seminal vesicle tissue and monospecific anti-P6-IgGs, we show that P6 is a secretory product of the seminal vesicles. Immunohistochemical experiments supported this finding. Immunoscreening of a lambda gt11 cDNA library derived from seminal vesicle poly(A)+RNA furnished a number of positive cDNA clones, from which clone pH42 was characterized by sequencing. The partial amino acid sequence of a CNBr-fragment of P6 permitted identification of the reading frame of clone pH42 encoding the precursor protein of P6. The P6 precursor contains a signal peptide of 23 amino acids followed by the mature P6 sequence of 76 amino acid residues. The cDNA sequence of pH42 was 80% homologous with that of the human monocyte-chemoattractant protein-1 (hMCP-1). The respective amino acid sequences for the precursor molecules are 72% identical. Northern analysis of seminal vesicle poly(A)+RNA using pH42 as probe probe identified a 0.9-kb P6 mRNA. Stimulation of P6 mRNA expression by phytohemagglutinin in bovine peripheral mononuclear leukocytes suggests that P6 is identical to bovine MCP-1. PMID:1721821

Wempe, F; Henschen, A; Scheit, K H

1991-11-01

25

Chimeric Bovine Respiratory Syncytial Virus with Attachment and Fusion Glycoproteins Replaced by Bovine Parainfluenza Virus Type 3 Hemagglutinin-Neuraminidase and Fusion Proteins  

Microsoft Academic Search

Chimeric bovine respiratory syncytial viruses (BRSV) expressing glycoproteins of bovine parainfluenza virus type 3 (BPIV-3) instead of BRSV glycoproteins were generated from cDNA. In the BRSV antigenome cDNA, the open reading frames of the major BRSV glycoproteins, attachment protein G and fusion protein F, were replaced individually or together by those of the BPIV-3 hemagglutinin-neuraminidase (HN) and\\/or fusion (F) glycoproteins.

MATTHIAS B. STOPE; AXEL KARGER; ULRIKE SCHMIDT; URSULA J. BUCHHOLZ

2001-01-01

26

Identification of candidate genes related to bovine marbling using protein-protein interaction networks.  

PubMed

Complex traits are determined by the combined effects of many loci and are affected by gene networks or biological pathways. Systems biology approaches have an important role in the identification of candidate genes related to complex diseases or traits at the system level. The present study systemically analyzed genes associated with bovine marbling score and identified their relationships. The candidate nodes were obtained using MedScan text-mining tools and linked by protein-protein interaction (PPI) from the Human Protein Reference Database (HPRD). To determine key node of marbling, the degree and betweenness centrality (BC) were used. The hub nodes and biological pathways of our network are consistent with the previous reports about marbling traits, and also suggest unknown candidate genes associated with intramuscular fat. Five nodes were identified as hub genes, which was consistent with the network analysis using quantitative reverse-transcription PCR (qRT-PCR). Key nodes of the PPI network have positive roles (PPAR?, C/EBP?, and RUNX1T1) and negative roles (RXRA, CAMK2A) in the development of intramuscular fat by several adipogenesis-related pathways. This study provides genetic information for identifying candidate genes for the marbling trait in bovine. PMID:21912507

Lim, Dajeong; Kim, Nam-Kuk; Park, Hye-Sun; Lee, Seung-Hwan; Cho, Yong-Min; Oh, Sung Jong; Kim, Tae-Hun; Kim, Heebal

2011-01-01

27

Engineered Lactobacillus rhamnosus GG expressing IgG-binding domains of protein G: Capture of hyperimmune bovine colostrum antibodies and protection against diarrhea in a mouse pup rotavirus infection model.  

PubMed

Rotavirus-induced diarrhea causes more than 500,000 deaths annually in the world, and although vaccines are being made available, new effective treatment strategies should still be considered. Purified antibodies derived from hyperimmune bovine colostrum (HBC), from cows immunized with rotavirus, were previously used for treatment of rotavirus diarrhea in children. A combination of HBC antibodies and a probiotic strain of Lactobacillus (L. rhamnosus GG) was also found to be more effective than HBC alone in reducing diarrhea in a mouse model of rotavirus infection. In order to further improve this form of treatment, L. rhamnosus GG was engineered to display surface expressed IgG-binding domains of protein G (GB1, GB2, and GB3) which capture HBC-derived IgG antibodies (HBC-IgG) and thus target rotavirus. The expression of IgG-binding domains on the surface of the bacteria as well as their binding to HBC-IgG and to rotavirus (simian strain RRV) was demonstrated by Western blot, flow cytometry, and electron microscopy. The prophylactic effect of engineered L. rhamnosus GG and anti-rotaviral activity of HBC antibodies was evaluated in a mouse pup model of RRV infection. The combination therapy with engineered L. rhamnosus GG (PG3) and HBC was significantly more effective in reducing the prevalence, severity, and duration of diarrhea in comparison to HBC alone or a combination of wild-type L. rhamnosus GG and HBC. The new therapy reduces the effective dose of HBC between 10 to 100-fold and may thus decrease treatment costs. This antibody capturing platform, tested here for the first time in vivo, could potentially be used to target additional gastrointestinal pathogens. PMID:24291196

Gnayd?n, Gke; Zhang, Ran; Hammarstrm, Lennart; Marcotte, Harold

2014-01-16

28

Comparison of the principal proteins in bovine, caprine, buffalo, equine and camel milk.  

PubMed

Proteomic analysis of bovine, caprine, buffalo, equine and camel milk highlighted significant interspecies differences. Camel milk was found to be devoid of ?-lactoglobulin, whereas ?-lactoglobulin was the major whey protein in bovine, buffalo, caprine, and equine milk. Five different isoforms of ?-casein were found in camel milk, analogous to the micro-heterogeneity observed for bovine ?-casein. Several spots observed in 2D-electrophoretograms of milk of all species could tentatively be identified as polypeptides arising from the enzymatic hydrolysis of caseins. The understanding gained from the proteomic comparison of these milks may be of relevance both in terms of identifying sources of hypoallergenic alternatives to bovine milk and detection of adulteration of milk samples and products. PMID:22365180

Hinz, Katharina; O'Connor, Paula M; Huppertz, Thom; Ross, R Paul; Kelly, Alan L

2012-05-01

29

Computational modelling of bovine ovarian follicle development  

PubMed Central

Background The development of ovarian follicles hinges on the timely exposure to the appropriate combination of hormones. Follicle stimulating hormone (FSH) and luteinizing hormone (LH) are both produced in the pituitary gland and are transported via the blood circulation to the thecal layer surrounding the follicle. From there both hormones are transported into the follicle by diffusion. FSH-receptors are expressed mainly in the granulosa while LH-receptors are expressed in a gradient with highest expression in the theca. How this spatial organization is achieved is not known. Equally it is not understood whether LH and FSH trigger distinct signalling programs or whether the distinct spatial localization of their G-protein coupled receptors is sufficient to convey their distinct biological function. Results We have developed a data-based computational model of the spatio-temporal signalling processes within the follicle and (i) predict that FSH and LH form a gradient inside the follicle, (ii) show that the spatial distribution of FSH- and LH-receptors can arise from the well known regulatory interactions, and (iii) find that the differential activity of FSH and LH may well result from the distinct spatial localisation of their receptors, even when both receptors respond with the same intracellular signalling cascade to their ligand. Conclusion The model integrates the large amount of published data into a consistent framework that can now be used to better understand how observed defects translate into failed follicle maturation. PMID:23856357

2013-01-01

30

Insulin regulates milk protein synthesis at multiple levels in the bovine mammary gland  

Microsoft Academic Search

The role of insulin in milk protein synthesis is unresolved in the bovine mammary gland. This study examined the potential\\u000a role of insulin in the presence of two lactogenic hormones, hydrocortisone and prolactin, in milk protein synthesis. Insulin\\u000a was shown to stimulate milk protein gene expression, casein synthesis and 14C-lysine uptake in mammary explants from late pregnant cows. A global

Karensa K. Menzies; Christophe Lefvre; Keith L. Macmillan; Kevin R. Nicholas

2009-01-01

31

Proteomics-Based Systems Biology Modeling of Bovine Germinal Vesicle Stage Oocyte and Cumulus Cell Interaction  

PubMed Central

Background Oocytes are the female gametes which establish the program of life after fertilization. Interactions between oocyte and the surrounding cumulus cells at germinal vesicle (GV) stage are considered essential for proper maturation or programming of oocytes, which is crucial for normal fertilization and embryonic development. However, despite its importance, little is known about the molecular events and pathways involved in this bidirectional communication. Methodology/Principal Findings We used differential detergent fractionation multidimensional protein identification technology (DDF-Mud PIT) on bovine GV oocyte and cumulus cells and identified 811 and 1247 proteins in GV oocyte and cumulus cells, respectively; 371 proteins were significantly differentially expressed between each cell type. Systems biology modeling, which included Gene Ontology (GO) and canonical genetic pathway analysis, showed that cumulus cells have higher expression of proteins involved in cell communication, generation of precursor metabolites and energy, as well as transport than GV oocytes. Our data also suggests a hypothesis that oocytes may depend on the presence of cumulus cells to generate specific cellular signals to coordinate their growth and maturation. Conclusions/Significance Systems biology modeling of bovine oocytes and cumulus cells in the context of GO and protein interaction networks identified the signaling pathways associated with the proteins involved in cell-to-cell signaling biological process that may have implications in oocyte competence and maturation. This first comprehensive systems biology modeling of bovine oocytes and cumulus cell proteomes not only provides a foundation for signaling and cell physiology at the GV stage of oocyte development, but are also valuable for comparative studies of other stages of oocyte development at the molecular level. PMID:20574525

Peddinti, Divyaswetha; Memili, Erdogan; Burgess, Shane C.

2010-01-01

32

Is double C2 protein (DOC2) expressed in bovine adrenal medulla? A commercial anti-DOC2 monoclonal antibody recognizes a major bovine mitochondrial antigen.  

PubMed Central

We have examined the expression in bovine adrenal medulla of double C2 protein (DOC2), a vesicular protein which associates with intracellular phospholipid and Ca(2+) and is implicated in the modulation of regulated exocytosis. Extensive reverse transcription-PCR, Northern blot analyses and in vitro translation reactions have been combined with immunological studies to provide data to suggest that neither DOC2alpha nor DOC2beta is expressed at detectable levels in bovine adrenal chromaffin cells, and that a widely used monoclonal antibody directed against DOC2 also recognizes mitochondrial complex III core protein 2. PMID:10998344

Duncan, R R; Apps, D K; Learmonth, M P; Shipston, M J; Chow, R H

2000-01-01

33

The requirement for protein kinase C delta (PRKCD) during preimplantation bovine embryo development.  

PubMed

Protein kinase C (PKC) delta (PRKCD) is a member of the novel PKC subfamily that regulates gene expression in bovine trophoblast cells. Additional functions for PRKCD in early embryonic development in cattle have not been fully explored. The objectives of this study were to describe the expression profile of PRKCD mRNA in bovine embryos and to examine its biological roles during bovine embryo development. Both PRKCD mRNA and protein are present throughout early embryo development and increases in mRNA abundance are evident at morula and blastocyst stages. Phosphorylation patterns are consistent with detection of enzymatically active PRKCD in bovine embryos. Exposure to a pharmacological inhibitor (rottlerin) during early embryonic development prevented development beyond the eight- to 16-cell stage. Treatment at or after the 16-cell stage reduced blastocyst development rates, total blastomere numbers and inner cell mass-to-trophoblast cell ratio. Exposure to the inhibitor also decreased basal interferon tau (IFNT) transcript abundance and abolished fibroblast growth factor-2 induction of IFNT expression. Furthermore, trophoblast adhesion and proliferation was compromised in hatched blastocysts. These observations provide novel insights into PRKCD mRNA expression profiles in bovine embryos and provide evidence for PRKCD-dependent regulation of embryonic development, gene expression and post-hatching events. PMID:25116760

Yang, Qi-En; Ozawa, Manabu; Zhang, Kun; Johnson, Sally E; Ealy, Alan D

2014-08-13

34

The effect of bovine whey protein on ectopic bone formation in young growing rats  

Microsoft Academic Search

The beneficial effect of bovine whey protein (WP) on bone metabolism has been shown in adult human subjects and ovariectomised rats. However, its effect on bone formation in earlier life, particularly during periods of bone mineral accrual, has not been investigated. Twenty-one male rats (4 weeks old, Wistar strain) were randomised by weight into three groups of seven rats each

Owen Kelly; Siobhan Cusack; Kevin D. Cashman

2003-01-01

35

~ristalsof bovine chyrnotrypsin. Enzymes are proteins specialized to catalyze biological reac-  

E-print Network

Figure 8-1 ~ristalsof bovine chyrnotrypsin. 1 Enzymes are proteins specialized to catalyze of biochemistry is the history of en- zyme research. The name enzyme ("in yeast") was not used until 1877- furic acid. Although Louis Pasteur recognized that fermentation is catalyzed by enzymes, he postulated

Vallino, Joseph J.

36

THz spectroscopy and molecular modeling of bovine serum albumin under various hydration conditions  

NASA Astrophysics Data System (ADS)

Bovine serum albumin (BSA) is the most abundant protein in bovine plasma; its three dimensional structure is yet unknown. We investigated the structure and dynamics of BSA in lyophilized samples, in 10% w/w and 50% w/w BSA aqueous solutions using THz spectroscopy and molecular modeling. THz spectra were recorded with a spectral resolution of 7.4 GHz. Theoretical spectra were simulated using a structural model of BSA based on the homology with the known structure of human serum albumin (HSA). The agreement between simulated THz spectra and THz spectra recorded experimentally allowed us to validate the BSA model and the solution models. Based on these models we investigated the flexibility of dry BSA and of BSA with one hydration layer. The hydrated structure of BSA is less flexible than the structure free of water molecules, except for residues 54 - 104 that are more mobile in the hydrated structure. We also investigated the fluctuations of the water molecules within the first hydration layer and identified two groups of water molecules: one that exhibits small fluctuations and one of highly mobile water molecules. These molecules are associated to highly mobile regions from the proteins and move in positive correlation with the neighboring protein regions. We also propose a BSA dimerization model in which the molecules strongly interact. The fluctuations of the BSA monomers and of their first hydration layer were investigated. The two molecules display similar fluctuation patterns, but one of them is slightly more flexible.

Mernea, Maria; Calborean, Octavian; Petrescu, Livia; Zatreanu, Diana; Sandu, Oana; Dascalu, Traian; Mihailescu, Dan Florin

2012-02-01

37

THz spectroscopy and molecular modeling of bovine serum albumin under various hydration conditions  

NASA Astrophysics Data System (ADS)

Bovine serum albumin (BSA) is the most abundant protein in bovine plasma; its three dimensional structure is yet unknown. We investigated the structure and dynamics of BSA in lyophilized samples, in 10% w/w and 50% w/w BSA aqueous solutions using THz spectroscopy and molecular modeling. THz spectra were recorded with a spectral resolution of 7.4 GHz. Theoretical spectra were simulated using a structural model of BSA based on the homology with the known structure of human serum albumin (HSA). The agreement between simulated THz spectra and THz spectra recorded experimentally allowed us to validate the BSA model and the solution models. Based on these models we investigated the flexibility of dry BSA and of BSA with one hydration layer. The hydrated structure of BSA is less flexible than the structure free of water molecules, except for residues 54 - 104 that are more mobile in the hydrated structure. We also investigated the fluctuations of the water molecules within the first hydration layer and identified two groups of water molecules: one that exhibits small fluctuations and one of highly mobile water molecules. These molecules are associated to highly mobile regions from the proteins and move in positive correlation with the neighboring protein regions. We also propose a BSA dimerization model in which the molecules strongly interact. The fluctuations of the BSA monomers and of their first hydration layer were investigated. The two molecules display similar fluctuation patterns, but one of them is slightly more flexible.

Mernea, Maria; Calborean, Octavian; Petrescu, Livia; Zatreanu, Diana; Sandu, Oana; Dascalu, Traian; Mihailescu, Dan Florin

2011-09-01

38

Comparative phosphorylation of calmodulin from trypanosomatids and bovine brain by calmodulin-binding protein kinases.  

PubMed

Calmodulin (CaM), a major intracellular Ca2+ receptor protein, has been identified and partially characterized in several trypanosomatids. The amino acid sequences of CaM from Trypanosoma cruzi and Trypanosoma brucei are known, while that from Leishmania mexicana is not. CaM from T. cruzi contains 18 amino acid substitutions, as compared with CaM from bovine brain. In addition, CaM from bovine brain contains two tyrosine residues (Tyr-99 and Tyr-138), while CaM from T. cruzi only contains Tyr-138. In the present work we show that a monoclonal antibody developed against the carboxyl-terminal region of bovine brain CaM fails to recognize CaM from both T. cruzi and L. mexicana. CaM from both parasites and from bovine brain were phosphorylated in vitro by a preparation of CaM-binding protein kinases enriched in the epidermal growth factor (EGF) receptor. Phosphoamino acids analysis demonstrated EGF-dependent phosphorylation of tyrosine residues in bovine brain CaM, while only trace amounts of tyrosine phosphorylation were detected in CaM from both trypanosomatids. These results demonstrate that the EGF receptor tyrosine kinase targets Tyr-99, but not Tyr-138, as the single major phosphorylatable residue of CaM. On the other hand, and in contrast to bovine brain CaM, there is a significant phosphorylation of serine residues in CaM from trypanosomatids which is activated by the EGF receptor via a protein-serine/threonine kinase cascade. PMID:9827017

Benaim, G; Cervino, V; Villalobo, A

1998-07-01

39

Osteoinductivity of partially purified bovine, ostrich and emu bone morphogenetic proteins in vitro.  

PubMed

The aim of this study was to observe the osteogenic activity of native bone morphogenetic proteins (BMPs) obtained from different species including bovine, ostrich and emu sources in order to compare mammalian and avian BMPs. Rat mesenchymal progenitor marrow stromal cells and pre-osteoblastic C2C12 cell cultures, were exposed to the native BMPs and alkaline phosphatase (ALP) and creatine kinase (CK) levels were determined by assay. The results showed that the ALP activity in C2C12 cultures was elevated by bovine BMP by 2- to 10-fold (p < 0.05-0.001) from day 3 during 14 days. There were no significant differences in avian BMP related elevations of ALP activity except with ostrich BMPs at day 14 (p < 0.05). However, exposure of MSCs cultures to BMPs derived from bovine, ostrich or emu sources resulted in elevated ALP from day 3 (p < 0.05). Bovine BMP resulted in more ALP elevation than with either of the avian BMPs. All of BMPs elevated Creatine kinase (CK) activity from day 1 and climbed until peaking at day 7. Compared with control cultures, CK was elevated more with exposure to emu BMP and was more elevated with greater statistical significance than with bovine and ostrich BMP before day 5. These higher levels remained until day 14 (p < 0.05). The results of this study suggest that both bovine and avian BMPs are able to stimulate osteogenesis in mature osteoblasts in vitro. The strongest synergistic effect on osteogenesis was detected in cells stimulated with bovine BMP. Avian BMPs had lower effects on ALP and CK activity, emu BMP being more effective than ostrich BMP. PMID:21630431

Hu, ZhenMing; Peel, Sean A F; Lindholm, Tom C; Sndor, George K B; Clokie, Cameron M L; Su, Yan

2011-09-01

40

Protein Hydrolysates from Non-bovine and Plant Sources Replaces Tryptone in Microbiological Media  

NASA Astrophysics Data System (ADS)

Tryptone (pancreatic digest of casein) is a common ingredient in laboratory and fermentation media for growing wild-type and genetically modified microorganisms. Many of the commercially manufactured products such as human growth hormone, antibiotics, insulin, etc. are produced by recombinant strains grown on materials derived from bovine sources. With the emergence of Bovine Spongiform Encephalopathy (BSE) and the consequent increase in Food and Drug Administration (FDA) regulations, elimination of materials of bovine origin from fermentation media is of paramount importance. To achieve this objective, a number of protein hydrolysates derived from non-bovine animal and plant sources were evaluated. Tryptone in Luria-Bertani (LB) broth was replaced with an equal quantity of alternate protein hydrolysates. Four of the six hydrolysates (one animal and three from plants) were found to efficiently replace the tryptone present in LB-medium as measured by growth rate and growth yield of a recombinant Escherichia coli strain. In addition, we have determined plasmid stability, inducibility and activity of the plasmid encoded ?-galactosidase in the recombinant strain grown in the presence of various protein hydrolysates.

Ranganathan, Yamini; Patel, Shifa; Pasupuleti, Vijai K.; Meganathan, R.

41

Genomic Heritability of Bovine Growth Using a Mixed Model  

PubMed Central

This study investigated heritability for bovine growth estimated with genomewide single nucleotide polymorphism (SNP) information obtained from a DNA microarray chip. Three hundred sixty seven Korean cattle were genotyped with the Illumina BovineSNP50 BeadChip, and 39,112 SNPs of 364 animals filtered by quality assurance were analyzed to estimate heritability of body weights at 6, 9, 12, 15, 18, 21, and 24 months of age. Restricted maximum likelihood estimate of heritability was obtained using covariance structure of genomic relationships among animals in a mixed model framework. Heritability estimates ranged from 0.58 to 0.76 for body weights at different ages. The heritability estimates using genomic information in this study were larger than those which had been estimated previously using pedigree information. The results revealed a trend that the heritability for body weight increased at a younger age (6 months). This suggests an early genetic evaluation for bovine growth using genomic information to increase genetic merits of animals. PMID:25358309

Ryu, Jihye; Lee, Chaeyoung

2014-01-01

42

Immunocytochemical localization of pyrazine-binding protein in bovine nasal mucosa.  

PubMed

Polyclonal antibodies have been raised against purified bovine pyrazine-binding protein, a protein that binds the odorant 2-isobutyl-3-methoxypyrazine. These antibodies have been utilized in immunocytochemical experiments to localize the pyrazine-binding protein in bovine nasal mucosa. Tissue fragments, macroscopically identified as olfactory and respiratory mucosa, were fixed in Bouin's fluid and embedded in paraffin. Consecutive serial sections were processed for immunofluorescence studies and restained either with haematoxylin-eosin or with periodic acid Schiff-Alcian Blue. In both olfactory and respiratory mucosa, only seromucous tubulo-acinar glands were specifically labelled. These glands are located in the lamina propria underlying typical respiratory epithelium, even in those tissues that are macroscopically defined as olfactory mucosa. PMID:3545483

Avanzini, F; Bignetti, E; Bordi, C; Carfagna, G; Cavaggioni, A; Ferrari, G; Sorbi, R T; Tirindelli, R

1987-02-01

43

A bovine model for polycystic ovary syndrome  

Technology Transfer Automated Retrieval System (TEKTRAN)

Polycystic ovary syndrome (PCOS) results in the greatest single cause of anovulatory infertility in reproductive age women (affecting 5-10%). Previously, research groups have created animal models utilizing non-human primates and sheep to better understand the mechanisms involved in PCOS. However, c...

44

Production and properties of health-promoting proteins and peptides from bovine colostrum and milk.  

PubMed

The high nutritive value and diverse functional properties of milk proteins are well known. Beyond these qualities, milk proteins have attracted growing scientific and commercial interest as a source of biologically active molecules. Such proteins are found in abundance in colostrum which is the initial milk secreted by mammalian species during late pregnancy and the first few days after birth of the offspring. The best characterized colostrum-based bioactive proteins include alpha-lactalbumin, beta-lactoglobulin, immunoglobulins, lactoferrin, lactoperoxidase and growth factors. All of them can nowadays be enriched and purified on an industrial scale from bovine colostral whey or cheese whey. These native proteins exhibit a wide range of biological activities that are known to affect the digestive function, metabolic responses to absorbed nutrients, growth and development of organs and disease resistance. Also, some of these proteins may prove beneficial in reduction of the risks of chronic human diseases reflected by the metabolic syndrome. It is speculated that such potentially beneficial effects are partially attributed to bioactive peptides derived from intact proteins. These peptides can be liberated during gastrointestinal digestion or fermentation of milk by starter cultures. The efficacy of a few peptides has been established in animal and human studies and the number of commercial products supplemented with specific milk peptides is envisaged to increase on global markets. Bovine colostrum appears as a highly potential source of biologically active native proteins and peptide fractions for inclusion as health-promoting ingredients in various food applications. PMID:24200017

Korhonen, H J

2013-01-01

45

The effect of myofibrillar protein interaction on the tenderness of bovine muscle subjected to cold-shortening and postmortem conditioning  

E-print Network

THE EFFECT OF MYOFIBRILLAR PROTEIN INTERACTION ON THE TENDERNESS OF BOVINE MUSCLE SUBJECTED TO COLD-SHORTENING AND POSTMORTEM CONDITIONING A Thesis by MICHELE ANDREA POLLARD Submitted to the Graduate College of Texas ARM University... in partial fulfillment of the requirement for the degree of MASTER OF SCIENCE August 1983 Major Subject: Food Science and Technology THE EFFECT OF MYOFIBRILLAR PROTEIN INTERACTION ON THE TENDERNESS OF BOVINE MUSCLE SUBJECTED TO COLD...

Pollard, Michele Andrea

2012-06-07

46

A bovine acellular scaffold for vocal fold reconstruction in a rat model #  

PubMed Central

With a rat model of vocal fold injury, this study examined the in vivo host response to an acellular xenogeneic scaffold derived from the bovine vocal fold lamina propria, and the potential of the scaffold for constructive tissue remodeling. Bilateral wounds were created in the posterior vocal folds of 20 rats, and bovine acellular scaffolds were implanted into the wounds unilaterally, with the contralateral vocal folds as control. The rats were humanely sacrificed after 3 days, 7 days, 1 month, and 3 months, and the coronal sections of their larynges were examined histologically. Expressions of key matrix proteins including collagen I, collagen III, elastin, fibronectin, hyaluronic acid, and glycosaminoglycans were quantified with digital image analysis. Significant infiltration of host inflammatory cells and host fibroblasts in the scaffold implant was observed in the acute stage of wound repair (3 days and 7 days post-surgery). The mean relative densities of collagen I, collagen III, and glycosaminoglycans in the implanted vocal folds were significantly higher than those in the control after 3 days, followed by gradual decreases over 3 months. Histological results showed that the scaffolds were apparently degraded by 3 months, with no fibrotic tissue formation or calcification. These preliminary findings suggested that the bovine acellular scaffold could be a potential xenograft for vocal fold regeneration. PMID:19165789

Xu, Chet C.; Chan, Roger W.; Weinberger, Debra G.; Efune, Guy; Pawlowski, Karen S.

2008-01-01

47

Cross-Reactivity Between the Soybean Protein P34 and Bovine Caseins  

PubMed Central

Purpose Soy-based formulas are widely used as dairy substitutes to treat milk allergy patients. However, reactions to soy have been reported in a small proportion of patients with IgE-mediated milk allergies. The aim of this work was to explore whether P34, a mayor soybean allergen, is involved in this cross-reactivity. Methods In vitro recognition of P34 was evaluated by immunoblotting, competitive ELISA and basophil activation tests (BAT) using sera from allergic patients. In vivo cross-reactivity was examined using an IgE-mediated milk allergy mouse model. Results P34 was recognized by IgE antibodies from the sera of milk allergic patients, casein-specific monoclonal antibodies, and sera from milk-allergic mice. Spleen cells from sensitized mice incubated with milk, soy or P34 secreted IL-5 and IL-13, while IFN-? remained unchanged. In addition, the cutaneous test was positive with cow's milk proteins (CMP) and P34 in the milk allergy mouse model. Moreover, milk-sensitized mice developed immediate symptoms following sublingual exposure to P34. Conclusions Our results demonstrate that P34 shares epitopes with bovine casein, which is responsible for inducing hypersensitivity symptoms in milk allergic mice. This is the first report of the in vivo cross-allergenicity of P34. PMID:25553264

Smaldini, Paola Lorena; Curciarello, Renata; Cauerhff, Ana; Fossati, Carlos Alberto

2015-01-01

48

Production and Functional Analysis of Recombinant Bovine Morphogenic Protein 15  

E-print Network

kDa protein. Bioactivity and BMP receptor signaling specificity were ascertained using in vitro treatment of HeLa cells and Western blotting for the BMP signaling molecule phosphorylated-SMAD 1/5. Inhibition of this signaling cascade using...

Burns, Gregory Willis

2013-11-21

49

Differential synaptic distribution of the scaffold proteins Cask and Caskin1 in the bovine retina.  

PubMed

Scaffold proteins organize pre- and postsynaptic compartments and align pre- and postsynaptic events. Cask is a multi-domain scaffold protein essential for brain synaptic functions. Caskin1 is a recently discovered, brain-specific Cask-interacting multi-domain protein of unknown function. In the present study, we determined the localization of these scaffold proteins in the bovine retina. The retina contains tonically active ribbon synapses and conventional synapses. We found Cask highly enriched in virtually all retinal synapses. Cask was localized in close vicinity to the active zone protein RIM1/2 in ribbon and conventional synapses. Caskin1 is also enriched in retinal synapses but is present only in a subset of Cask-positive synapses. These findings suggest that Cask plays an important role in all retinal synapses. In contrast, Caskin1 appears to execute more specialized functions in distinct sets of retinal synapses, possibly for neuronal pathway formation and stabilization of distinct synaptic contacts. PMID:25123431

Anjum, Rizwana; Ayoubian, Hiresh; Schmitz, Frank

2014-09-01

50

In vivo delivery of bovine viral diahorrea virus, E2 protein using hollow mesoporous silica nanoparticles  

NASA Astrophysics Data System (ADS)

Our work focuses on the application of mesoporous silica nanoparticles as a combined delivery vehicle and adjuvant for vaccine applications. Here we present results using the viral protein, E2, from bovine viral diarrhoea virus (BVDV). BVDV infection occurs in the target species of cattle and sheep herds worldwide and is therefore of economic importance. E2 is a major immunogenic determinant of BVDV and is an ideal candidate for the development of a subunit based nanovaccine using mesoporous silica nanoparticles. Hollow type mesoporous silica nanoparticles with surface amino functionalisation (termed HMSA) were characterised and assessed for adsorption and desorption of E2. A codon-optimised version of the E2 protein (termed Opti-E2) was produced in Escherichia coli. HMSA (120 nm) had an adsorption capacity of 80 ?g Opti-E2 per mg HMSA and once bound E2 did not dissociate from the HMSA. Immunisation studies in mice with a 20 ?g dose of E2 adsorbed to 250 ?g HMSA was compared to immunisation with Opti-E2 (50 ?g) together with the traditional adjuvant Quillaja saponaria Molina tree saponins (QuilA, 10 ?g). The humoral responses with the Opti-E2/HMSA nanovaccine although slightly lower than those obtained for the Opti-E2 + QuilA group demonstrated that HMSA particles are an effective adjuvant that stimulated E2-specific antibody responses. Importantly the cell-mediated immune responses were consistently high in all mice immunised with Opti-E2/HMSA nanovaccine formulation. Therefore we have shown the Opti-E2/HMSA nanoformulation acts as an excellent adjuvant that gives both T-helper 1 and T-helper 2 mediated responses in a small animal model. This study has provided proof-of-concept towards the development of an E2 subunit nanoparticle based vaccine.Our work focuses on the application of mesoporous silica nanoparticles as a combined delivery vehicle and adjuvant for vaccine applications. Here we present results using the viral protein, E2, from bovine viral diarrhoea virus (BVDV). BVDV infection occurs in the target species of cattle and sheep herds worldwide and is therefore of economic importance. E2 is a major immunogenic determinant of BVDV and is an ideal candidate for the development of a subunit based nanovaccine using mesoporous silica nanoparticles. Hollow type mesoporous silica nanoparticles with surface amino functionalisation (termed HMSA) were characterised and assessed for adsorption and desorption of E2. A codon-optimised version of the E2 protein (termed Opti-E2) was produced in Escherichia coli. HMSA (120 nm) had an adsorption capacity of 80 ?g Opti-E2 per mg HMSA and once bound E2 did not dissociate from the HMSA. Immunisation studies in mice with a 20 ?g dose of E2 adsorbed to 250 ?g HMSA was compared to immunisation with Opti-E2 (50 ?g) together with the traditional adjuvant Quillaja saponaria Molina tree saponins (QuilA, 10 ?g). The humoral responses with the Opti-E2/HMSA nanovaccine although slightly lower than those obtained for the Opti-E2 + QuilA group demonstrated that HMSA particles are an effective adjuvant that stimulated E2-specific antibody responses. Importantly the cell-mediated immune responses were consistently high in all mice immunised with Opti-E2/HMSA nanovaccine formulation. Therefore we have shown the Opti-E2/HMSA nanoformulation acts as an excellent adjuvant that gives both T-helper 1 and T-helper 2 mediated responses in a small animal model. This study has provided proof-of-concept towards the development of an E2 subunit nanoparticle based vaccine. Electronic supplementary information (ESI) available: Desorption studies of Opti-E2 bound HMSA. See DOI: 10.1039/c4nr01202j

Mahony, D.; Cavallaro, A. S.; Mody, K. T.; Xiong, L.; Mahony, T. J.; Qiao, S. Z.; Mitter, N.

2014-05-01

51

The minotaur proteome: avoiding cross-species identifications deriving from bovine serum in cell culture models.  

PubMed

Cell culture is a fundamental tool in proteomics where mammalian cells are cultured in vitro using a growth medium often supplemented with 5-15% FBS. Contamination by bovine proteins is difficult to avoid because of adherence to the plastic vessel and the cultured cells. We have generated peptides from bovine serum using four sample preparation methods and analyzed the peptides by high mass accuracy LC-MS/MS. Distinguishing between bovine and human peptides is difficult because of a considerable overlap of identical tryptic peptide sequences. Pitfalls in interpretation, different database search strategies to minimize erroneous identifications and an augmented contaminant database are presented. PMID:20641139

Bunkenborg, Jakob; Garca, Guadalupe Espadas; Paz, Marcia Ivonne Pea; Andersen, Jens S; Molina, Henrik

2010-08-01

52

A conformational isomer of bovine pancreatic trypsin inhibitor protein produced by refolding  

NASA Astrophysics Data System (ADS)

Refolding of the bovine pancreatic trypsin inhibitor protein (BPTI) after reduction of its three cysteine disulphide linkages can occur when the reduced protein is placed in a suitable oxidizing medium (ref. 1 and refs therein). The refolding process has been studied by trapping chemically intermediates which contain only one or two disulphide bonds (ref. 1 and refs therein). We report here that during structural studies of these intermediates by NMR, we have found that complete re-oxidation of the protein results in substantial quantities of a metastable folded species which is identical to native BPTI in its covalent bonding (including the disulphide bonds) but possesses a somewhat different conformation. The existence of such a species is supported by circular dichroism measurements on refolded BPTI2. This novel form of BPTI is of considerable interest because it can be used to provide information about the folding mechanism and conformational stability of the protein.

States, D. J.; Dobson, C. M.; Karplus, M.; Creighton, T. E.

1980-08-01

53

Serum-derived bovine immunoglobulin/protein isolate: postulated mechanism of action for management of enteropathy  

PubMed Central

The health and performance of the gastrointestinal tract is influenced by the interaction of a variety of factors, including diet, nutritional status, genetics, environment, stress, the intestinal microbiota, immune status, and gut barrier. Disruptions in one or more of these factors can lead to enteropathy or intestinal disorders that are known to occur in concert with certain disease states or conditions such as irritable bowel syndrome or human immunodeficiency virus (HIV) infection. Nutritional support in the form of a medical food along with current therapies could help manage the adverse effects of enteropathy, which include effects on nutrient digestion, absorption, and metabolism, as well as utilization of nutrients from foodstuffs. Numerous studies have demonstrated that oral administration of plasma- or serum-derived protein concentrates containing high levels of immunoglobulins can improve weight management, normalize gut barrier function, and reduce the severity of enteropathy in animals. Recent trials in humans provide preliminary evidence that a serum-derived bovine immunoglobulin/protein isolate is safe and improves symptoms, nutritional status, and various biomarkers associated with enteropathy in patients with HIV infection or diarrhea-predominant irritable bowel syndrome. This review summarizes data from preclinical and clinical studies with immunoglobulin-containing plasma/serum protein concentrates, with a focus on the postulated mode of action of serum-derived bovine immunoglobulin/protein isolate for patients with enteropathy. PMID:24904221

Petschow, Bryon W; Burnett, Bruce; Shaw, Audrey L; Weaver, Eric M; Klein, Gerald L

2014-01-01

54

Protein and nucleotide contamination of bovine liver catalase used in culture medium explains growth of Trypanosoma cruzi.  

PubMed

Commercially available bovine liver catalase has been used to supplement chemically defined medium for growth of Trypanosoma cruzi. The protein extract was found to be contaminated with 25 to 30 protein bands as well as DNA and RNA polymers. PMID:2451330

O'Daly, J A; Rodrguez, M B

1987-01-01

55

Cooperation between bovine leukaemia virus transactivator protein and Ha-ras oncogene product in cellular transformation.  

PubMed Central

Human T-lymphotropic viruses (HTLV-I and -II) and bovine leukaemia virus (BLV) express transactivator proteins able to increase long terminal repeat (LTR) directed viral expression. These transacting factors are though to be involved in the induction of leukaemia by these viruses. Transfection of BLV transactivator p34tax together with Ha-ras immortalizes and transforms rat embryo fibroblasts, in vitro. The transformed cell induce tumours in nude mice. These data emphasize the causal role exerted by p34tax in in vivo tumorigenesis. Images Fig. 1. Fig. 2. Fig. 3. PMID:2158445

Willems, L; Heremans, H; Chen, G; Portetelle, D; Billiau, A; Burny, A; Kettmann, R

1990-01-01

56

E3 protein of bovine coronavirus is a receptor-destroying enzyme with acetylesterase activity  

SciTech Connect

In addition to members of the Orthomyxoviridae and Paramyxoviridae, several coronaviruses have been shown to possess receptor-destroying activities. Purified bovine coronavirus (BCV) preparations have an esterase activity which inactivates O-acetylsialic acid-containing receptors on erythrocytes. Diisopropyl fluorophosphate (DFP) completely inhibits this receptor-destroying activity of BCV, suggesting that the viral enzyme is a serine esterase. Treatment of purified BCV with (/sup 3/H)DFP and subsequent sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the proteins revealed that the esterase/receptor-destroying activity of BCV is associated with the E3 protein was specifically phosphorylated. This finding suggests that the esterase/receptor-destroying activity of BCV is associated with the E3 protein. Furthermore, treatment of BCV with DFP dramatically reduced its infectivity in a plaque assay. It is assumed that the esterase activity of BCV is required in an early step of virus replication, possible during virus entry or uncoating.

Vlasak, R.; Luytjes, W.; Leider, J.; Spaan, W.; Palese, P.

1988-12-01

57

Domain swapping creates a third putative combining site in bovine odorant binding protein dimer.  

PubMed

In mammals, odorant binding proteins may play an important role in the transport of odors towards specific olfactory receptors on sensory neurones across the aqueous compartment of the nasal mucus. We have solved the X-ray structure of such a transport protein, bovine odorant binding protein (OBP) at 2.0 A resolution. The beta-barrel of OBP is similar to that of lipocalins, but OBP dimer association results from domain swapping, an observation unique among the lipocalins. The alpha-helix of each monomer stacks against the beta-barrel of the other monomer. Contrary to previous reports, each monomer has an internal buried cavity which could accommodate a naturally occurring molecule. Besides this cavity, an open cavity is located at the dimer interface. Data in solution suggest that this central cavity may be a binding site created by domain swapping. PMID:8836103

Tegoni, M; Ramoni, R; Bignetti, E; Spinelli, S; Cambillau, C

1996-10-01

58

Lumbar intertransverse-process spinal arthrodesis with use of a bovine bone-derived osteoinductive protein. A preliminary report.  

PubMed

The use of a bovine bone-derived osteoinductive protein extract as a bone-graft substitute was evaluated in a rabbit model of intertransverse process arthrodesis of the lumbar spine. Forty-five adult New Zealand White rabbits had arthrodesis between the fifth and sixth lumbar vertebrae with use of one of three graft materials: autogenous iliac-crest bone, osteoinductive protein delivered in an allogeneic demineralized bone matrix/collagen carrier, or demineralized bone matrix/collagen carrier or demineralized bone matrix/collagen carrier without osteoinductive protein. Fusion was assessed by manual palpation, radiography, biomechanical testing, and light microscopy at two and five weeks after the operation. At two weeks, light microscopic analysis of the arthrodesis site in which osteoinductive protein had been used showed that most of the demineralized bone matrix was still present, with small amounts of membranous and endochondral bone formation at the peripheral margins of the implant. Light microscopic analysis of the five-week specimens showed increased new-bone formation and a more homogeneous and mature fusion mass with the osteoinductive bone protein than with the autogenous bone graft. At five weeks, the fusions with the osteoinductive protein extract were characterized by more secondary spongiosa, with formation of bone marrow centrally and a cortical rim peripherally. Of the thirty-five rabbits that were examined at five weeks, all ten in the group that had received osteoinductive bone protein had a solid fusion, but the rate of fusion was significantly less in the other two groups: eight of thirteen rabbits (p = 0.05) in the group that had received autogenous bone graft and two of twelve rabbits (p = 0.0001) in the group that had received demineralized bone matrix/collagen carrier without osteoinductive bone protein. The use of osteoinductive bone protein resulted in stronger (p = 0.02) and stiffer (p = 0.005) fusions compared with those obtained with the use of autogenous iliac-crest graft. PMID:7673292

Boden, S D; Schimandle, J H; Hutton, W C

1995-09-01

59

The Protein Model Portal  

Microsoft Academic Search

Structural Genomics has been successful in determining the structures of many unique proteins in a high throughput manner.\\u000a Still, the number of known protein sequences is much larger than the number of experimentally solved protein structures. Homology\\u000a (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins.\\u000a Thereby, experimental structure determination efforts and

Konstantin Arnold; Florian Kiefer; Jrgen Kopp; James N. D. Battey; Michael Podvinec; John D. Westbrook; Helen M. Berman; Lorenza Bordoli; Torsten Schwede

2009-01-01

60

Fluorescent probing of protein bovine serum albumin stability and denaturation using polarity sensitive spectral response of a charge transfer probe.  

PubMed

The polarity sensitive photo-induced intra-molecular charge transfer (ICT) fluorescence probe (E)-3-(4-methylamino-phenyl)-acrylic acid ethyl ester (MAPAEE) has been used to study the model protein Bovine Serum Albumin (BSA) in its native and thermal and urea induced denatured states. The interaction between BSA and the regular surfactant Sodium Dodecyl Sulphate (SDS) as well as the biologically relevant steroid-based amphiphile Sodium Deoxycholate (NaDC) has also been very keenly followed using this ICT probe. The variation of micellar properties of both SDS and NaDC with increasing ionic strengths and in presence of the chaotrope urea has also been well documemted by the same probe. Steady-state spectroscopy, FRET, and fluorescence anisotropy measurements have been used to gain better insight into these processes and the molecule MAPAEE to be a full-bodied fluorescent probe for studying such intricate biological systems, their properties and interactions. PMID:20922468

Ghosh, Shalini; Jana, Sankar; Nath, Debnarayan; Guchhait, Nikhil

2011-01-01

61

Protein solubility modeling  

NASA Technical Reports Server (NTRS)

A thermodynamic framework (UNIQUAC model with temperature dependent parameters) is applied to model the salt-induced protein crystallization equilibrium, i.e., protein solubility. The framework introduces a term for the solubility product describing protein transfer between the liquid and solid phase and a term for the solution behavior describing deviation from ideal solution. Protein solubility is modeled as a function of salt concentration and temperature for a four-component system consisting of a protein, pseudo solvent (water and buffer), cation, and anion (salt). Two different systems, lysozyme with sodium chloride and concanavalin A with ammonium sulfate, are investigated. Comparison of the modeled and experimental protein solubility data results in an average root mean square deviation of 5.8%, demonstrating that the model closely follows the experimental behavior. Model calculations and model parameters are reviewed to examine the model and protein crystallization process. Copyright 1999 John Wiley & Sons, Inc.

Agena, S. M.; Pusey, M. L.; Bogle, I. D.

1999-01-01

62

Nicotinic Acid Increases Adiponectin Secretion from Differentiated Bovine Preadipocytes through G-Protein Coupled Receptor Signaling.  

PubMed

The transition period in dairy cows (3 weeks prepartum until 3 weeks postpartum) is associated with substantial mobilization of energy stores, which is often associated with metabolic diseases. Nicotinic acid (NA) is an antilipolytic and lipid-lowering compound used to treat dyslipidaemia in humans, and it also reduces non-esterified fatty acids in cattle. In mice the G-protein coupled receptor 109A (GPR109A) ligand NA positively affects the secretion of adiponectin, an important modulator of glucose and fat metabolism. In cattle, the corresponding data linking NA to adiponectin are missing. Our objective was to examine the effects of NA on adiponectin and AMPK protein abundance and the expression of mRNAs of related genes such as chemerin, an adipokine that enhances adiponectin secretion in vitro. Differentiated bovine adipocytes were incubated with pertussis toxin (PTX) to verify the involvement of GPR signaling, and treated with 10 or 15 M NA for 12 or 24 h. NA increased adiponectin concentrations (p ? 0.001) and the mRNA abundances of GPR109A (p ? 0.05) and chemerin (p ? 0.01). Pre-incubation with PTX reduced the adiponectin response to NA (p ? 0.001). The NA-stimulated secretion of adiponectin and the mRNA expression of chemerin in the bovine adipocytes were suggestive of GPR signaling-dependent improved insulin sensitivity and/or adipocyte metabolism in dairy cows. PMID:25411802

Kopp, Christina; Hosseini, Afshin; Singh, Shiva P; Regenhard, Petra; Khalilvandi-Behroozyar, Hamed; Sauerwein, Helga; Mielenz, Manfred

2014-01-01

63

In Vitro and In Vivo Oncogenic Potential of Bovine Leukemia Virus G4 Protein  

PubMed Central

In addition to the genes involved in the structure of the viral particle, the bovine leukemia virus (BLV) genome contains a region called X which contains at least four genes. Among them, the tax and rex genes, respectively, are involved in transcriptional and posttranscriptional regulation of viral transcription. Two other genes, R3 and G4, were identified after cloning of the corresponding mRNAs from BLV-infected lymphocytes. Although the function of the two latter genes is still unknown, they appear to have important roles, since deletion of them restricts viral propagation in vivo. In order to assess the oncogenic potential of the R3 and G4 proteins, we first analyzed their ability to immortalize and/or transform primary rat embryo fibroblasts (Refs). In this assay, the G4 but not the R3 protein cooperated with the Ha-ras oncogene to induce tumors in nude mice. It thus appears that G4 exhibited oncogenic potential in vitro. To extend these observations in vivo, the pathology induced by recombinant viruses with mutations in G4 and in R3 and G4 was next evaluated with the sheep animal model. Viral propagation, as measured by semiquantitative PCR, appeared to be reduced when the R3 and G4 genes were deleted. These observations confirm and extend our previous data underlining the biological function of these genes. In addition, we present the results of a clinical survey that involves 39 sheep infected with six different BLV recombinants. Over a period of 40 months, 83% of the sheep infected with a wild-type virus developed leukemias and/or lymphosarcomas. In contrast, none out of 13 sheep infected with viruses with mutations in G4 or in R3 and G4 developed disease. We conclude that in addition to its oncogenic potential in vitro, G4 is required for pathogenesis in vivo. These observations should help us gain insight into the process of leukemogenesis induced by the related human T-cell leukemia virus type 1. PMID:9499124

Kerkhofs, Pierre; Heremans, Hubertine; Burny, Arsne; Kettmann, Richard; Willems, Luc

1998-01-01

64

The platelet-derived growth factor receptor as a target of the bovine papillomavirus E5 protein  

Microsoft Academic Search

The 44-amino acid E5 protein of bovine papillomavirus is a homo-dimeric, transmembrane protein that transforms cells by activating the platelet-derived growth factor receptor in a ligand-independent fashion. The E5 protein induces receptor activation by forming a stable complex with the receptor, thereby inducing receptor dimerization, trans-phosphorylation of tyrosine residues in the cytoplasmic domain of the receptor, and recruitment of

Daniel DiMaio; Char-Chang Lai; Dawn Mattoon

2000-01-01

65

Relief of amplification inhibition in PCR with bovine serum albumin or T4 gene 32 protein  

SciTech Connect

The benefits of adding bovine serum albumin (BSA) or T4 gene 32 proteins (gp32) to PCR were evaluated with reaction mixtures containing substances that inhibit amplification. Whereas 10- to 1,000-fold more FeCl{sub 3}, hemin, fulvic acids, humic acids, tannic acids, or extracts from feces, freshwater, or marine water were accommodated in PCR when either 400 ng of BSA per {mu}l was included in the reactions, neither BSA nor gp32 relieved interference significantly when minimum inhibitory levels of bile salts, bilirubin, EDTA, NaCl, sodium dodecyl sulfate, or Triton X-100 were present. Use of BSA and gp32 together offered no more relief of inhibition than either alone at its optimal level, and neither protein had any noticeable effect on amplification in the absence of inhibitors. 21 refs., 3 figs.

Kreader, C.A. [Environmental Protection Agency, Cincinnati, OH (United States)

1996-03-01

66

Proteomic analysis of bovine brain G protein gamma subunit processing heterogeneity.  

PubMed

We characterized the variable processing of the G protein gamma subunit isoforms associated with bovine brain G proteins, a primary mediator of cellular communication. Ggamma subunits were isolated from purified brain G proteins and characterized by Edman sequencing, by MALDI MS, by chemical and/or enzymatic fragmentation assayed by MALDI MS, and by MS/MS fragmentation and sequencing. Multiple forms of six different Ggamma isoforms were detected. Significant variation in processing was found at both the amino termini and particularly the carboxyl termini of the proteins. All Ggamma isoforms contain a carboxyl-terminal CAAX motif for prenylation, carboxyl-terminal proteolysis, and carboxymethylation. Characterization of these proteins indicates significant variability in the normal processing of all of these steps in the prenylation reaction, including a new variation of prenyl processing resulting from cysteinylation of the carboxyl terminus. These results have multiple implications for intracellular signaling mechanisms by G proteins, for the role of prenyl processing variation in cell signaling, and for the site of action and consequences of drugs that target the prenylation modification. PMID:16332732

Cook, Lana A; Schey, Kevin L; Wilcox, Michael D; Dingus, Jane; Ettling, Rebecca; Nelson, Troy; Knapp, Daniel R; Hildebrandt, John D

2006-04-01

67

Fibrillins and latent TGF? binding proteins in bovine ovaries of offspring following high or low protein diets during pregnancy of dams  

Microsoft Academic Search

The microsatellite D19S884, located in intron 55 of fibrillin-3 (FBN3) gene, associates with polycystic ovary syndrome (PCOS) in familial studies. The family of fibrillin proteins (FBN1-3), which includes latent TGF-? binding proteins (LTBP-1 to -4), are extracellular matrix proteins. We localized and examined the expression of these proteins in the adult bovine ovaries (n=710 per group, average age 681 days)

Mark J. Prodoehl; Helen F. Irving-Rodgers; Wendy M. Bonner; Tracy M. Sullivan; Gina C. Micke; Mark A. Gibson; Vivienne E. Perry; Raymond J. Rodgers

2009-01-01

68

Identification of an outer membrane protein of Fusobacterium necrophorum subsp. necrophorum that binds with high affinity to bovine endothelial cells.  

PubMed

Fusobacterium necrophorum, a Gram-negative anaerobe, is the primary etiologic agent of liver abscesses in cattle. There are two subspecies; subsp. necrophorum and subsp. funduliforme, which differ in morphological, biochemical, molecular characteristics, and virulence. The subsp. necrophorum, which is more virulent, occurs more frequently in liver abscesses than the subsp. funduliforme. Bacterial adhesion to the host cell surface is critical to the pathogenesis of several bacterial infections, and in F. necrophorum, outer membrane proteins (OMP) have been shown to mediate adhesion to bovine endothelial cells. The objective of this study was to identify potential adhesins that are involved in adhesion of F. necrophorum subsp. necrophorum to the host cells. An OMP of 42.4kDa, which binds with high affinity to the bovine endothelial cells and is recognized by the sera from cattle with liver abscesses, was identified. N-terminal sequencing of the protein showed 96% homology to the FomA protein of F. nucleatum. The PCR analysis showed that this fomA gene was present in several strains of subsp. necrophorum, subsp. funduliforme of bovine and subsp. funduliforme of human origin. The purified native and recombinantly expressed protein when preincubated with the endothelial cells, prevented the attachment of subsp. necrophorum significantly. In addition, the polyclonal antibody produced against the protein prevented the binding of subsp. necrophorum to bovine endothelial cells. PMID:25601800

Kumar, Amit; Menon, Sailesh; Nagaraja, T G; Narayanan, Sanjeev

2015-03-23

69

Bone Morphogenetic Protein 15 in the Pro-Mature Complex Form Enhances Bovine Oocyte Developmental Competence  

PubMed Central

Developmental competence of in vitro matured (IVM) oocytes needs to be improved and this can potentially be achieved by adding recombinant bone morphogenetic protein 15 (BMP15) or growth differentiation factor (GDF9) to IVM. The aim of this study was to determine the effect of a purified pro-mature complex form of recombinant human BMP15 versus the commercially available bioactive forms of BMP15 and GDF9 (both isolated mature regions) during IVM on bovine embryo development and metabolic activity. Bovine cumulus oocyte complexes (COCs) were matured in vitro in control medium or treated with 100 ng/ml pro-mature BMP15, mature BMP15 or mature GDF9 +/? FSH. Metabolic measures of glucose uptake and lactate production from COCs and autofluorescence of NAD(P)H, FAD and GSH were measured in oocytes after IVM. Following in vitro fertilisation and embryo culture, day 8 blastocysts were stained for cell numbers. COCs matured in medium +/? FSH containing pro-mature BMP15 displayed significantly improved blastocyst development (57.73.9%, 43.54.2%) compared to controls (43.32.4%, 28.93.7%) and to mature GDF9+FSH (36.13.0%). The mature form of BMP15 produced intermediate levels of blastocyst development; not significantly different to control or pro-mature BMP15 levels. Pro-mature BMP15 increased intra-oocyte NAD(P)H, and reduced glutathione (GSH) levels were increased by both forms of BMP15 in the absence of FSH. Exogenous BMP15 in its pro-mature form during IVM provides a functional source of oocyte-secreted factors to improve bovine blastocyst development. This form of BMP15 may prove useful for improving cattle and human artificial reproductive technologies. PMID:25058588

Sudiman, Jaqueline; Sutton-McDowall, Melanie L.; Ritter, Lesley J.; White, Melissa A.; Mottershead, David G.; Thompson, Jeremy G.; Gilchrist, Robert B.

2014-01-01

70

Bone morphogenetic protein 15 in the pro-mature complex form enhances bovine oocyte developmental competence.  

PubMed

Developmental competence of in vitro matured (IVM) oocytes needs to be improved and this can potentially be achieved by adding recombinant bone morphogenetic protein 15 (BMP15) or growth differentiation factor (GDF9) to IVM. The aim of this study was to determine the effect of a purified pro-mature complex form of recombinant human BMP15 versus the commercially available bioactive forms of BMP15 and GDF9 (both isolated mature regions) during IVM on bovine embryo development and metabolic activity. Bovine cumulus oocyte complexes (COCs) were matured in vitro in control medium or treated with 100 ng/ml pro-mature BMP15, mature BMP15 or mature GDF9 +/- FSH. Metabolic measures of glucose uptake and lactate production from COCs and autofluorescence of NAD(P)H, FAD and GSH were measured in oocytes after IVM. Following in vitro fertilisation and embryo culture, day 8 blastocysts were stained for cell numbers. COCs matured in medium +/- FSH containing pro-mature BMP15 displayed significantly improved blastocyst development (57.73.9%, 43.54.2%) compared to controls (43.32.4%, 28.93.7%) and to mature GDF9+FSH (36.13.0%). The mature form of BMP15 produced intermediate levels of blastocyst development; not significantly different to control or pro-mature BMP15 levels. Pro-mature BMP15 increased intra-oocyte NAD(P)H, and reduced glutathione (GSH) levels were increased by both forms of BMP15 in the absence of FSH. Exogenous BMP15 in its pro-mature form during IVM provides a functional source of oocyte-secreted factors to improve bovine blastocyst development. This form of BMP15 may prove useful for improving cattle and human artificial reproductive technologies. PMID:25058588

Sudiman, Jaqueline; Sutton-McDowall, Melanie L; Ritter, Lesley J; White, Melissa A; Mottershead, David G; Thompson, Jeremy G; Gilchrist, Robert B

2014-01-01

71

The Quaternary Structure of the Recombinant Bovine Odorant-Binding Protein Is Modulated by Chemical Denaturants  

PubMed Central

A large group of odorant-binding proteins (OBPs) has attracted great scientific interest as promising building blocks in constructing optical biosensors for dangerous substances, such as toxic and explosive molecules. Native tissue-extracted bovine OBP (bOBP) has a unique dimer folding pattern that involves crossing the ?-helical domain in each monomer over the other monomers ?-barrel. In contrast, recombinant bOBP maintaining the high level of stability inherent to native tissue bOBP is produced in a stable native-like state with a decreased tendency for dimerization and is a mixture of monomers and dimers in a buffered solution. This work is focused on the study of the quaternary structure and the folding-unfolding processes of the recombinant bOBP in the absence and in the presence of guanidine hydrochloride (GdnHCl). Our results show that the recombinant bOBP native dimer is only formed at elevated GdnHCl concentrations (1.5 M). This process requires re-organizing the protein structure by progressing through the formation of an intermediate state. The bOBP dimerization process appears to be irreversible and it occurs before the protein unfolds. Though the observed structural changes for recombinant bOBP at pre-denaturing GdnHCl concentrations show a local character and the overall protein structure is maintained, such changes should be considered where the protein is used as a sensitive element in a biosensor system. PMID:24409322

Stepanenko, Olga V.; Stepanenko, Olesya V.; Staiano, Maria; Kuznetsova, Irina M.; Turoverov, Konstantin K.; DAuria, Sabato

2014-01-01

72

cDNA cloning of bovine midkine and production of the recombinant protein, which affects in vitro maturation of bovine oocytes.  

PubMed

In the present study, we cloned bovine midkine (bMK) cDNA by RT- and RACE-PCR, and determined its nucleotide sequence. The nucleotide and deduced amino acid sequences of bMK showed a high degree of homology to those of mouse and human MK. Moreover, a large amount of recombinant bMK (rbMK) was produced using a baculovirus expression system and the protein was purified to homogeneity by heparin affinity chromatography. To examine whether treatment with rbMK during in vitro maturation (IVM) of bovine cumulus-enclosed oocytes affects their nuclear maturation and postfertilization development to the blastocyst stage, bovine cumulus-enclosed oocytes obtained from slaughterhouse-derived ovaries were cultured for 24 hr in IVM medium without (control) or with various concentrations (50-400 ng/ml) of rbMK, followed by in vitro fertilization (IVF) and culture. Although rbMK treatment during IVM did not affect the rates of nuclear maturation and postfertilization cleavage of oocytes, rbMK at all experimental concentrations significantly (P < 0.05) increased the blastocyst yields per tested and per cleaved oocyte compared to the control. Next, it was examined whether heparitinase (HTN) treatment of cumulus-enclosed oocytes would affect the enhancing activity of rbMK during IVM on the developmental competence of oocyte after IVF. The enhancing activity of rbMK was completely suppressed by HTN (1.0 mU/ml) treatment. These results indicate that the presence of rbMK during IVM of bovine cumulus-enclosed oocytes can enhance their developmental competence to the blastocyst stage after IVF and suggest that heparan sulfate chains on the cell surface of cumulus cells and/or oocytes are required for bMK to exert its effect. PMID:10954861

Ikeda, S; Nishikimi, A; Ichihara-Tanaka, K; Muramatsu, T; Yamada, M

2000-09-01

73

Bovine Brain: An in vitro Translational Model in Developmental Neuroscience and Neurodegenerative Research.  

PubMed

Animal models provide convenient and clinically relevant tools in the research on neurodegenerative diseases. Studies on developmental disorders extensively rely on the use of laboratory rodents. The present mini-review proposes an alternative translational model based on the use of fetal bovine brain tissue. The bovine (Bos taurus) possesses a large and highly gyrencephalic brain and the long gestation period (41?weeks) is comparable to human pregnancy (38-40?weeks). Primary cultures obtained from fetal bovine brain constitute a validated in vitro model that allows examinations of neurons and/or glial cells under controlled and reproducible conditions. Physiological processes can be also studied on cultured bovine neural cells incubated with specific substrates or by electrically coupled electrolyte-oxide-semiconductor capacitors that permit direct recording from neuronal cells. Bovine neural cells and specific in vitro cell culture could be an alternative in comparative neuroscience and in neurodegenerative research, useful for studying development of normal and altered circuitry in a long gestation mammalian species. Use of bovine tissues would promote a substantial reduction in the use of laboratory animals. PMID:25072040

Peruffo, Antonella; Cozzi, Bruno

2014-01-01

74

The Effect of Electrical Stimulation on the Water-Holding Capacity and Protein Denaturation of Two Bovine Muscles1  

Microsoft Academic Search

The effect of low-voltage electrical stimulation on the water-holding capacity and protein denaturation of bovine longissimus thoracis and semi- membranosus was studied in eight electrically stimu- lated (85 V, 14 Hz, 15 s; immediately after slaughter) and eight nonstimulated Friesian Holstein bull car- casses. At 24 h postmortem longissimus thoracis and semimembranosus were sampled for drip loss, thaw loss, filter

M. J. A. den Hertog-Meischke; F. J. M. Smulders; J. G. van Logtestijn; F. van Knapen

75

Rheology of globular proteins: apparent yield stress, high shear rate viscosity and interfacial viscoelasticity of bovine serum albumin solutions  

E-print Network

biological functions, including maintaining blood pH and osmotic pressure,2 as well as transporting ligands circulation.1 The concentration of human serum albumin (HSA) in blood plasma is $40 mg ml?1 ($0.6 mM). Bovine are the most abundant among the constituent proteins in mammalian blood.1 Serum albumins participate in various

76

A role for protein tyrosine kinase in the steroidogenic pathway of angiotensin II in bovine zona glomerulosa cells  

Microsoft Academic Search

Stimulation of aldosterone synthesis in bovine adrenal zona glomerulosa (ZGB) cells by angiotensin II (AngII) is believed to be mediated by the phospholipase C (PLC) pathway that results in the increase of cytosolic free calcium concentration and in the activation of protein kinase C (PKC). However, the cell proliferation and contraction associated with AngII action are known to be mediated

V. Bodart; H. Ong; A. De Lan

1995-01-01

77

Similar Signature of the Prion Protein in Natural Sheep Scrapie and Bovine Spongiform Encephalopathy-Linked Diseases  

Microsoft Academic Search

It has been suggested that specific molecular features could characterize the protease-resistant prion protein (PrP res) detected in animal species as well as in humans infected by the infectious agent strain that causes bovine spongiform encephalopathy (BSE). Studies of glycoform patterns in such diseases in French cattle and cheetahs, as well as in mice infected by isolates from both species,

THIERRY G. M. BARON; JEAN-YVES MADEC; DIDIER CALAVAS

1999-01-01

78

Assessing the Susceptibility of Transgenic Mice Overexpressing Deer Prion Protein to Bovine Spongiform Encephalopathy  

PubMed Central

Several transgenic mouse models have been developed which facilitate the transmission of chronic wasting disease (CWD) of cervids and allow prion strain discrimination. The present study was designed to assess the susceptibility of the prototypic mouse line, Tg(CerPrP)1536+/?, to bovine spongiform encephalopathy (BSE) prions, which have the ability to overcome species barriers. Tg(CerPrP)1536+/? mice challenged with red deer-adapted BSE resulted in 90% to 100% attack rates, and BSE from cattle failed to transmit, indicating agent adaptation in the deer. PMID:24257620

Vickery, Christopher M.; Lockey, Richard; Holder, Thomas M.; Thorne, Leigh; Beck, Katy E.; Wilson, Christina; Denyer, Margaret; Sheehan, John; Marsh, Sarah; Webb, Paul R.; Dexter, Ian; Norman, Angela; Popescu, Emma; Schneider, Amanda; Holden, Paul; Griffiths, Peter C.; Plater, Jane M.; Dagleish, Mark P.; Martin, Stuart; Telling, Glenn C.; Simmons, Marion M.

2014-01-01

79

Use and relevance of a bovine mammary gland explant model to study infection responses in bovine mammary tissue.  

PubMed

Our aim was to develop an explant model to define more precisely the early response of bovine mammary epithelial cells to infection. Therefore we investigated the mRNA expression encoding for some soluble immunological factors in lipopolysaccharide (LPS)-treated bovine mammary gland explants. Explants were taken out from the mammary gland of eight lactating cows after slaughter then incubated with LPS (10 mug/ml) for 6 h. The mRNA expression of alpha-lactalbumin (alpha-la), various cytokines, tumour necrosis factor (TNF)-alpha, interleukin (IL)-1beta, IL-6, IL-8, and two immunoglobulin receptors, the neonatal Fc receptor (FcRn) and polymeric immunoglobulin receptor (pIGR), were assessed with qPCR before and after 3 h and 6 h of LPS challenge. Both immunoglobulin receptors and alpha-la increased at 3 h then recovered their initial level at 6 h whereas IL-1beta, IL-6 and IL-8 increased only after 6 h (P<0.05). Surprisingly, TNF-alpha transcripts did not show any regulation in response to the LPS treatment. We nevertheless concluded that our model was valid to examine the short-term response of mammary epithelial cell challenged with LPS. PMID:16978438

Rabot, Aline; Wellnitz, Olga; Meyer, Heinrich H D; Bruckmaier, Rupert M

2007-02-01

80

Grafting of bovine serum albumin proteins on plasma-modified polymers for potential application in tissue engineering  

NASA Astrophysics Data System (ADS)

In this work, an influence of bovine serum albumin proteins grafting on the surface properties of plasma-treated polyethylene and poly- l-lactic acid was studied. The interaction of the vascular smooth muscle cells with the modified polymer surface was determined. The surface properties were characterized by X-ray photoelectron spectroscopy, atomic force microscopy, nano-LC-ESI-Q-TOF mass spectrometry, electrokinetic analysis, and goniometry. One of the motivations for this work is the idea that by the interaction of the cell with substrate surface, the proteins will form an interlayer between the cell and the substrate. It was proven that when interacting with the plasma-treated high-density polyethylene and poly- l-lactic acid, the bovine serum albumin protein is grafted on the polymer surface. Since the proteins are bonded to the substrate surface, they can stimulate cell adhesion and proliferation.

Kaslkov, Nikola Slepi?kov; Slepi?ka, Petr; Kolsk, Zde?ka; Hoda?ov, Petra; Ku?kov, t?pnka; vor?k, Vclav

2014-04-01

81

Grafting of bovine serum albumin proteins on plasma-modified polymers for potential application in tissue engineering  

PubMed Central

In this work, an influence of bovine serum albumin proteins grafting on the surface properties of plasma-treated polyethylene and poly-l-lactic acid was studied. The interaction of the vascular smooth muscle cells with the modified polymer surface was determined. The surface properties were characterized by X-ray photoelectron spectroscopy, atomic force microscopy, nano-LC-ESI-Q-TOF mass spectrometry, electrokinetic analysis, and goniometry. One of the motivations for this work is the idea that by the interaction of the cell with substrate surface, the proteins will form an interlayer between the cell and the substrate. It was proven that when interacting with the plasma-treated high-density polyethylene and poly-l-lactic acid, the bovine serum albumin protein is grafted on the polymer surface. Since the proteins are bonded to the substrate surface, they can stimulate cell adhesion and proliferation. PMID:24708858

2014-01-01

82

Biochemical characterization of bovine brain myristoyl-CoA:protein N-myristoyltransferase type 2.  

PubMed

Protein N-myristoylation is a lipidic modification which refers to the covalent attachment of myristate, a 14-carbon saturated fatty acid, to the N-terminal glycine residue of a number of mammalian, viral, and fungal proteins. In this paper, we have cloned the gene coding for myristoyl-CoA:protein N-myristoyltransferase (NMT) from Bos tarus brain. The open reading frame codes for a 410-amino-acid protein and overexpressed in Escherichia coli. Kinetic studies suggested that bovine brain NMT2 and human NMT1 show significant differences in their peptide substrate specificities. The metal ion Ca(2+) had stimulatory effects on NMT2 activity while Mn(2+) and Zn(2+) inhibited the enzyme activity. In addition, NMT2 activity was inhibited by various organic solvents and other detergents while NMT1 had a stimulatory effect. Biochemical characterization suggested that both forms of NMT have unique characteristics. Further analysis towards functional role NMT2 will lead the development of therapeutic target for the progression of various diseases such as cancer, cardiovascular diseases, and neurodegenerative diseases. PMID:19746168

Selvakumar, Ponniah; Lakshmikuttyamma, Ashakumary; Sharma, Rajendra K

2009-01-01

83

TanfordKirkwood electrostatics for protein modeling  

PubMed Central

Solvent plays a significant role in determining the electrostatic potential energy of proteins, most notably through its favorable interactions with charged residues and its screening of electrostatic interactions. These energetic contributions are frequently ignored in computational protein design and protein modeling methodologies because they are difficult to evaluate rapidly and accurately. To address this deficiency, we report a revised form of the original TanfordKirkwood continuum electrostatic model [Tanford, C. & Kirkwood, J.?G. (1957) J. Am. Chem. Soc. 79, 53335339], which accounts for the effects of solvent polarization on charged atoms in proteins. The TanfordKirkwood model was modified to increase its speed and to improve its sensitivity to the details of protein structure. For the 37 electrostatic self-energies of the polar side-chains in bovine pancreatic trypsin inhibitor, and their 666 interaction energies, the modified TanfordKirkwood potential of mean force differs from a computationally intensive numerical potential (DelPhi) by root-mean-square errors of 0.6 kcal/mol and 0.08 kcal/mol, respectively. The TanfordKirkwood approach makes possible a realistic treatment of electrostatics in computationally demanding protein modeling calculations. For example, pH titration calculations for ovomucoid third domain that model polar side-chain relaxation (including >2 1023 rotamer conformations of the protein) provide pKa values of unprecedented accuracy. PMID:10500144

Havranek, James J.; Harbury, Pehr B.

1999-01-01

84

Hydrogen Exchange and Protein Hydration: The Deuteron Spin Relaxation Dispersions of Bovine Pancreatic Trypsin Inhibitor and Ubiquitin  

Microsoft Academic Search

Water deuteron (2H) spin relaxation was used to study hydrogen exchange hydration, and protein dynamics in aqueous soltuions of the globular proteins bovine pancreatic trypsin inhibitor (BPTI) and ubiquitin. The frequency dispersion of the longitudinal2H relaxation rate was measured in the pD range 2 to 11 at 27C. In contrast to the previously reported water17O relaxation dispersion from the same

Vladimir P. Denisov; Bertil Halle

1995-01-01

85

Effectiveness of extruded rapeseed associated with an alfalfa protein concentrate in enhancing the bovine milk fatty acid composition  

Microsoft Academic Search

Linseed and rapeseed, good sources of 18:3 n-3 and cis9-18:1, respectively, have been shown to improve the bovine milk fatty acid (FA) profile. However, rapeseed, unlike linseed, has little effect on the concentration of 18:3 n-3 in milk fat. Alfalfa protein concentrate (APC), besides being a valuable protein source for milk production, contains lipids rich in 18:3 n-3. Therefore, this

Q. C. Dang Van; L. Bejarano; E. Mignolet; D. Coulmier; E. Froidmont; Y. Larondelle; M. Focant

2011-01-01

86

Adhesion of Fusobacterium necrophorum to bovine endothelial cells is mediated by outer membrane proteins.  

PubMed

Fusobacterium necrophorum, a Gram-negative anaerobe, is frequently associated with suppurative and necrotic infections of animals and humans. The organism is a major bovine pathogen, and in cattle, the common fusobacterial infections are hepatic abscesses, foot rot, and necrotic laryngitis. The species comprises two subspecies: F. necrophorum subsp. necrophorum and F. necrophorum subsp. funduliforme. Bacterial adhesion to the host cell surface is a critical initial step in the pathogenesis, and outer membrane proteins (OMP) play an important role in adhesion and establishment of certain Gram-negative bacterial infections. The means by which F. necrophorum attaches to epithelial or endothelial cells has not been determined. We evaluated whether OMP of F. necrophorum, isolated from a liver abscess, mediated adhesion to bovine endothelial cells (adrenal gland capillary endothelial cell line). The extent of binding of subsp. necrophorum to the endothelial cells was higher than that of F. necrophorum subsp. funduliforme. Trypsin treatment of bacterial cells decreased their binding to endothelial cells indicating the protein nature of adhesins. Preincubation of endothelial cells with OMP extracted from F. necrophorum decreased the binding of bacterial cells. In addition, binding of each subspecies to endothelial cells was inhibited by polyclonal antibodies raised against respective OMP and the antibody-mediated inhibition was subspecies specific. The western blot analysis of OMP bound to endothelial cells with anti-OMP antibodies showed four OMP of 17, 24, 40 and 74 kDa. We conclude that OMP of F. necrophorum play a role in adhesion of bacterial cells to the endothelial cells. PMID:23153522

Kumar, Amit; Gart, Elena; Nagaraja, T G; Narayanan, Sanjeev

2013-03-23

87

The influence of protein fractions from bovine colostrum digested in vivo and in vitro on human intestinal epithelial cell proliferation.  

PubMed

Colostrum consists of a number of biologically active proteins and peptides that influence physiological function and development of a neonate. The present study investigated the biological activity of peptides released from first day bovine colostrum through in vitro and in vivo enzymatic digestion. This was assessed for proliferative activity using a human intestinal epithelial cell line, T84. Digestion of the protein fraction of bovine colostrum in vitro was conducted with the enzymes pepsin, chymosin and trypsin. Pepsin and chymosin digests yielded protein fractions with proliferative activity similar to that observed with undigested colostrum and the positive control foetal calf serum (FCS). In contrast trypsin digestion significantly (P<005) decreased colostral proliferative activity when co-cultured with cells when compared with undigested colostrum. The proliferative activity of undigested colostrum protein and abomasal whey protein digesta significantly increased (P<005) epithelial cell proliferation in comparison to a synthetic peptide mix. Bovine colostrum protein digested in vivo was collected from different regions of the gastrointestinal tract (GIT) in newborn calves fed either once (n=3 calves) or three times at 12-h intervals (n=3 calves). Digesta collected from the distal duodenum, jejunum and colon of calves fed once, significantly (P<005) stimulated cell proliferation in comparison with comparable samples collected from calves fed multiple times. These peptide enriched fractions are likely to yield candidate peptides with potential application for gastrointestinal repair in mammalian species. PMID:24433585

Morgan, Alison J; Riley, Lisa G; Sheehy, Paul A; Wynn, Peter C

2014-02-01

88

Spectral [corrected] studies on the cadmium-ion-binding properties of bovine brain S-100b protein.  

PubMed

The effect of Cd2+ binding on bovine brain S-100b protein was studied using c.d. u.v. difference spectroscopy and fluorescence measurements. At pH 7.5, S-100b protein binds two Cd2+ ions per monomer with a Kd value of 3 x 10(-5) M. Addition of Cd2+ resulted in perturbing the single tyrosine residue (Tyr17) in the protein as indicated by u.v. difference spectroscopy and aromatic c.d. measurements. In the presence of Cd2+, the tyrosine residue moves to a more non-polar environment, since a red shift was observed in the u.v. difference spectrum. When the protein was excited at 278 nm, the tyrosine fluorescence emission maximum was centred at 306 nm. Cd2+ addition resulted in an increase in intrinsic fluorescence intensity. Fluorescence titration with Cd2+ indicated the protein binds Cd2+ with a Kd value of 3 x 10(-5) M. 2-p-Toluidinylnaphthalene-6-sulphonate-labelled protein, when excited at 345 nm, had a fluorescence emission maximum at 440 nm. Addition of Cd2+ to labelled protein resulted in a 5-fold increase in fluorescence intensity accompanied by a 5 nm blue shift in the emission maximum, suggesting that the probe, in the presence of Cd2+, moves to a hydrophobic domain. U.v. difference spectroscopic studies indicated a unique Cd2(+)-binding site on the protein, since Cd2+ addition yielded a large positive absorption band in the 240 nm region that is not found with either Ca2+ or Zn2- ions. Similar absorption bands have been observed in Cd-protein complexes such as Cd-metallothionein [Vasak, Kagi & Hill (1981) Biochemistry 20, 2852-2856] and also in model complexes of Cd2+ with 2-mercaptoethanol. This absorption band is believed to arise as a result of charge-transfer transitions between the thiolate and Cd2+. Of the two Cd2- -binding sites on the beta-chain, one must be located at the N-terminal end near the single tyrosine residue, since Cd2- and Zn2+ produced similar effects on the intrinsic protein fluorescence. The other Cd2+ site which is unique to Cd2+ must be Cys84, located at the C-terminal end. PMID:2039467

Donato, H; Mani, R S; Kay, C M

1991-05-15

89

Identification of anti-adipogenic proteins in adult bovine serum suppressing 3T3-L1 preadipocyte differentiation  

PubMed Central

Adipocyte differentiation is a complex developmental process forming adipocytes from various precursor cells. The murine 3T3-L1 preadipocyte cell line has been most frequently used in the studies of adipocyte differentiation. Differentiation of 3T3-L1 preadipocytes includes a medium containing fetal bovine serum (FBS) with hormonal induction. In this study, we observed that differentiation medium containing adult bovine serum (ABS) instead of FBS did not support differentiation of preadipocytes. Impaired adipocyte differentiation was due to the presence of a serum protein factor in ABS that suppresses differentiation of preadipocytes. Using a proteomic analysis, alpha-2-macroglobulin and paraoxonase/arylesterase 1, which were previously shown to suppress differentiation of preadipocytes, were identified as anti-adipogenic proteins. Although their functional mechanisms have not yet been elucidated, the anti-adipogenic effects of these proteins are discussed. [BMB Reports 2013; 46(12): 582-587] PMID:24195790

Park, Jeongho; Park, Jihyun; Nahm, Sang-Soep; Choi, Inho; Kim, Jihoe

2013-01-01

90

Persistent infection with bovine herpesvirus type 1: rabbit model.  

PubMed Central

Persistent infection with bovine herpesvirus type 1 (BHV-1) was established in all rabbits after conjunctival inoculation of virus. Spontaneous reactivations of BHV-1 with and without the appearance of recurrent ocular lesions were observed in persistently infected rabbits. BHV-1 was reactivated predictably and shed from all persistently infected rabbits after the administration of dexamethasone. During all reactivations, BHV-1 isolation was restricted to the inoculated eye. PMID:6274801

Rock, D L; Reed, D E

1982-01-01

91

Protein Model Database  

SciTech Connect

The phenomenal success of the genome sequencing projects reveals the power of completeness in revolutionizing biological science. Currently it is possible to sequence entire organisms at a time, allowing for a systemic rather than fractional view of their organization and the various genome-encoded functions. There is an international plan to move towards a similar goal in the area of protein structure. This will not be achieved by experiment alone, but rather by a combination of efforts in crystallography, NMR spectroscopy, and computational modeling. Only a small fraction of structures are expected to be identified experimentally, the remainder to be modeled. Presently there is no organized infrastructure to critically evaluate and present these data to the biological community. The goal of the Protein Model Database project is to create such infrastructure, including (1) public database of theoretically derived protein structures; (2) reliable annotation of protein model quality, (3) novel structure analysis tools, and (4) access to the highest quality modeling techniques available.

Fidelis, K; Adzhubej, A; Kryshtafovych, A; Daniluk, P

2005-02-23

92

Subcellular Localization of the Bovine Leukemia Virus R3 and G4 Accessory Proteins  

PubMed Central

Bovine leukemia virus (BLV) is a complex retrovirus that belongs to the Deltaretrovirus genus, which also includes Human T-cell leukemia virus type 1 (HTLV-1). Both viruses contain an X region coding for at least four proteins: Tax and Rex, which are involved in transcriptional and posttranscriptional regulation, respectively, and the accessory proteins R3 and G4 (for BLV) and p12I, p13II, and p30II (for HTLV-1). The present study was aimed at characterizing the subcellular localization of BLV R3 and G4. The results of immunofluorescence experiments on transfected HeLa Tat cells demonstrated that R3 is located in the nucleus and in cellular membranes, as previously reported for HTLV-1 p12I. In contrast, G4, like p13II, is localized both in the nucleus and in mitochondria. In addition, we have shown that G4 harbors a mitochondrial targeting signal consisting of a hydrophobic region and an amphipathic ?-helix. Thus, despite a lack of significant primary sequence homology, R3 and p12I and G4 and p13II exhibit similar targeting properties, suggesting possible overlap in their functional properties. PMID:12097596

Lefbvre, Laurent; Ciminale, Vincenzo; Vanderplasschen, Alain; D'Agostino, Donna; Burny, Arsne; Willems, Luc; Kettmann, Richard

2002-01-01

93

Isolation, purification and characterization of antioxidant peptidic fractions from a bovine liver sarcoplasmic protein thermolysin hydrolyzate.  

PubMed

Sarcoplasmic proteins isolated from bovine livers were hydrolyzed using the enzyme thermolysin at 37C for 2h. The hydrolyzates were filtered through molecular weight cut off membranes (MWCO) and filtrates were obtained. The water activity (a(w)) of unhydrolysed sarcoplasmic protein, full hydrolyzates, 10-kDa and 3-kDa filtrates were below the limit necessary for microbial growth. The antioxidant activities of both filtrates and fractions were assessed using the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity assay, the ferric ion reducing antioxidant power (FRAP) assay and the Fe(2+) chelating ability assay. RP-HPLC was used for purification of the full hydrolyzates, the 10-kDa and the 3-kDa filtrates. The peptidic content of the full hydrolyzates, the 10-kDa and the 3-kDa filtrates were assessed using the Dumas method and peptide contents of each fraction were characterized using electrospray quadrupole time-of-flight (ESI-Q-TOF) mass spectrometry with the resultant spectrum analysed using the software programmes Protein Lynx Global Server 2.4. and TurboSEQUEST. Similarities between the amino acid composition of characterized peptides from each fraction and previously reported antioxidant peptides were found. This study demonstrates that meat by-product such as liver can be utilised as raw material for the generation of bioactive peptides with demonstrated antioxidant activities in vitro using the enzyme thermolysin. It is significant as it presents a potential opportunity for meat processors to use their waste streams for the generation of bioactive peptides for potential functional food use. PMID:21129427

Di Bernardini, Roberta; Rai, Dilip K; Bolton, Declan; Kerry, Joseph; O'Neill, Eileen; Mullen, Anne Maria; Harnedy, Pdraign; Hayes, Maria

2011-02-01

94

Bovine hepatic and adipose retinol-binding protein gene expression and relationship with tumor necrosis factor-?.  

PubMed

Retinol-binding protein (RBP) is the main transport system for retinol in circulation, is a relatively small protein with one binding site for retinol in the all-trans form, and is bound to transthyretin. The objectives of this study were to characterize the temporal pattern of bovine hepatic mRNA expression of RBP during the periparturient period and to determine if a relationship exists between the expression of RBP and that of tumor necrosis factor (TNF)-? in dairy cows. In experiment 1, we assessed hepatic mRNA expression of RBP during the periparturient period. Liver tissues were sampled from periparturient dairy cows (n=9) at -21, -4, +1, +7, and +21 relative to parturition and frozen in liquid N(2). Total RNA was extracted from each tissue sample and cDNA was generated. Gene expressions of RBP and ?-actin (as a housekeeping gene) were measured as relative quantity using reverse transcription-PCR. Data were analyzed using cycle threshold values, adjusted to ?-actin, and significance was determined at P<0.05. Serum samples (-21, -4, +1, +7, and +21 relative to parturition) were analyzed for retinol concentration using a standard HPLC-based method. Cows had variable expression of hepatic RBP and serum retinol over the transition period, with a decline near parturition and a rebound toward prepartum levels later in lactation. In experiment 2, liver and visceral (intestinal) adipose tissues were sampled from dairy cows (n=28) at slaughter. Expression of RBP and TNF-? was detected in all samples and variations among cows were highly significant for both genes. Across tissues, expression of RBP was positively correlated with that of TNF-? (r=0.60). Within adipose tissue, expression of RBP and TNF-? was weakly correlated (r=0.23), whereas in hepatic tissue, expression was strongly correlated (r=0.62). In experiment 3, late-lactation dairy Holstein cows were blocked by parity and feed intake, and randomly assigned to control, recombinant bovine (rb)TNF challenge, or pair-fed control treatment (n=5/treatment). Cows were injected with either rbTNF (subcutaneous injection of 2 g/kg of body weight in saline) or sterile saline (control and pair-fed control animals) once daily for 7d. Liver biopsy was performed on d 7 and samples were processed for expression of RBP and TNF-?. Although TNF challenge caused an upregulation of hepatic TNF-? expression, as expected, it did not alter hepatic RBP expression. Overall, the temporal pattern of hepatic RBP gene expression during the periparturient period followed, to a great extent, that of plasma retinol. Although a strong positive correlation was previously detected between bovine hepatic RBP and TNF-? transcripts, rbTNF challenge did not cause alter RBP expression. These observations collectively imply that regulation of RBP at the transcription level is influenced by physiological state but may be independent from that of transthyretin, which is altered by proinflammatory stimuli (such as TNF-?) via induction of transcription factor nuclear factor-interleukin 6. PMID:23040032

Rezamand, P; Watts, J S; Hunt, K M; Bradford, B J; Mamedova, L K; Morey, S D

2012-12-01

95

Two bovine models of osteogenesis imperfecta exhibit decreased apatite crystal size  

Microsoft Academic Search

SummaryIn recent years advances have been made in detailing the changes in both collagen and noncollagenous proteins caused by a\\u000a variety of mutations leading to osteogenesis imperfecta. Much less, however, is known about the mineral phase in the affected\\u000a bone. In this report, we measured the crystallinity of the apatite in bovine OI bone. Line broadening of the 002 reflection

L. W. Fisher; E. D. Eanes; L. J. Denholm; B. R. Heywood; J. D. Termine

1987-01-01

96

Differential effects of flavonoids on bovine kidney low molecular mass protein tyrosine phosphatase.  

PubMed

Among the structurally related flavonoids tested on the bovine kidney low molecular weight protein tyrosine phosphatase (LMrPTP) activity, quercetin activated by about 2.6-fold the p-nitrophenyl-phosphate (p-NPP)-directed reaction, in contrast to morin that acted as a competitive inhibitor, with Ki values of 87, 73 and 50 microM for p-NPP, FMN, and tyrosine-phosphate, respectively. Other related flavonoids, such as rutin, kaempferol, catechin, narigin, phloretin and taxifolin did not significantly affect the LMrPTP activity. The positions of the hydroxyl groups in the structures of the flavonoids were important for their distinct effects on LMrPTP activity. The hydroxyl groups at C3' and C4' and the presence of a double bond at C2 and C3 were essential for the activating effect of quercetin. The absence of the 3'-OH (kaempferol), absence of the double bond (taxifolin) and the presence of the sugar rutinose at the 3-OH (rutin) suppressed the effect of quercetin. The C2'- and C4'-hydroxyl groups, the presence of the double bond, and a C4-ketone group were important requirements for the inhibitory effects of morin. PMID:17059175

Miranda, Mrcio A; Okamoto, Andr K; Ferreira, Carmen V; Silva, Thelma L; Granjeiro, Jos M; Aoyama, Hiroshi

2006-08-01

97

Chemical structure of the arabinogalactan protein from gum ghatti and its interaction with bovine serum albumin.  

PubMed

Exudate gums, because of their beneficial properties, have been significant items of international trade in various industries for centuries. This manuscript sets out to gain insight into the fine structural details of an arabinogalactan protein (AGP) of gum ghatti (Anogeissus latifolia gum). The presence of a highly branched 554 kDa AGP having 1,6-linked Galp, 1,2-linked Manp, 1,3-linked Araf and 1,4-linked GlcpA main chain, substituted at O-4,6 of 1,2-linked Manp, and O-3/O-3,4 of 1,6-linked Galp residues by Araf, Arap and Galp units was revealed by chemical, chromatographic, ESMS, and NMR analyses. In particular, ESMS analysis of per acetylated oligomeric fragments derived from AGP by Smith degradation followed by acetylation was described as a commanding tool for providing critical structural information on a spectrum of glycerol tagged oligosaccharides. In addition, formation of an electrostatically driven complex between the isolated AGP and bovine serum albumin resulting in changes in the microenvironment around the tryptophan residues of BSA was established. A moderate radical scavenging activity comparable with those of standard antioxidants was observed from the AGP fraction (?94% at 1 mg/mL) that could be valuable in foods or pharmaceutical products as alternatives to synthetic antioxidants. PMID:25498648

Ghosh, Kanika; Ray, Sayani; Ghosh, Debjani; Ray, Bimalendu

2015-03-01

98

A comparative analysis of rapid methods for purification and refolding of recombinant bovine prion protein  

Technology Transfer Automated Retrieval System (TEKTRAN)

Bacterially-produced recombinant prion protein (rPrP) is a frequently used model system for the study of the properties of wild-type and mutant prion proteins by biochemical and biophysical approaches. A range of approaches have been developed for the purification and refolding of untagged, overexpr...

99

Oral administration of bovine whey proteins to mice elicits opposing immunoregulatory responses and is adjuvant dependent.  

PubMed

Most studies investigating the induction of oral tolerance (OT) use purified proteins such as ovalbumin (OVA), bovine serum albumin (BSA) and beta-lactoglobulin (beta-LG). Little information is available regarding the induction of OT to a protein mixture, e.g. cow's milk. In this study we compared the regulatory mechanisms induced after the oral administration of a whey protein concentrate (WP) derived from cow's milk following immunization with two different adjuvants, complete Freund's adjuvant (CFA) and alum. OVA was used as a control antigen. Animals were given a single feed of these proteins at an equivalent dose of 1 mg/g body weight before they were immunized seven days later with the antigen in Freund's adjuvant or alum. Delayed type hypersensitivity (DTH) responses were suppressed by both a feed of WP and OVA after immunization with CFA. However, only OVA feeding suppressed antigen specific IgG responses. In an attempt to investigate whether WP would tolerize the more susceptible IgE responses, alum immunization replaced CFA as the adjuvant used for systemic immunizations. WP, after a single feed, significantly primed for DTH and IgE responses indicating oral sensitization to WP. In contrast, OVA suppressed DTH, IgE and IgG responses. Antigen specific proliferation of mononuclear cells was suppressed in mice fed OVA, but primed in those fed with WP. In addition cells taken from sensitized mice fed WP up-regulated levels of specific interleukin (IL) -4, -10 and -12 in vitro whereas these cytokines were suppressed in cultures from tolerant WP fed mice. Global suppression was obtained in cultures from tolerant OVA fed mice. TGF-beta was not detected in draining PLN cell cultures of either tolerant or sensitized mice. These data suggest that a whey protein mixture induces divergent responses following immunization with either CFA or alum despite being fed at an identical dose. We suggest that that the choice of the adjuvant may determine the immunoregulatory outcome and this is also reflected by the systemic cytokine profile. PMID:15030512

Afuwape, A O; Turner, M W; Strobel, S

2004-04-01

100

Small-angle neutron scattering study of differences in phase behavior of silica nanoparticles in the presence of lysozyme and bovine serum albumin proteins  

NASA Astrophysics Data System (ADS)

The differences in phase behavior of anionic silica nanoparticles (88 ) in the presence of two globular proteins [cationic lysozyme (molecular weight (MW) 14.7 kD) and anionic bovine serum albumin (BSA) (MW 66.4 kD)] have been studied by small-angle neutron scattering. The measurements were carried out on a fixed concentration (1 wt %) of Ludox silica nanoparticles with varying concentrations of proteins (0-5 wt %) at pH = 7. It is found that, despite having different natures (opposite charges), both proteins can render to the same kind of aggregation of silica nanoparticles. However, the concentration regions over which the aggregation is observed are widely different for the two proteins. Lysozyme with very small amounts (e.g., 0.01 wt %) leads to the aggregation of silica nanoparticles. On the other hand, silica nanoparticles coexist with BSA as independent entities at low protein concentrations and turn to aggregates at high protein concentrations (>1 wt %). In the case of lysozyme, the charge neutralization by the protein on the nanoparticles gives rise to the protein-mediated aggregation of the nanoparticles. The nanoparticle aggregates coexist with unaggregated nanoparticles at low protein concentrations, whereas, they coexist with a free protein at higher protein concentrations. For BSA, the nonadsorbing nature of the protein produces the depletion force that causes the aggregation of the nanoparticles at higher protein concentrations. The evolution of the interaction is modeled by the two Yukawa potential, taking account of both attractive and repulsive terms of the interaction in these systems. The nanoparticle aggregation is found to be governed by the short-range attraction for lysozyme and the long-range attraction for BSA. The aggregates are characterized by the diffusion limited aggregate type of mass fractal morphology.

Yadav, Indresh; Kumar, Sugam; Aswal, V. K.; Kohlbrecher, J.

2014-03-01

101

Small-angle neutron scattering study of differences in phase behavior of silica nanoparticles in the presence of lysozyme and bovine serum albumin proteins.  

PubMed

The differences in phase behavior of anionic silica nanoparticles (88) in the presence of two globular proteins [cationic lysozyme (molecular weight (MW) 14.7 kD) and anionic bovine serum albumin (BSA) (MW 66.4 kD)] have been studied by small-angle neutron scattering. The measurements were carried out on a fixed concentration (1wt%) of Ludox silica nanoparticles with varying concentrations of proteins (0-5wt%) at pH=7. It is found that, despite having different natures (opposite charges), both proteins can render to the same kind of aggregation of silica nanoparticles. However, the concentration regions over which the aggregation is observed are widely different for the two proteins. Lysozyme with very small amounts (e.g., 0.01wt%) leads to the aggregation of silica nanoparticles. On the other hand, silica nanoparticles coexist with BSA as independent entities at low protein concentrations and turn to aggregates at high protein concentrations (>1wt%). In the case of lysozyme, the charge neutralization by the protein on the nanoparticles gives rise to the protein-mediated aggregation of the nanoparticles. The nanoparticle aggregates coexist with unaggregated nanoparticles at low protein concentrations, whereas, they coexist with a free protein at higher protein concentrations. For BSA, the nonadsorbing nature of the protein produces the depletion force that causes the aggregation of the nanoparticles at higher protein concentrations. The evolution of the interaction is modeled by the two Yukawa potential, taking account of both attractive and repulsive terms of the interaction in these systems. The nanoparticle aggregation is found to be governed by the short-range attraction for lysozyme and the long-range attraction for BSA. The aggregates are characterized by the diffusion limited aggregate type of mass fractal morphology. PMID:24730839

Yadav, Indresh; Kumar, Sugam; Aswal, V K; Kohlbrecher, J

2014-03-01

102

Crystal structures of bovine odorant-binding protein in complex with odorant molecules.  

PubMed

The structure of bovine odorant-binding protein (bOBP) revealed a striking feature of a dimer formed by domain swapping [Tegoni, M., Ramoni, R., Bignetti, E., Spinelli, S. & Cambillau, C. (1996) Nat. Struct. Biol.3, 863-867; Bianchet, M.A., Bains, G., Pelosi, P., Pevsner, J., Snyder, S.H., Monaco, H.L. & Amzel, L.M. (1996) Nat. Struct. Biol.3, 934-939] and the presence of a naturally occuring ligand [Ramoni, R., Vincent, F., Grolli, S., Conti, V., Malosse, C., Boyer, F.D., Nagnan-Le Meillour, P., Spinelli, S., Cambillau, C. & Tegoni, M. (2001) J. Biol. Chem.276, 7150-7155]. These features led us to investigate the binding of odorant molecules with bOBP in solution and in the crystal. The behavior of odorant molecules in bOBP resembles that observed with porcine OBP (pOBP), although the latter is monomeric and devoid of ligand when purified. The odorant molecules presented K(d) values with bOBP in the micromolar range. Most of the X-ray structures revealed that odorant molecules interact with a common set of residues forming the cavity wall and do not exhibit specific interactions. Depending on the ligand and on the monomer (A or B), a single residue--Phe89--presents alternate conformations and might control cross-talking between the subunits. Crystal data on both pOBP and bOBP, in contrast with binding and spectroscopic studies on rat OBP in solution, reveal an absence of significant conformational changes involving protein loops or backbone. Thus, the role of OBP in signal triggering remains unresolved. PMID:15373829

Vincent, Florence; Ramoni, Roberto; Spinelli, Silvia; Grolli, Stefano; Tegoni, Mariella; Cambillau, Christian

2004-10-01

103

Prostaglandin E synthase interacts with inducible heat shock protein 70 after heat stress in bovine primary dermal fibroblast cells.  

PubMed

Exposure to heat stress in dairy cows leads to undesired side effects that are reflected by complex alterations in endocrine parameters, such as reduced progesterone, estradiol, and thyroid hormone concentrations. These endocrine maladaptation leads to failure to resume cyclicity, a poor uterine environment and inappropriate immune responses in postpartum dairy cows. Prostaglandins (PG's) are lipid mediators, which serve as signal molecules in response to various external stimuli as well as to cell-specific internal signal molecules. A central role in PG synthesis plays prostaglandin E synthase (PGES) that catalyzes the isomerization of PGH2 to PGE2 .The present study was conducted to investigate heat stress associated PGES expression. Expression of PGES and inducible heat shock protein 70 (HSP70), as a putative chaperonic protein, was studied in bovine primary fibroblasts under different heat shock conditions. Bovine primary fibroblasts produce PGE2 at homoiothermical norm temperature (38.5C in bovine), but reduce PGE2 production rates under extreme heat stress (at 45C for 6 h). By contrast, PGE2 production rates are maintained after a milder heat stress (at 41.5C for 6 h). PGE2 synthesis is abolished by application of cyclooxygenase inhibitor indomethacin, indicating de novo synthesis. Heat stress increases HSP70 but not PGES protein concentrations. HSP70 physically interacts with PGES and the PGES-HSP70 complex did not dissociate upon heat stress at 45C even after returning the cells to 37C. The PGE2 production negatively correlates with the portion of PGES-HSP70 complex. These results suggest a protein interaction between HSP70 and PGES in dermal fibroblast cells. Blockage of PGES protein by HSP70 seems to interfere with the regulatory processes essential for cellular adaptive protection. 2014 International Society for Advancement of Cytometry. PMID:25412999

Richter, Constanze; Viergutz, Torsten; Schwerin, Manfred; Weitzel, Joachim M

2015-01-01

104

Osmotically unresponsive water fraction on proteins: non-ideal osmotic pressure of bovine serum albumin as a function of pH and salt concentration.  

PubMed

How much does protein-associated water differ in colligative properties (freezing point, boiling point, vapor pressure and osmotic behavior) from pure bulk water? This question was approached by studying the globular protein bovine serum albumin (BSA), using changes in pH and salt concentration to alter its native structural conformation and state of aggregation. BSA osmotic pressure was investigated experimentally and analyzed using the molecular model of Fullerton et al. [Biochem Cell Biol 1992;70(12):1325]. Analysis yielded both the extent of osmotically unresponsive water (OUW) and the effective molecular weight values of the membrane-impermeable BSA solute. Manipulation of BSA conformation and aggregation by membrane-penetrating cosolutes show that alterations in pH and salt concentration change the amount of bulk water that escapes into BSA from a minimum of 1.4 to a maximum of 11.7 g water per g dry mass BSA. PMID:16376113

Fullerton, Gary D; Kanal, Kalpana M; Cameron, Ivan L

2006-01-01

105

Critical examination of the colloidal particle model of globular proteins.  

PubMed

Recent studies of globular protein solutions have uniformly adopted a colloidal view of proteins as particles, a perspective that neglects the polymeric primary structure of these biological macromolecules, their intrinsic flexibility, and their ability to sample a large configurational space. While the colloidal perspective often serves as a useful idealization in many cases, the macromolecular identity of proteins must reveal itself under thermodynamic conditions in which the native state is no longer stable, such as denaturing solvents and high protein concentrations where macromolecules tend to have screened excluded volume, charge, and hydrodynamic interactions. Under extreme pH conditions, charge repulsion interactions within the protein chain can overcome the attractive hydrogen-bonding interactions, holding it in its native globular state. Conformational changes can therefore be expected to have great significance on the shear viscosity and other rheological properties of protein solutions. These changes are not envisioned in conventional colloidal protein models and we have initiated an investigation of the scattering and rheological properties of model proteins. We initiate this effort by considering bovine serum albumin because it is a globular protein whose solution properties have also been extensively investigated as a function of pH, temperature, ionic strength, and concentration. As we anticipated, near-ultraviolet circular dichroism measurements and intrinsic viscosity measurements clearly indicate that the bovine serum albumin tertiary structure changes as protein concentration and pH are varied. Our findings point to limited validity of the colloidal protein model and to the need for further consideration and quantification of the effects of conformational changes on protein solution viscosity, protein association, and the phase behavior. Small-angle Neutron Scattering measurements have allowed us to assess how these conformational changes influence protein size, shape, and interprotein interaction strength. PMID:25650939

Sarangapani, Prasad S; Hudson, Steven D; Jones, Ronald L; Douglas, Jack F; Pathak, Jai A

2015-02-01

106

Modeling and docking the endothelin G-protein-coupled receptor.  

PubMed Central

A model of the endothelin G-protein-coupled receptor (ET(A)) has been constructed using a segmented approach. The model was produced using a bovine rhodopsin model as a template for the seven transmembrane alpha-helices. The three cytoplasmic loop regions and the C-terminal region were modeled on NMR structures of corresponding segments from bovine rhodopsin. The three extracellular loops were modeled on homologous loop regions in other proteins of known structure. The N-terminal region was modeled as a three-helix domain based on its homology with a hydrolase protein. To test the model, the FTDOCK algorithm was used to predict the ligand-binding site for the crystal structure of human endothelin. The site of docking is consistent with mutational and biochemical data. The principal sites of interaction in the endothelin ligand all lie on one face of a helix that has been implicated by structure-activity relationship studies as being essential for binding. As further support for the model, attempts to dock bigET, an inactive precursor to endothelin that does not bind to the receptor, found no sites for tight binding. The model of the receptor-ligand complex produced forms a basis for rational drug design of agonists and antagonists for this G-protein-coupled receptor. PMID:11106614

Orry, A J; Wallace, B A

2000-01-01

107

Isolation, Purification and Characterization of Fatty-Acid-Binding Protein from Milk Fat Globule Membrane: Effect of Bovine Growth Hormone Treatment  

Microsoft Academic Search

Fatty-acid-binding protein (FABP) was purified from bovine milk fat globule membrane (MFGM) by ion-exchange chromatography on DEAE-Sepharose and by gel-filtration on Sephadex G-50. Purified FABP was similar to bovine mammary gland heart (H)-type FABP\\/ mammary derived growth inhibitor (MDGI). It inhibited growth of mammary epithelial cells at nanogram concentrations, had a relative molecular mass of 15 kDa, as determined by

2002-01-01

108

Effects of electrical stimulation on the myofibril protein degradation and fragmentation in bovine longissimus dorsi muscle and its relationship to tenderness  

E-print Network

EFFECTS OF ELECTRICAL STIMULATION ON THE MYOFIBRIL PROTEIN DEGRADATION AND FRAGMENTATION IN BOVINE LONGISSIMUS DORSI MUSCLE AND ITS RELATIONSHIP TO TENDERNESS A Thesis by Maria Lucia Salles Cunha Procknor Submitted to the Graduate College... IN BOVINE LONGISSIMUS DORSI MUSCLE AND ITS RELATIONSHIP TO TENDERNESS A Thesis by MARIA LUCIA SALLES CUNHA PROCKNOR Approved as to style and content by: Thayne R. Dutson (Co-Chairman) Jeffrey W. Savell (Co-Chairman) Konrad A. Eugster (Member...

Procknor, Maria Lucia Salles Cunha

2012-06-07

109

Involvement of the cyclic AMP-responsive element binding protein in bovine leukemia virus expression in vivo.  

PubMed Central

The TAR element (Tax-responsive element; also called TxRE) is a major determinant of the regulation of bovine leukemia virus (BLV) expression. In order to gain insight into the mechanisms of viral expression, complexes formed between proteins and the TAR enhancer DNA were analyzed by gel retardation assays. We report here that nuclear lysates from ex vivo-isolated B lymphocytes contain proteins that specifically bind to TAR. An antibody directed toward the cyclic AMP-responsive element binding (CREB) protein supershifted a complex (C1) present only in BLV-infected B lymphocytes. The CREB protein thus appears to be a major transcription factor involved in BLV expression in vivo. Images PMID:8057465

Adam, E; Kerkhofs, P; Mammerickx, M; Kettmann, R; Burny, A; Droogmans, L; Willems, L

1994-01-01

110

A Bovine Model of Respiratory Chlamydia psittaci Infection: Challenge Dose Titration  

PubMed Central

This study aimed to establish and evaluate a bovine respiratory model of experimentally induced acute C. psittaci infection. Calves are natural hosts and pathogenesis may resemble the situation in humans. Intrabronchial inoculation of C. psittaci strain DC15 was performed in calves aged 23 months via bronchoscope at four different challenge doses from 106 to 109 inclusion-forming units (ifu) per animal. Control groups received either UV-inactivated C. psittaci or cell culture medium. While 106 ifu/calf resulted in a mild respiratory infection only, the doses of 107 and 108 induced fever, tachypnea, dry cough, and tachycardia that became apparent 23 days post inoculation (dpi) and lasted for about one week. In calves exposed to 109 ifu C. psittaci, the respiratory disease was accompanied by severe systemic illness (apathy, tremor, markedly reduced appetite). At the time point of most pronounced clinical signs (3 dpi) the extent of lung lesions was below 10% of pulmonary tissue in calves inoculated with 106 and 107 ifu, about 15% in calves inoculated with 108 and more than 30% in calves inoculated with 109 ifu C. psittaci. Beside clinical signs and pathologic lesions, the bacterial load of lung tissue and markers of pulmonary inflammation (i.e., cell counts, concentration of proteins and eicosanoids in broncho-alveolar lavage fluid) were positively associated with ifu of viable C. psittaci. While any effect of endotoxin has been ruled out, all effects could be attributed to infection by the replicating bacteria. In conclusion, the calf represents a suitable model of respiratory chlamydial infection. Dose titration revealed that both clinically latent and clinically manifest infection can be reproduced experimentally by either 106 or 108 ifu/calf of C. psittaci DC15 while doses above 108 ifu C. psittaci cannot be recommended for further studies for ethical reasons. This defined model of different clinical expressions of chlamydial infection allows studying host-pathogen interactions. PMID:22299031

Reinhold, Petra; Ostermann, Carola; Liebler-Tenorio, Elisabeth; Berndt, Angela; Vogel, Anette; Lambertz, Jacqueline; Rothe, Michael; Rttger, Anke; Schubert, Evelyn; Sachse, Konrad

2012-01-01

111

Protein kinase C potentiates homologous desensitization of the beta2-adrenoceptor in bovine tracheal smooth muscle.  

PubMed

Preincubation (30 min) of bovine tracheal smooth muscle with various concentrations (0.1, 1 and 10 microM) of fenoterol decreased isoprenaline-induced maximal relaxation (E(max)) of methacholine-contracted preparations in a concentration dependent fashion, indicating desensitization of the beta(2)-adrenoceptor. Preincubation with 1 microM of the protein kinase C (PKC) activator phorbol 12-myristate 13-acetate (PMA) caused a small but significant decrease in isoprenaline-induced E(max), indicating activated PKC-mediated heterologous beta(2)-adrenoceptor desensitization. To investigate the capacity of activated PKC to regulate homologous desensitization, we incubated the smooth muscle strips with the combination of both 1 microM PMA and 1 microM fenoterol. This combined treatment synergistically decreased the isoprenaline-induced maximal relaxation, as compared to the individual effects of PMA and fenoterol alone, indicating a common pathway for heterologous and homologous desensitization. Moreover, the specific PKC-inhibitor 2-[1-(3-dimethylaminopropyl)-1H-indol-3-yl]-3-(1H-indol-3-yl) maleimide (GF 109203X) markedly increased the potency and E(max) of isoprenaline for all conditions used, including control conditions, and the synergistic effects of PMA and fenoterol were completely prevented. In conclusion, the present study demonstrates that homologous desensitization of the beta(2)-adrenergic receptor can be enhanced by PKC activation. For the first time we have provided evidence that this concept is functionally operative in airway smooth muscle, and it may explain the reduced bronchodilator response to beta(2)-adrenoceptor agonists in patients with asthma during a severe exacerbation. PMID:16324695

Boterman, Mark; Smits, Steven R J G; Meurs, Herman; Zaagsma, Johan

2006-01-01

112

Cation dependency of the hydrolytic activity of activated bovine Protein C  

SciTech Connect

The hydrolytic activity of activated bovine plasma Protein C (APC) is dependent upon monovalent or divalent cations. The kinetics of APC activity were examined with a variety of monovalent and divalent cations, and significant differences were observed. Similar studies were performed with des(1-41, light chain)APC (GDAPC), from which all ..gamma..-carboxyglutamic acid residues have been removed. These studies provided useful information concerning the cation dependency. Divalent cations apparently stimulate APC and GDAPC kinetic activity through association at a single ..gamma..-carboxyglutamic acid-independent high affinity binding site. A Mn(II) binding site of this nature of GDAPC was determined by EPR spectroscopy, to possess a dissociation constant of 53 +/- 8 uM. Monovalent cations stimulate GDAPC activity through association at an apparently single binding site that is distinct from the divalent cation site. The monovalent cation , Tl(I), was determined, by /sup 205/Tl(I) NMR spectroscopy, to bind to APC and GDAPC with dissociation constants of 16 +/- 8 mM and 32+/- 11 mM, respectively. Both NMR and EPR spectroscopy have been utilized to estimate topographical relationships between divalent cation sites, monovalent cation sites, and the active site of GDAPC. By observing the paramagnetic effects of either Mn(II) or an active site directed spin-label on the longitudinal relaxation rates of Tl(I) nuclei bound to this enzyme, the average interatomic distance between Mn(II) and Tl(I) was calculated to be 8.3 +/- 0.3 A, and the average distance between Tl(I) and the spin-label free electron was estimated to be 3.8 +/- 0.2 A.

Hill, K.A.W.

1986-01-01

113

Conservative mutations in the immunosuppressive region of the bovine leukemia virus transmembrane protein affect fusion but not infectivity in vivo.  

PubMed

Many retroviruses, including bovine leukemia virus (BLV), contain a highly conserved region located about 40 amino acids downstream from the fusion peptide within the sequence of the external domain of the transmembrane (TM) protein. This region is notably thought to be involved in the presentation of the NH2-terminal peptide to allow cell fusion. By using hydrophobic cluster analysis and by analogy with the influenza A hemagglutinin structures, the core of the TM structure including this particular region was predicted to consist, in the BLV and other retroviral envelope proteins, of an alpha-helix followed by a loop region, both docked against a subsequent alpha-helix that forms a triple-stranded coiled coil. The loop region could undergo, as in hemagglutinin, a major refolding into an alpha-helix integrating the coiled coil structure and putting the fusion peptide to one tip of the molecule. Based on this model, we have identified amino acids that may be essential to the BLV TM structure, and a series of mutations were introduced in the BLV env gene of an infectious molecular clone. A first series of mutations was designed to disturb the coiled coil structure (substitutions with proline residues), whereas others would maintain the general TM structure. When expressed by Semliki Forest virus recombinants, all the mutated envelope proteins were stable and efficiently synthesized in baby hamster kidney cells. Both proline-substituted and conservative mutants were strongly affected in their capacity to fuse to CC81 indicator cells. In addition, it appeared that the integrity of the TM coiled coil structure is essential for envelope protein multimerization, as analyzed by metrizamide gradient centrifugation. Finally, to gain insight into the role of this coiled coil in the infectious potential of BLV in vivo, the mutated TM genes were introduced in an infectious and pathogenic molecular clone and injected into sheep. It appeared that only the conservative mutations (A60V and A64S) allowed maintenance of viral infectivity in vivo. Since these mutations destroyed the ability to induce syncytia, we conclude that efficient fusion capacity of the recombinant envelopes is not a prerequisite for the infectious potential of BLV in vivo. Viral propagation of these mutants was strongly affected in some of the infected sheep. However, the proviral loads within half of the infected animals (2 out of 2 for A60V and 1 out of 4 for A64S) were close to the wild-type levels. In these sheep, it thus appears that the A60V and A64S mutants propagate efficiently despite being unable to induce syncytia in cell culture. PMID:9582317

Gatot, J S; Callebaut, I; Mornon, J P; Portetelle, D; Burny, A; Kerkhofs, P; Kettmann, R; Willems, L

1998-05-22

114

Experimental ruminant models for bovine neosporosis: what is known and what is needed.  

PubMed

At present, bovine neosporosis is an important worldwide concern because of its wide geographic distribution and economic impact. Abortion is the main clinical sign of bovine neosporosis in both dairy and beef cattle. Ruminant challenge models are critical to evaluate potential vaccine candidates to help tackle bovine neosporosis and to study pathogenesis and host responses to infection. Several research groups have developed ruminant models of Neospora caninum infection independently of others, resulting in a high degree of variability due to the use of different species of animals, breeds, strains/isolates of N. caninum, doses, routes and times of inoculation. Standardization is greatly needed to advance research in a more collaborative, timely and efficient manner. In the absence of widely accepted international guidelines, this manuscript serves to summarize and discuss the different models and parameters currently in use. Parameters essential for the development of non-pregnant and pregnant ruminant models are outlined and the main knowledge gaps are identified. This information could act as the basis to develop a consensus for international standard guidelines for ruminant models of neosporosis that would be helpful for researchers in this field worldwide. PMID:24926962

Benavides, Julio; Collantes-Fernndez, Esther; Ferre, Ignacio; Prez, Valentn; Campero, Carlos; Mota, Rinaldo; Innes, Elisabeth; Ortega-Mora, Luis M

2014-09-01

115

Osmotically unresponsive water fraction on proteins: Non-ideal osmotic pressure of bovine serum albumin as a function of pH and salt concentration  

Microsoft Academic Search

How much does protein-associated water differ in colligative properties (freezing point, boiling point, vapor pressure and osmotic behavior) from pure bulk water? This question was approached by studying the globular protein bovine serum albumin (BSA), using changes in pH and salt concentration to alter its native structural conformation and state of aggregation. BSA osmotic pressure was investigated experimentally and analyzed

Gary D. Fullerton; Kalpana M. Kanal; Ivan L. Cameron

2006-01-01

116

Lipid modifications of microsomes isolated from villus and crypt zones of bovine intestinal mucosa: relationship with fatty acid binding protein.  

PubMed

The present studies were conducted to examine the fatty acid composition of microsomal lipids of bovine small intestine. Microsomes and cytosol were isolated from mucosal scrapings enriched with villus and crypts cells, and the following studies were conducted to: 1) analyse fatty acids from microsomal lipids; 2) incorporate 1-14C oleic acid to microsomal lipids; and 3) bind 1-14C oleic acid to cytosolic proteins of villus and crypt zone. The results of these studies demonstrated that: (1) the major unsaturated fatty acids of microsomes were oleic (C18:1 n-9), linoleic (C18:2 n-6) and arachidonic acids (C20:4 n-6), which increased from crypt to villus tip of the bovine intestinal mucosa; (2) gel filtration chromatography indicated that the low-molecular weight cytosolic proteins obtained from superficial mucosal scrapings contained the greatest oleic acid binding activity; (3) the incorporation of 1-14C oleic acid to microsomes was higher in phospholipids, triglycerides and cholesterol esters from villus than in crypts zones; (4) the protein content of cytosol and microsomes was longer in villus zones than in crypts zones; (5) the peroxidizability index showed the highest value in villus microsomes. PMID:9224550

Furlan, L; Catala, A

1997-02-01

117

Polymer-Induced Heteronucleation for Protein Single Crystal Growth: Structural Elucidation of Bovine Liver Catalase and Concanavalin A Forms  

SciTech Connect

Obtaining single crystals for X-ray diffraction remains a major bottleneck in structural biology; when existing crystal growth methods fail to yield suitable crystals, often the target rather than the crystallization approach is reconsidered. Here we demonstrate that polymer-induced heteronucleation, a powerful technique that has been used for small molecule crystallization form discovery, can be applied to protein crystallization by optimizing the heteronucleant composition and crystallization formats for crystallizing a wide range of protein targets. Applying these advances to two benchmark proteins resulted in dramatically increased crystal size, enabling structure determination, for a half century old form of bovine liver catalase (BLC) that had previously only been characterized by electron microscopy, and the discovery of two new forms of concanavalin A (conA) from the Jack bean and accompanying structural elucidation of one of these forms.

Foroughi, Leila M.; Kang, You-Na; Matzger, Adam J. (Michigan)

2012-05-09

118

Alternative pathway fof bovine complement Immunochemical studies on factor B-like serum protein and its conversion product B gamma 2.  

PubMed Central

Rabbits produced antibodies to a factor B-like serum protein (factor Bbov), its conversion product B gamma 2 and some other bovine serum proteins after repeated immunization with zymosan which previously had been incubated with fresh bovine serum. Such antisera were used to monitor purification of B gamma 2 from fresh bovine sera incubated with zxymosan. Subsequently, antisera specific for factor Bbov and B gamma 2 were produced. Antiserum produced against B gamma 2 cross-reacted with factor Bbov. Functional assays for factor Bbov were carried out in a hemolytic system with guinea pig erythrocytes in EGTA buffer. Heat inactivation (56 degrees C/5 min) of bovine serum destroyed the antigenicity of factor Bbov but not that of B gamma 2. Factor Bbov had an apparent molecular weight of 95,000 and B gamma 2 a molecular weight of 40,000 daltons. Conversion of factor Bbov to B gamma 2 was determined qualitatively by immunoelectrophoresis and quantitatively by radial immunodiffusion. Conversion of factor Bbov to B gamma 2 in bovine serum, in the presence of zymosan or cobra venom factor (CoVF) required Mg++ but not Ca++, did not occur in heat inactivated (56 degrees C/5 min) serum and was maximal, but not complete, when fresh bovine serum was incubated with zymosan (20 mg/mL) at 37 for two hours. Images Fig. 1. Fig. 2 Fig. 3. Fig. 4. Fig. 6. Fig. 7. PMID:6176300

Tabel, H

1981-01-01

119

Continuous Age-Structured Model for Bovine Tuberculosis in African buffalo  

NASA Astrophysics Data System (ADS)

The paper deals with a model of the spread of bovine tuberculosis in the buffalo population in the Kruger National Park in South Africa. The model uses continuous age structure and it is formulated in terms of partial differential equations using eight epidemiological classes (compartments). More precisely, the age density for each class at time t satisfies a one way wave equation, where the age is the space variable. The continuous age model discussed here is derived from a 2006 age groups model by P. C. Cross and W. M. Getz.

Anguelov, R.; Kojouharov, H.

2009-10-01

120

Infection of the upper respiratory tract of hamsters by the bovine parainfluenza virus type 3 BN-1 strain expressing enhanced green fluorescent protein.  

PubMed

Bovine parainfluenza virus type 3 (BPIV3) is an important pathogen associated with bovine respiratory disease complex (BRDC). We have generated a recombinant BPIV3 expressing enhanced green fluorescent protein (rBPIV3-EGFP) based on the BN-1 strain isolated in Japan. After intranasal infection of hamsters with rBPIV3-EGFP, EGFP fluorescence was detected in the upper respiratory tract including the nasal turbinates, pharynx, larynx, and trachea. In the nasal turbinates, rBPIV3-EGFP attained high titers (>10(6) TCID50/g of tissue) 2-4 days after infection. Ciliated epithelial cells in the nasal turbinates and trachea were infected with rBPIV3-EGFP. Histopathological analysis indicated that mucosal epithelial cells in bronchi were shed by 6 days after infection, leaving non-ciliated cells, which may have increased susceptibility to bacterial infection leading to the development of BRDC. These data indicate that rBPIV3-EGFP infection of hamsters is a useful small animal model for studying the development of BPIV3-associated BRDC. PMID:25543964

Ohkura, Takashi; Minakuchi, Moeko; Sagai, Mami; Kokuho, Takehiro; Konishi, Misako; Kameyama, Ken-Ichiro; Takeuchi, Kaoru

2015-02-01

121

Influence of metal ions on phosphatidylcholine bovine serum albumin model membrane, an FTIR study  

NASA Astrophysics Data System (ADS)

FTIR spectroscopy was used to study the interaction of K +, Ca 2+ and Eu 3+ ions and the Phosphatidylcholine (PC)-bovine serum albumin (BSA) complex. First, a PC-BSA interaction system was constructed. The analytical results of transmission electron microscope (TEM), quasi-elastic light scattering (QELS) techniques and FTIR-ATR spectroscopy indicated that PC molecules interacted with BSA in aqueous solutions. However, IR inspection was limited for aqueous solutions. Solid experimental condition was then employed, and FTIR spectra showed that the PC and BSA molecules incorporated with each other, which could represent their interactions in solutions. Then, the influence of metal ions on PC-BSA system was studied in solid experimental conditions, and FTIR spectroscopy was used in this study. The spectral results showed that: (1) K +, Ca 2+ and Eu 3+ ions all decreased the rigidities of acyl chains of PC in PC-BSA systems. (2) The interactions between Ca 2+, Eu 3+ ions and the hydrophilic phosphate ester and carbonyl ester groups of PC were stronger than that of K + ions, while the influent modes of Ca 2+ and Eu 3+ ions on these regions were different. (3) When the relative molar content of Eu 3+ ions to PC ( Ri/p) reached 2, the coordination effect between Eu 3+ ions and PO2- groups of PC was saturated. (4) The addition of these ions increased the content of ?-helix structures of BSA, and decreased the content of ?-turn structures. By comparing these results with the interactions of K +, Ca 2+, Eu 3+ ions with phospholipid system in the absence of protein, some special characters were discovered in the acyl regions of PC, while their interactions results with the hydrophilic regions of PC were alike. It might be interpreted that these metal ions influenced the acyl chains of PC mediated from BSA molecules, and coordinated directly with the hydrophilic regions of PC. As for biological membrane was a system included both phospholipid and proteins, these characters suggested that phospholipid-protein mixture system could be a better model in the studies of interaction between metal ions and biological membranes using FTIR spectroscopy.

Wang, Fan; Yang, Zhanlan; Zhou, Yong; Weng, Shifu; Zhang, Li; Wu, Jinguang

2006-08-01

122

The S protein of bovine coronavirus is a hemagglutinin recognizing 9-O-acetylated sialic acid as a receptor determinant.  

PubMed Central

The S protein of bovine coronavirus (BCV) has been isolated from the viral membrane and purified by gradient centrifugation. Purified S protein was identified as a viral hemagglutinin. Inactivation of the cellular receptors by sialate 9-O-acetylesterase and generation of receptors by sialylation of erythrocytes with N-acetyl-9-O-acetylneuraminic acid (Neu5,9Ac2) indicate that S protein recognizes 9-O-acetylated sialic acid as a receptor determinant as has been shown previously for intact virions. The second glycoprotein of BCV, HE, which has been thought previously to be responsible for the hemagglutinating activity of BCV, is a less efficient hemagglutinin; it agglutinates mouse and rat erythrocytes, but in contrast to S protein, it is unable to agglutinate chicken erythrocytes, which contain a lower level of Neu5,9Ac2 on their surface. S protein is proposed to be responsible for the primary attachment of virus to cell surface. S protein is proposed to be responsible for the primary attachement of virus to cell surface receptors. The potential of S protein as a probe for the detection of Neu5,9Ac2-containing glycoconjugates is demonstrated. Images PMID:1920630

Schultze, B; Gross, H J; Brossmer, R; Herrler, G

1991-01-01

123

Oncoviral Bovine Leukemia Virus G4 and Human T-Cell Leukemia Virus Type 1 p13II Accessory Proteins Interact with Farnesyl Pyrophosphate Synthetase  

PubMed Central

G4 and p13II are accessory proteins encoded by the X region of bovine leukemia virus and human T-cell leukemia virus type 1 (HTLV-1), respectively. Disruption of the G4 and p13II open reading frames interferes with viral spread in animal model systems, indicating that the corresponding proteins play a key role in viral replication. In addition, G4 is oncogenic in primary cell cultures and is absolutely required for efficient onset of leukemogenesis in sheep. To gain insight into the function of these proteins, we utilized the yeast two-hybrid system to identify protein partners of G4. Results revealed that G4 interacts with farnesyl pyrophosphate synthetase (FPPS), a protein involved in the mevalonate/squalene pathway and in synthesis of FPP, a substrate required for prenylation of Ras. The specificity of the interaction was verified by glutathione S-transferase (GST) pull-down assays and by coimmunoprecipitation experiments. Furthermore, confocal microscopy showed that the subcellular localization of G4 was profoundly affected by FPPS. The G4 protein itself was not prenylated, at least in rabbit reticulocyte lysate-based assays. The domain of G4 required for binding to FPPS was restricted to an amphipathic ?-helix rich in arginine residues. Subtle mutation of this ?-helix abrogated G4 oncogenic potential in vitro, providing a biological relevance for FPPS-G4 complex formation in cells. Finally, HTLV-1 p13II was also found to specifically interact with FPPS (in yeast as well as in GST pull-down assays) and to colocalize with G4 in mitochondria, suggesting a functional analogy between these oncoviral accessory proteins. Identification of FPPS as a molecular partner for p13II and G4 accessory proteins opens new prospects for treatment of retrovirus-induced leukemia. PMID:11773414

Lefbvre, Laurent; Vanderplasschen, Alain; Ciminale, Vincenzo; Heremans, Hubertine; Dangoisse, Olivier; Jauniaux, Jean-Claude; Toussaint, Jean-Franois; Zelnik, Vlado; Burny, Arsne; Kettmann, Richard; Willems, Luc

2002-01-01

124

Exploring hydrophobic subdomain IIA of the protein bovine serum albumin in the native, intermediate, unfolded, and refolded states by a small fluorescence molecular reporter.  

PubMed

A simple intramolecular charge transfer (ICT) compound, 5-(4-dimethylamino-phenyl)-penta-2,4-dienoic acid methyl ester (DPDAME), has been documented to be a potential molecular reporter for probing microheterogeneous environments of a model transport protein bovine serum albumin (BSA) using spectroscopic techniques. Meteoric modifications to the emission profile of DPDAME upon addition of BSA come out to be a result of its binding to hydrophobic subdomain IIA. The highly polarity-sensitive ICT emission of DPDAME is found to be a proficient extrinsic molecular reporter for efficient mapping of native, intermediate, unfolded, and refolded states of the protein. Experimental data coupled with a reinforcing support from theoretical simulation using CHARMM22 software confirm the binding site of the probe to be the subdomain IIA of BSA, while FRET study reveals a remarkably close approach of our extrinsic molecular reporter to Trp-212 (in domain IIA): the distance between DPDAME and Trp-212 is 1.437 nm. The caliber of DPDAME as an external fluorescence marker also extends to the depiction of protein-surfactant (BSA-SDS) interaction to commendable fruition. Additionally, the protective action of small amounts of SDS on urea-denatured protein is documented by polarity-sensitive ICT emission of the probe. The present study also reflects the enhancement of the stability of BSA with respect to chemically induced denaturation by urea as a result of binding to the probe DPDAME. PMID:20397640

Paul, Bijan Kumar; Samanta, Anuva; Guchhait, Nikhil

2010-05-13

125

Increasing the X-ray Diffraction Power of Protein Crystals by Dehydration: The Case of Bovine Serum Albumin and a Survey of Literature Data  

PubMed Central

Serum albumin is one of the most widely studied proteins. It is the most abundant protein in plasma with a typical concentration of 5 g/100 mL and the principal transporter of fatty acids in plasma. While the crystal structures of human serum albumin (HSA) free and in complex with fatty acids, hemin, and local anesthetics have been characterized, no crystallographic models are available on bovine serum albumin (BSA), presumably because of the poor diffraction power of existing hexagonal BSA crystals. Here, the crystallization and diffraction data of a new BSA crystal form, obtained by the hanging drop method using MPEG 5K as precipitating agent, are presented. The crystals belong to space group C2, with unit-cell parameters a = 216.45 , b = 44.72 , c = 140.18 , ? = 114.5. Dehydration was found to increase the diffraction limit of BSA crystals from ~8 to 3.2 , probably by improving the packing of protein molecules in the crystal lattice. These results, together with a survey of more than 60 successful cases of protein crystal dehydration, confirm that it can be a useful procedure to be used in initial screening as a method of improving the diffraction limits of existing crystals. PMID:22489183

Krauss, Irene Russo; Sica, Filomena; Mattia, Carlo Andrea; Merlino, Antonello

2012-01-01

126

sup 1 H NMR study of the influence of hydrophobic contacts on protein-prosthetic group recognition in bovine and rat ferricytochrome b sub 5  

SciTech Connect

The proton nuclear magnetic resonance spectra of the soluble fragment of native bovine and genetically engineered wild-type rat ferricytochrome b{sub 5} reconstituted with a wide variety of hemes chemically modified at 2- and/or 4-positions have been recorded and analyzed. While all but one nonsymmetric heme yielded comparable amounts of the two heme orientations immediately after reconstitution, the relative proportion of the two orientations at equilibrium varied widely. The unpaired spin density distribution in the heme {pi} system leads to substituent hyperfine shift patterns in these paramagnetic complexes that are completely diagnostic of the heme orientation in the protein matrix. An empirical assignment strategy is outlined and applied which allows unequivocal assignment of the absolute orientation of a derivatized heme within the protein matrix. Using a series of hemes lacking 2-fold symmetry solely due to a single substitution, the preferences for localized site occupation of vinyls, methyls, and hydrogens are developed. The differences in this heme orientational preference among bovine, rat, and chicken ferricytochromes b{sub 5} could be correlated with the relative steric bulk of the residues at positions 23 and 25. Detailed thermodynamic analysis of the orientational preferences of native protoheme reveals that, while the same orientation as found in X-ray crystal structures of bovine cytochrome b{sub 5} predominate at 25{degree}C in both proteins, the preference in the bovine protein is primarily for enthalpic reasons while in the rat protein the preference is due to entropic factors.

Lee, K-B.; La Mar, G.N.; Kehres, L.A.; Fujinari, E.M.; Smith, K.M. (Univ. of California, Davis (USA)); Pochapsky, T.C.; Sligar, S.G. (Univ. of Illinois, Urbana (USA))

1990-10-01

127

A novel in vitro bovine cartilage punch model for assessing the regeneration of focal cartilage defects with biocompatible bacterial nanocellulose  

PubMed Central

Introduction Current therapies for articular cartilage defects fail to achieve qualitatively sufficient tissue regeneration, possibly because of a mismatch between the speed of cartilage rebuilding and the resorption of degradable implant polymers. The present study focused on the self-healing capacity of resident cartilage cells in conjunction with cell-free and biocompatible (but non-resorbable) bacterial nanocellulose (BNC). This was tested in a novel in vitro bovine cartilage punch model. Methods Standardized bovine cartilage discs with a central defect filled with BNC were cultured for up to eight weeks with/without stimulation with transforming growth factor-?1 (TGF-?1. Cartilage formation and integrity were analyzed by histology, immunohistochemistry and electron microscopy. Content, release and neosynthesis of the matrix molecules proteoglycan/aggrecan, collagen II and collagen I were also quantified. Finally, gene expression of these molecules was profiled in resident chondrocytes and chondrocytes migrated onto the cartilage surface or the implant material. Results Non-stimulated and especially TGF-?1-stimulated cartilage discs displayed a preserved structural and functional integrity of the chondrocytes and surrounding matrix, remained vital in long-term culture (eight weeks) without signs of degeneration and showed substantial synthesis of cartilage-specific molecules at the protein and mRNA level. Whereas mobilization of chondrocytes from the matrix onto the surface of cartilage and implant was pivotal for successful seeding of cell-free BNC, chondrocytes did not immigrate into the central BNC area, possibly due to the relatively small diameter of its pores (2 to 5 ?m). Chondrocytes on the BNC surface showed signs of successful redifferentiation over time, including increase of aggrecan/collagen type II mRNA, decrease of collagen type I mRNA and initial deposition of proteoglycan and collagen type II in long-term high-density pellet cultures. Although TGF-?1 stimulation showed protective effects on matrix integrity, effects on other parameters were limited. Conclusions The present bovine cartilage punch model represents a robust, reproducible and highly suitable tool for the long-term culture of cartilage, maintaining matrix integrity and homoeostasis. As an alternative to animal studies, this model may closely reflect early stages of cartilage regeneration, allowing the evaluation of promising biomaterials with/without chondrogenic factors. PMID:23673274

2013-01-01

128

A bovine model of respiratory Chlamydia psittaci infection: challenge dose titration.  

PubMed

This study aimed to establish and evaluate a bovine respiratory model of experimentally induced acute C. psittaci infection. Calves are natural hosts and pathogenesis may resemble the situation in humans. Intrabronchial inoculation of C. psittaci strain DC15 was performed in calves aged 2-3 months via bronchoscope at four different challenge doses from 10(6) to 10(9) inclusion-forming units (ifu) per animal. Control groups received either UV-inactivated C. psittaci or cell culture medium. While 10(6) ifu/calf resulted in a mild respiratory infection only, the doses of 10(7) and 10(8) induced fever, tachypnea, dry cough, and tachycardia that became apparent 2-3 days post inoculation (dpi) and lasted for about one week. In calves exposed to 10(9) ifu C. psittaci, the respiratory disease was accompanied by severe systemic illness (apathy, tremor, markedly reduced appetite). At the time point of most pronounced clinical signs (3 dpi) the extent of lung lesions was below 10% of pulmonary tissue in calves inoculated with 10(6) and 10(7) ifu, about 15% in calves inoculated with 10(8) and more than 30% in calves inoculated with 10(9) ifu C. psittaci. Beside clinical signs and pathologic lesions, the bacterial load of lung tissue and markers of pulmonary inflammation (i.e., cell counts, concentration of proteins and eicosanoids in broncho-alveolar lavage fluid) were positively associated with ifu of viable C. psittaci. While any effect of endotoxin has been ruled out, all effects could be attributed to infection by the replicating bacteria. In conclusion, the calf represents a suitable model of respiratory chlamydial infection. Dose titration revealed that both clinically latent and clinically manifest infection can be reproduced experimentally by either 10(6) or 10(8) ifu/calf of C. psittaci DC15 while doses above 10(8) ifu C. psittaci cannot be recommended for further studies for ethical reasons. This defined model of different clinical expressions of chlamydial infection allows studying host-pathogen interactions. PMID:22299031

Reinhold, Petra; Ostermann, Carola; Liebler-Tenorio, Elisabeth; Berndt, Angela; Vogel, Anette; Lambertz, Jacqueline; Rothe, Michael; Rttger, Anke; Schubert, Evelyn; Sachse, Konrad

2012-01-01

129

SimulatingWater MOLECULAR DYNAMICS MODEL of bovine pancreatic  

E-print Network

of water that would scarcely wet the point of a pin. The money was not to buy the vanish- ingly small is found in the pancreases of cattle. BPTI is a fa- vorite subject of computer modelers simply because

Levitt, Michael

130

Comparative Protein Structure Modeling Using Modeller  

PubMed Central

Functional characterization of a protein sequence is one of the most frequent problems in biology. This task is usually facilitated by accurate three-dimensional (3-D) structure of the studied protein. In the absence of an experimentally determined structure, comparative or homology modeling can sometimes provide a useful 3-D model for a protein that is related to at least one known protein structure. Comparative modeling predicts the 3-D structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described. PMID:18428767

Eswar, Narayanan; Marti-Renom, Marc A.; Madhusudhan, M.S.; Eramian, David; Shen, Min-yi; Pieper, Ursula

2014-01-01

131

Identification of low-abundance proteins of bovine colostral and mature milk using two-dimensional electrophoresis followed by microsequencing and mass spectrometry.  

PubMed

We identified several low-abundance proteins of bovine colostrum and mature milk using the immunoabsorption technique and two-dimensional electrophoresis (2-DE) followed by microsequencing and mass spectrometry. Two major milk proteins, beta-casein and immunoglobulin G (IgG), were effectively removed from the milk using immunoabsorbents. Milk samples before and after immunoabsorption were separated by 2-DE. Protein identification of the spots on 2-DE was performed by either gel comparison, microsequencing, matrix-assisted laser desorption/ionization-time of flight mass-spectrometry (MALDI-TOF-MS), peptide mass fingerprinting or peptide sequencing using tandem MS by hybrid quadrupole/orthogonal acceleration time of flight-MS (Q-TOF). Significant differences in protein patterns were observed between the low-abundance proteins of colostrum and mature milk. In addition, several low-abundance proteins including fibrinogen beta-chain, chitinase 3-like 1, alpha-antitrypsin, complement C3 alpha-chain, gelsolin and apolipoprotein H were observed only in colostrum. However, the level of beta-casein fragments increased significantly during this lactation period. alpha-Lactalbumin and beta-lactoglobulin as well as some low-abundance proteins including bovine serum albumin, serotransferrin and lactoferrin were identified in both colostral and mature milk. Low-abundance proteins in bovine colostrum may have special physiologic relevance to the health and development of calves early in lactation. PMID:11981865

Yamada, Masamichi; Murakami, Kouki; Wallingford, John C; Yuki, Yoshikazu

2002-04-01

132

Identification of immune genes and proteins involved in the response of bovine mammary tissue to Staphylococcus aureus infection  

PubMed Central

Background Mastitis in dairy cattle results from infection of mammary tissue by a range of micro-organisms but principally coliform bacteria and Gram positive bacteria such as Staphylococcus aureus. The former species are often acquired by environmental contamination while S. aureus is particularly problematic due to its resistance to antibiotic treatments and ability to reside within mammary tissue in a chronic, subclinical state. The transcriptional responses within bovine mammary epithelial tissue subjected to intramammary challenge with S. aureus are poorly characterised, particularly at the earliest stages of infection. Moreover, the effect of infection on the presence of bioactive innate immune proteins in milk is also unclear. The nature of these responses may determine the susceptibility of the tissue and its ability to resolve the infection. Results Transcriptional profiling was employed to measure changes in gene expression occurring in bovine mammary tissues sampled from three dairy cows after brief and graded intramammary challenges with S. aureus. These limited challenges had no significant effect on the expression pattern of the gene encoding ?-casein but caused coordinated up-regulation of a number of cytokines and chemokines involved in pro-inflammatory responses. In addition, the enhanced expression of two genes, S100 calcium-binding protein A12 (S100A12) and Pentraxin-3 (PTX3) corresponded with significantly increased levels of their proteins in milk from infected udders. Both genes were shown to be expressed by mammary epithelial cells grown in culture after stimulation with lipopolysaccharide. There was also a strong correlation between somatic cell count, a widely used measure of mastitis, and the level of S100A12 in milk from a herd of dairy cows. Recombinant S100A12 inhibited growth of Escherichia coli in vitro and recombinant PTX3 bound to E. coli as well as C1q, a subunit of the first component of the complement cascade. Conclusion The transcriptional responses in infected bovine mammary tissue, even at low doses of bacteria and short periods of infection, probably reflect the combined contributions of gene expression changes resulting from the activation of mammary epithelial cells and infiltrating immune cells. The secretion of a number of proinflammatory cytokines and chemokines from mammary epithelial cells stimulated by the bacteria serves to trigger the recruitment and activation of neutrophils in mammary tissue. The presence of S100A12 and PTX3 in milk from infected udder quarters may increase the anti-bacterial properties of milk thereby helping to resolve the mammary tissue infection as well as potentially contributing to the maturation of the newborn calf epithelium and establishment of the newborn gut microbial population. PMID:18513449

Lutzow, Ylva C Strandberg; Donaldson, Laurelea; Gray, Christian P; Vuocolo, Tony; Pearson, Roger D; Reverter, Antonio; Byrne, Keren A; Sheehy, Paul A; Windon, Ross; Tellam, Ross L

2008-01-01

133

Bovine adipose triglyceride lipase is not altered and adipocyte fatty acid binding protein is increased by dietary flaxseed  

Technology Transfer Automated Retrieval System (TEKTRAN)

In this paper, we report the full length coding sequence of bovine ATGL cDNA are reported and analyze its expression in bovine tissues. Similar to human, mouse, and pig ATGL sequences, bovine ATGL has a highly conserved patatin domain that is necessary for lipolytic function in mice and humans. Thi...

134

High-resolution X-ray crystal structure of bovine H-protein using the high-pressure cryocooling method  

PubMed Central

Recently, many technical improvements in macromolecular X-ray crystallography have increased the number of structures deposited in the Protein Data Bank and improved the resolution limit of protein structures. Almost all high-resolution structures have been determined using a synchrotron radiation source in conjunction with cryocooling techniques, which are required in order to minimize radiation damage. However, optimization of cryoprotectant conditions is a time-consuming and difficult step. To overcome this problem, the high-pressure cryocooling method was developed (Kim et al., 2005 ?) and successfully applied to many protein-structure analyses. In this report, using the high-pressure cryocooling method, the X-ray crystal structure of bovine H-protein was determined at 0.86? resolution. Structural comparisons between high- and ambient-pressure cryocooled crystals at ultra-high resolution illustrate the versatility of this technique. This is the first ultra-high-resolution X-ray structure obtained using the high-pressure cryocooling method. PMID:24121354

Higashiura, Akifumi; Ohta, Kazunori; Masaki, Mika; Sato, Masaru; Inaka, Koji; Tanaka, Hiroaki; Nakagawa, Atsushi

2013-01-01

135

Evaluation of Multiplexed Foot-and-Mouth Disease Nonstructural Protein Antibody Assay Against Standardized Bovine Serum Panel  

SciTech Connect

Liquid array technology has previously been used to show proof-of-principle of a multiplexed non structural protein serological assay to differentiate foot-and-mouth infected and vaccinated animals. The current multiplexed assay consists of synthetically produced peptide signatures 3A, 3B and 3D and recombinant protein signature 3ABC in combination with four controls. To determine diagnostic specificity of each signature in the multiplex, the assay was evaluated against a naive population (n = 104) and a vaccinated population (n = 94). Subsequently, the multiplexed assay was assessed using a panel of bovine sera generated by the World Reference Laboratory for foot-and-mouth disease in Pirbright, UK. This sera panel has been used to assess the performance of other singleplex ELISA-based non-structural protein antibody assays. The 3ABC signature in the multiplexed assay showed comparative performance to a commercially available non-structural protein 3ABC ELISA (Cedi test{reg_sign}) and additional information pertaining to the relative diagnostic sensitivity of each signature in the multiplex is acquired in one experiment. The encouraging results of the evaluation of the multiplexed assay against a panel of diagnostically relevant samples promotes further assay development and optimization to generate an assay for routine use in foot-and-mouth disease surveillance.

Perkins, J; Parida, S; Clavijo, A

2007-05-14

136

Improvement of gluten-free bread properties by the incorporation of bovine plasma proteins and different saccharides into the matrix.  

PubMed

The aim of this work was to improve the quality of gluten-free bread, incorporating plasma bovine proteins concentrated by ultrafiltration and freeze-dried with saccharides (inulin and sucrose). The influence of these compounds on textural properties and final bread quality was assessed. The textural studies revealed that with the addition of proteins and inulin, homogeneous and smaller air cells were achieved improving the textural properties while the bread hardness was comparable with breads with gluten. The volume of gluten-free breads increased with increasing proteins and inulin concentrations, reaching a maximum at a protein concentration of 3.5% (w/w). The addition of the enhancers improved moisture retention of the loaves after cooking and an increase of lightness of crumb with respect to the control was observed. The sensory analysis found no statistically significant difference in sensory attributes evaluated with respect to the control, so these ingredients do not negatively affect the organoleptic properties of bread. PMID:25306343

Rodriguez Furln, Laura T; Prez Padilla, Antonio; Campderrs, Mercedes E

2015-03-01

137

Bovine Brain Diacylglycerol Lipase: Substrate Specificity and Activation by Cyclic AMP-dependent Protein Kinase  

Microsoft Academic Search

Diacylglycerol lipase (EC 3.1.1.3) was purified from bovine brain microsomes using multiple column chromatographic techniques.\\u000a The purified enzyme migrates as a single band on SDS-PAGE and has an apparent molecular weight of 27kDa. Substrate specificity\\u000a experiments using mixed molecular species of 1,2-diacyl-sn-glycerols indicate that low concentrations of Ca2+ and Mg2+ have no direct effect on enzymic activity and 1,2-diacyl-sn-glycerols are

Thad A. Rosenberger; Akhlaq A. Farooqui; Lloyd A. Horrocks

2007-01-01

138

Bovine Ephemeral Fever Rhabdovirus ?1 Protein Has Viroporin-Like Properties and Binds Importin ?1 and Importin 7  

PubMed Central

ABSTRACT Bovine ephemeral fever virus (BEFV) is an arthropod-borne rhabdovirus that is classified as the type species of the genus Ephemerovirus. In addition to the five canonical rhabdovirus structural proteins (N, P, M, G, and L), the large and complex BEFV genome contains several open reading frames (ORFs) between the G and L genes (?1, ?2/?3, ?, and ?) encoding proteins of unknown function. We show that the 10.5-kDa BEFV ?1 protein is expressed in infected cells and, consistent with previous predictions based on its structure, has the properties of a viroporin. Expression of a BEFV ?1-maltose binding protein (MBP) fusion protein in Escherichia coli was observed to inhibit cell growth and increase membrane permeability to hygromycin B. Increased membrane permeability was also observed in BEFV-infected mammalian cells (but not cells infected with an ?1-deficient BEFV strain) and in cells expressing a BEFV ?1-green fluorescent protein (GFP) fusion protein, which was shown by confocal microscopy to localize to the Golgi complex. Furthermore, the predicted C-terminal cytoplasmic domain of ?1, which contains a strong nuclear localization signal (NLS), was translocated to the nucleus when expressed independently, and in an affinity chromatography assay employing a GFP trap, the full-length ?1 was observed to interact specifically with importin ?1 and importin 7 but not with importin ?3. These data suggest that, in addition to its function as a viroporin, BEFV ?1 may modulate components of nuclear trafficking pathways, but the specific role thereof remains unclear. IMPORTANCE PMID:24257609

Joubert, D. Albert; Blasdell, Kim R.; Audsley, Michelle D.; Trinidad, Lee; Monaghan, Paul; Dave, Keyur A.; Lieu, Kim G.; Amos-Ritchie, Rachel; Jans, David A.; Moseley, Gregory W.; Gorman, Jeffrey J.

2014-01-01

139

Bovine viral diarrhea virus 2 infection activates the unfolded protein response in MDBK cells, leading to apoptosis.  

PubMed

Bovine viral diarrhea virus 2 (BVDV-2) strains are divided into cytopathic and non-cytopathic biotypes based on the ablity to induce cytopathic effects in cultured cells. The mechanism of cytopathogenicity of BVDV-2 is not well understood. We examined cytopathogenesis in MDBK cells resulting from BVDV-2 infections by microscopic examinations and microarray analysis. We found that BVDV-2 activates endoplasmic reticulum (ER) stress signaling pathways that contribute to apoptosis of infected cells. We also monitored the expression of ER stress marker gene by RT-PCR during BVDV-2 infection and demonstrated that infection of MDBK cells with a cytopathic strain of BVDV-2 induces glucose-regulated protein 78 expression. Infection with BVDV-2 also induces DNA-damage-inducible transcript 3 expression and downregulates the lectin-galactoside-binding soluble 1 level. These results show that cytopathic strains of BVDV-2 induce an ER stress response resulting in apoptosis. PMID:19578292

Maeda, Kouji; Fujihara, Masatoshi; Harasawa, Ry

2009-06-01

140

Modeling Protein Self Assembly  

ERIC Educational Resources Information Center

Understanding the structure and function of proteins is an important part of the standards-based science curriculum. Proteins serve vital roles within the cell and malfunctions in protein self assembly are implicated in degenerative diseases. Experience indicates that this topic is a difficult one for many students. We have found that the concept

Baker, William P.; Jones, Carleton Buck; Hull, Elizabeth

2004-01-01

141

Cellular distribution of bovine leukemia virus proteins gp51SU, Pr72 env, and Pr66 gag-pro in persistently infected cells  

Microsoft Academic Search

Monoclonal antibodies (mAbs) against bovine leukemia virus (BLV) mature proteins and precursors were used to map the localization of these proteins in persistently infected non-lymphocytic cell lines using immunofluorescence assay (IFA) and immuno-electron microscopy. IFA staining was observed in the basolateral surface of live FLK-BLV cells. When using a mAb against Pr66gag-pro, mottled pinpoint fluorescence was seen in the cell

Louie Llames; Joaquin Goyache; Ana Domenech; Ana V Montaa; Guillermo Suarez; Esperanza Gomez-Lucia

2001-01-01

142

Protein Hydration Dynamics in Aqueous Solution: A Comparison of Bovine Pancreatic Trypsin Inhibitor and Ubiquitin by Oxygen17 Spin Relaxation Dispersion  

Microsoft Academic Search

Water oxygen-17 spin relaxation was used to study hydration and dynamcs of the globular proteins bovine pancreatic trypsin inhibitor (BPTI) and ubiquitin in aqueous solution. The frequency dispersion of the longitudinal and transverse relaxation rates was measured over the Larmor frequency range 2.6 to 49|4ru|MHz in the pD range 2 to 11 at 27C. While the protein-induced relaxation enhancement was

Vladimir P. Denisov; Bertil Halle

1995-01-01

143

Cell Arrest and Cell Death in Mammalian Preimplantation Development: Lessons from the Bovine Model  

PubMed Central

Background The causes, modes, biological role and prospective significance of cell death in preimplantation development in humans and other mammals are still poorly understood. Early bovine embryos represent a very attractive experimental model for the investigation of this fundamental and important issue. Methods and Findings To obtain reference data on the temporal and spatial occurrence of cell death in early bovine embryogenesis, three-dimensionally preserved embryos of different ages and stages of development up to hatched blastocysts were examined in toto by confocal laser scanning microscopy. In parallel, transcript abundance profiles for selected apoptosis-related genes were analyzed by real-time reverse transcriptase-polymerase chain reaction. Our study documents that in vitro as well as in vivo, the first four cleavage cycles are prone to a high failure rate including different types of permanent cell cycle arrest and subsequent non-apoptotic blastomere death. In vitro produced and in vivo derived blastocysts showed a significant incidence of cell death in the inner cell mass (ICM), but only in part with morphological features of apoptosis. Importantly, transcripts for CASP3, CASP9, CASP8 and FAS/FASLG were not detectable or found at very low abundances. Conclusions In vitro and in vivo, errors and failures of the first and the next three cleavage divisions frequently cause immediate embryo death or lead to aberrant subsequent development, and are the main source of developmental heterogeneity. A substantial occurrence of cell death in the ICM even in fast developing blastocysts strongly suggests a regular developmentally controlled elimination of cells, while the nature and mechanisms of ICM cell death are unclear. Morphological findings as well as transcript levels measured for important apoptosis-related genes are in conflict with the view that classical caspase-mediated apoptosis is the major cause of cell death in early bovine development. PMID:21811561

Leidenfrost, Sandra; Boelhauve, Marc; Reichenbach, Myriam; Gngr, Tuna; Reichenbach, Horst-Dieter; Sinowatz, Fred; Wolf, Eckhard; Habermann, Felix A.

2011-01-01

144

Primary structure of bovine pituitary secretory protein I (chromogranin A) deduced from the cDNA sequence  

SciTech Connect

Secretory protein I (SP-I), also referred to as chromogranin A, is an acidic glycoprotein that has been found in every tissue of endocrine and neuroendocrine origin examined but never in exocrine or epithelial cells. Its co-storage and co-secretion with peptide hormones and neurotransmitters suggest that it has an important endocrine or secretory function. The authors have isolated cDNA clones from a bovine pituitary lambdagt11 expression library using an antiserum to parathyroid SP-I. The largest clone (SP4B) hybridized to a transcript of 2.1 kilobases in RNA from parathyroid, pituitary, and adrenal medulla. Immunoblots of bacterial lysates derived from SP4B lysognes demonstrated specific antibody binding to an SP4B/..beta..-galactosidase fusion protein (160 kDa) with a cDNA-derived component of 46 kDa. Radioimmunoassay of the bacterial lystates with SP-I antiserum yielded parallel displacement curves of /sup 125/I-labeled SP-I by the SP4B lysate and authentic SP-I. SP4B contains a cDNA of 1614 nucleotides that encodes a 449-amino acid protein (calculated mass, 50 kDa). The nucleotide sequences of the pituitary SP-I cDNA and adrenal medullary SP-I cDNAs are nearly identical. Analysis of genomic DNA suggests that pituitary, adrenal, and parathyroid SP-I are products of the same gene.

Ahn, T.G.; Cohn, D.V.; Gorr, S.U.; Ornstein, D.L.; Kashdan, M.A.; Levine, M.A.

1987-07-01

145

Investigation of the binding of Cr(III) complexes to bovine and human serum proteins: a proteomic approach.  

PubMed

Chromium (Cr) compounds are widely used in alloys manufacturing and forming processes. One of the main concerns in the use of cobalt-chromium (Co-Cr) alloy-based implants is the long-term fate of Co and Cr ions in the blood, organs, and urine of patients. Our previous studies have shown that Cr(III) forms complexes in different cell culture media, whereas Cr(VI) does not form any detectable structure under the same conditions. Because Cr(VI) is known to be more toxic than Cr(III), we hypothesized that the presence of serum proteins in the molecular structure of Cr(III) may be responsible for the difference in toxicity. We investigated the interaction of the Cr(III) complexes with serum proteins and their internalization by U937 macrophage-like cells. By using a proteomic approach, we showed that in the presence of fetal bovine serum, Cr(III) complexes interacted only with albumin, whereas they interacted mainly with albumin, transferrin, and immunoglobulins (Ig) in the presence of human serum (HS). Cr(III) complexes were more easily engulfed by U937 macrophage-like cells when they were formed with HS. To the best of our knowledge, this is the first report on the formation of Cr(III) complexes in the presence of serum proteins and the interaction of these complexes with U937 macrophage-like cells. (c) 2010 Wiley Periodicals, Inc. J Biomed Mater Res, 2010. PMID:20166223

Tkaczyk, Cathy; Huk, Olga L; Mwale, Fackson; Antoniou, John; Zukor, David J; Petit, Alain; Tabrizian, Maryam

2010-07-01

146

Protein  

MedlinePLUS

... juvenile or insulin-dependent diabetes), proteins found in cows milk have been implicated in the development of ... O., et al., Removal of Bovine Insulin From Cows Milk Formula and Early Initiation of Beta-Cell ...

147

Optimization and characterization of an in vitro bovine mammary cell culture system to study regulation of milk protein synthesis and mammary differentiation  

SciTech Connect

A long term bovine mammary cell culture system that maintains normal mammary cell function was established and optimized to study milk protein synthesis and secretion and mammary differentiation. This culture system used bovine mammary acini isolated from developing or lactating mammary gland by enzymatic dissociation, and cryopreserved until thawed and plated for growth in vitro for these studies. Cells in M199 with lactogenic hormones {plus minus} fetal calf serum (FCS) were cultured on plastic, 100ul and 500ul type I collagen, and Matrigel, or embedded within type I collagen. Cell morphology, cell number, and total TCA-precipitable {sup 35}S-labelled proteins were monitored. Milk protein ({alpha}{sub s,1}-casein, lactoferrin (LF), {alpha}-lactalbumin, and {beta}-lactoglobulin) secretion and intracellular levels were determined by an ELISA assay.

Talhouk, R.S.

1988-01-01

148

Economic risk analysis model for bovine viral diarrhea virus biosecurity in cow-calf herds.  

PubMed

A stochastic model was designed to calculate the cost-effectiveness of biosecurity strategies for bovine viral diarrhea virus (BVDV) in cow-calf herds. Possible sources of BVDV introduction considered were imported animals, including the calves of pregnant imports, and fenceline contact with infected herds, including stocker cattle raised in adjacent pastures. Spread of BVDV through the herd was modeled with a stochastic SIR model. Financial consequences of BVDV, including lost income, treatment costs, and the cost of biosecurity strategies, were calculated for 10 years, based on the risks of a herd with a user-defined import profile. Results indicate that importing pregnant animals and stockers increased the financial risk of BVDV. Strategic testing in combination with vaccination most decreased the risk of high-cost outbreaks in most herds. The choice of a biosecurity strategy was specific to the risks of a particular herd. PMID:24360189

Smith, Rebecca L; Sanderson, Michael W; Jones, Rodney; N'Guessan, Yapo; Renter, David; Larson, Robert; White, Brad J

2014-03-01

149

Molecular modelling of protein-protein/protein-solvent interactions  

NASA Astrophysics Data System (ADS)

The inner workings of individual cells are based on intricate networks of protein-protein interactions. However, each of these individual protein interactions requires a complex physical interaction between proteins and their aqueous environment at the atomic scale. In this thesis, molecular dynamics simulations are used in three theoretical studies to gain insight at the atomic scale about protein hydration, protein structure and tubulin-tubulin (protein-protein) interactions, as found in microtubules. Also presented, in a fourth project, is a molecular model of solvation coupled with the Amber molecular modelling package, to facilitate further studies without the need of explicitly modelled water. Basic properties of a minimally solvated protein were calculated through an extended study of myoglobin hydration with explicit solvent, directly investigating water and protein polarization. Results indicate a close correlation between polarization of both water and protein and the onset of protein function. The methodology of explicit solvent molecular dynamics was further used to study tubulin and microtubules. Extensive conformational sampling of the carboxy-terminal tails of 8-tubulin was performed via replica exchange molecular dynamics, allowing the characterisation of the flexibility, secondary structure and binding domains of the C-terminal tails through statistical analysis methods. Mechanical properties of tubulin and microtubules were calculated with adaptive biasing force molecular dynamics. The function of the M-loop in microtubule stability was demonstrated in these simulations. The flexibility of this loop allowed constant contacts between the protofilaments to be maintained during simulations while the smooth deformation provided a spring-like restoring force. Additionally, calculating the free energy profile between the straight and bent tubulin configurations was used to test the proposed conformational change in tubulin, thought to cause microtubule destabilization. No conformational change was observed but a nucleotide dependent 'softening' of the interaction was found instead, suggesting that an entropic force in a microtubule configuration could be the mechanism of microtubule collapse. Finally, to overcome much of the computational costs associated with explicit soIvent calculations, a new combination of molecular dynamics with the 3D-reference interaction site model (3D-RISM) of solvation was integrated into the Amber molecular dynamics package. Our implementation of 3D-RISM shows excellent agreement with explicit solvent free energy calculations. Several optimisation techniques, including a new multiple time step method, provide a nearly 100 fold performance increase, giving similar computational performance to explicit solvent.

Luchko, Tyler

150

Unraveling the binding mechanism of polyoxyethylene sorbitan esters with bovine serum albumin: a novel theoretical model based on molecular dynamic simulations.  

PubMed

To gain a better understanding of the interactions governing the binding mechanism of proteins with non-ionic surfactants, the association processes of Tween 20 and Tween 80 with the bovine serum albumin (BSA) protein were investigated using molecular dynamics (MD) simulations. Protein:surfactant molar ratios were chosen according to the critical micelle concentration (CMC) of each surfactant in the presence of BSA. It was found that both the hydrophilic and the hydrophobic groups of the BSA equally contribute to the surface area of interaction with the non-ionic surfactants. A novel theoretical model for the interactions between BSA and these surfactants at the atomic level is proposed, where both surfactants bind to non-specific domains of the BSA three-dimensional structure mainly through their polyoxyethylene groups, by hydrogen bonds and van der Waals interactions. This is well supported by the strong electrostatic and van der Waals interaction energies obtained in the calculations involving surfactant polyoxyethylene groups and different protein regions. The results obtained from the MD simulations suggest that the formation of surfactant clusters over the BSA structure, due to further cooperative self-assembly of Tween molecules, could increase the protein conformational stability. These results extend the current knowledge on molecular interactions between globular proteins and non-ionic surfactants, and contribute to the fine-tuning design of protein formulations using polysorbates as excipients for minimizing the undesirable effects of protein adsorption and aggregation. PMID:24309134

Delgado-Magnero, Karelia H; Valiente, Pedro A; Ruiz-Pea, Miriam; Prez-Gramatges, Aurora; Pons, Tirso

2014-04-01

151

Effectiveness of extruded rapeseed associated with an alfalfa protein concentrate in enhancing the bovine milk fatty acid composition.  

PubMed

Linseed and rapeseed, good sources of 18:3 n-3 and cis9-18:1, respectively, have been shown to improve the bovine milk fatty acid (FA) profile. However, rapeseed, unlike linseed, has little effect on the concentration of 18:3 n-3 in milk fat. Alfalfa protein concentrate (APC), besides being a valuable protein source for milk production, contains lipids rich in 18:3 n-3. Therefore, this experiment aimed at (1) evaluating the transfer efficiency of unsaturated FA (UFA), especially 18:3 n-3, of APC to bovine milk fat, and (2) evaluating whether extruded rapeseed (ER) associated with APC is as effective as extruded linseed (EL) in enhancing the bovine milk fat composition. Six lactating Holstein cows were used in a replicated 2 2 Latin square design with 2 iso-energy, iso-nitrogen and iso-FA corn silage-based diets (EL and ER-APC) and two 21-d periods. Extruded linseed, as main UFA source, was included in the first diet, whereas ER, as main UFA source, and APC, as supplemental 18:3 n-3, were included in the second diet. Diets were distributed as a restricted total mixed ration. Compared with the EL diet, the ER-APC diet, where ER was associated with APC, increased milk concentration of 18:3 n-3 (1.18 vs. 1.31% of FA) and cis9-18:1 (18.35 vs. 20.01% of FA). The apparent transfer efficiency of 18:3 n-3 from diet to milk was almost twice as much for the ER-APC diet than for the EL diet (7.4 vs. 3.8% of intake). Extruded linseed accounted for 84% of 18:3 n-3 provided in the EL diet, whereas ER and APC accounted for 33 and 38% of 18:3 n-3 provided in the ER-APC diet, respectively. Because both EL and ER underwent extrusion in similar conditions, these results suggest that 18:3 n-3 of EL in the EL diet and ER in the ER-APC diet were subjected to more extensive ruminal biohydrogenation than 18:3 n-3 of APC in the ER-APC diet. This experiment shows that corn silage-based diets supplemented with ER as the main UFA source, associated with APC as supplemental 18:3 n-3, are as effective as corn silage-based diets supplemented with EL as the main UFA source, in increasing bovine milk UFA and 18:3 n-3 contents. Furthermore, at similar levels of dietary incorporation, this experiment shows that the ruminal bypass of 18:3 n-3 is higher for APC compared with EL. PMID:21787936

Dang Van, Q C; Bejarano, L; Mignolet, E; Coulmier, D; Froidmont, E; Larondelle, Y; Focant, M

2011-08-01

152

Effects of electrical stimulation high temperature pre-rigor conditioning on myofibrillar proteins of bovine muscle  

E-print Network

were electrophoretically separated on SDS gals and d nsitometrically quantitated to determine the effect of each treat- menp on the myofi'ori1lar proteins. To determine the effect of pH on myofibrillaz. proteins, eight stcznthmandibu1aris muscles... protein on SDS gels from myofibrils of high temperature conditioned ~l' *' . . 1 . *?d60 6. P 31 The relative percentage of each myofibrillar. protein on SDS gals from myofibrils of high temperature conditioned semimembranosus muscle removed 60 hr...

Adams, Keith LeRoy

2012-06-07

153

Proteins at interfaces : the adsorption of human plasma albumin and bovine pancreas ribonuclease on polystyrene latices  

Microsoft Academic Search

The adsorption from (aqueous) solution of proteins is very complex. The interfacial behaviour of proteins is determined by the properties of, and the mutual interactions between, the adsorbing interface, the protein molecules, the solvent (water) molecules and other solutes (e.g. ions). Virtually all kinds of interactions are involved, viz. electrostatic, hydrogen bonding, hydrophobic, van der Waals, etcetera.Due to the intricate

W. Norde

1976-01-01

154

Optimal concentration of hyaluronan and plant protein in different culture systems for in vitro maturation of bovine oocytes.  

PubMed

With a view to search for optimal concentration of hyaluronan (HA) and plant protein (PP) in different culture systems for in vitro maturation of bovine oocytes, cumulus-oocyte complexes (COCs) were matured in vitro in 2 culture systems (first co-cultured with granulose cells and estrus calf serum (ECS) in 2 mL volume, second without co-culture where ECS was replaced by exogenous hormones and BSA or PP in 100 microL dose under mineral oil). Seven types of media were used; 3 in first system and 4 in second system. To evaluate HA and PP effect on oocytes after in vitro culture an estimation of meiosis stage and a level of DNA fragmentation was performed by TUNEL staining. The highest meiotic maturation (84%) was observed in oocytes cultured in medium enriched with ECS in co-culture with granulose cells (1st system). The lowest meiotic maturation was noted in medium with addition of BSA (43%). The addition of HA in the medium enriched with BSA significantly increased the rate of matured oocytes (67%) and also didn't affect the chromatin quality of individual oocytes. The addition of HA to the culture medium supplemented with a PP decreased the rate of matured oocytes to 54% but no statistical differences were noted. The results of the present study showed that HA supplementation didn't have a detrimental impact on oocyte chromatin integrity and improved bovine oocytes' meiotic maturation in medium supplemented only with BSA without co-culture of granulose cells. PMID:23986966

Opiela, Jolanta; Latasiewicz, Ewa; Smorag, Zdzis?aw

2012-12-01

155

Bovine ephemeral fever rhabdovirus ?1 protein has viroporin-like properties and binds importin ?1 and importin 7.  

PubMed

Bovine ephemeral fever virus (BEFV) is an arthropod-borne rhabdovirus that is classified as the type species of the genus Ephemerovirus. In addition to the five canonical rhabdovirus structural proteins (N, P, M, G, and L), the large and complex BEFV genome contains several open reading frames (ORFs) between the G and L genes (?1, ?2/?3, ?, and ?) encoding proteins of unknown function. We show that the 10.5-kDa BEFV ?1 protein is expressed in infected cells and, consistent with previous predictions based on its structure, has the properties of a viroporin. Expression of a BEFV ?1-maltose binding protein (MBP) fusion protein in Escherichia coli was observed to inhibit cell growth and increase membrane permeability to hygromycin B. Increased membrane permeability was also observed in BEFV-infected mammalian cells (but not cells infected with an ?1-deficient BEFV strain) and in cells expressing a BEFV ?1-green fluorescent protein (GFP) fusion protein, which was shown by confocal microscopy to localize to the Golgi complex. Furthermore, the predicted C-terminal cytoplasmic domain of ?1, which contains a strong nuclear localization signal (NLS), was translocated to the nucleus when expressed independently, and in an affinity chromatography assay employing a GFP trap, the full-length ?1 was observed to interact specifically with importin ?1 and importin 7 but not with importin ?3. These data suggest that, in addition to its function as a viroporin, BEFV ?1 may modulate components of nuclear trafficking pathways, but the specific role thereof remains unclear. Although rhabdovirus accessory genes occur commonly among arthropod-borne rhabdoviruses, little is known of their functions. Here, we demonstrate that the BEFV ?1 ORF encodes a protein which has the structural and functional characteristics of a viroporin. We show that ?1 localizes in the Golgi complex and increases cellular permeability. We also show that BEFV ?1 binds importin ?1 and importin 7, suggesting that it may have a yet unknown role in modulating nuclear trafficking. This is the first functional analysis of an ephemerovirus accessory protein and of a rhabdovirus viroporin. PMID:24257609

Joubert, D Albert; Blasdell, Kim R; Audsley, Michelle D; Trinidad, Lee; Monaghan, Paul; Dave, Keyur A; Lieu, Kim G; Amos-Ritchie, Rachel; Jans, David A; Moseley, Gregory W; Gorman, Jeffrey J; Walker, Peter J

2014-02-01

156

Bovine Spongiform Encephalopathy  

Technology Transfer Automated Retrieval System (TEKTRAN)

Bovine spongiform encephalopathy (BSE) is caused by a novel contagion, known to as a prion. Prions are proteins capable of converting a normal cellular protein into a prion, thereby propagating an infection. BSE is the first known prion zoonotic. As such it has attracted broad scientific and, to a r...

157

Characterization of the Interaction between Eupatorin and Bovine Serum Albumin by Spectroscopic and Molecular Modeling Methods  

PubMed Central

This study investigated the interaction between eupatorin and bovine serum albumin (BSA) using ultraviolet-visible (UV-vis) absorption, fluorescence, synchronous fluorescence, circular dichroism (CD) spectroscopies, and molecular modeling at pH 7.4. Results of UV-vis and fluorescence spectroscopies illustrated that BSA fluorescence was quenched by eupatorin via a static quenching mechanism. Thermodynamic parameters revealed that hydrophobic and electrostatic interactions played major roles in the interaction. Moreover, the efficiency of energy transfer, and the distance between BSA and acceptor eupatorin, were calculated. The effects of eupatorin on the BSA conformation were analyzed using UV-vis, CD, and synchronous fluorescence. Finally, the binding of eupatorin to BSA was modeled using the molecular docking method. PMID:23839090

Xu, Hongliang; Yao, Nannan; Xu, Haoran; Wang, Tianshi; Li, Guiying; Li, Zhengqiang

2013-01-01

158

Characterization of the Interaction between Eupatorin and Bovine Serum Albumin by Spectroscopic and Molecular Modeling Methods.  

PubMed

This study investigated the interaction between eupatorin and bovine serum albumin (BSA) using ultraviolet-visible (UV-vis) absorption, fluorescence, synchronous fluorescence, circular dichroism (CD) spectroscopies, and molecular modeling at pH 7.4. Results of UV-vis and fluorescence spectroscopies illustrated that BSA fluorescence was quenched by eupatorin via a static quenching mechanism. Thermodynamic parameters revealed that hydrophobic and electrostatic interactions played major roles in the interaction. Moreover, the efficiency of energy transfer, and the distance between BSA and acceptor eupatorin, were calculated. The effects of eupatorin on the BSA conformation were analyzed using UV-vis, CD, and synchronous fluorescence. Finally, the binding of eupatorin to BSA was modeled using the molecular docking method. PMID:23839090

Xu, Hongliang; Yao, Nannan; Xu, Haoran; Wang, Tianshi; Li, Guiying; Li, Zhengqiang

2013-01-01

159

Development and utilization of a bovine type I collagen microfibril model.  

PubMed

The structure of fibrous collagen, a long triple helix that self-associates in a staggered array to form a matrix of fibrils, fibers and fiber bundles, makes it uniquely suitable as a scaffold for biomaterial engineering. A major challenge for this application is to stabilize collagen structure by means that are acceptable for the end use. The bovine type I collagen microfibril model, built by computer assisted modeling, comprised of five right-handed triple helices in a left-handed super coil containing gap and overlap regions as well as the nonhelical telopeptides is a tool for predicting or visualizing chemistry to stabilize the matrix, insert an active agent, or otherwise modify collagen. PMID:23131209

Brown, Eleanor M

2013-02-01

160

Generation of the Bovine Viral Diarrhea Virus E0 Protein in Transgenic Astragalus and Its Immunogenicity in Sika Deer  

PubMed Central

The bovine viral diarrhea virus (BVDV), a single-stranded RNA virus, can cause fatal diarrhea syndrome, respiratory problems, and reproductive disorders in herds. Over the past few years, it has become clear that the BVDV infection rates are increasing and it is likely that an effective vaccine for BVDV will be needed. In this study, transgenic Astragalus was used as an alternative productive platform for the expression of glycoprotein E0. The immunogenicity of glycoprotein E0 expressed in transgenic Astragalus was detected in deer. The presence of pBI121-E0 was confirmed by polymerase chain reaction (PCR), transcription was verified by reverse transcription- (RT-) PCR, and recombinant protein expression was confirmed by ELISA and Western blot analyses. Deer that were immunized subcutaneously with the transgenic plant vaccine developed specific humoral and cell-mediated immune responses against BVDV. This study provides a new method for a protein with weak immunogenicity to be used as part of a transgenic plant vaccine. PMID:24963321

Gao, Yugang; Zang, Pu; Liu, Qun; Wei, Gongqing

2014-01-01

161

Selective binding of proteins on functional nanoparticles via reverse charge parity model: an in vitro study  

NASA Astrophysics Data System (ADS)

The conformation of proteins absorbed on nanoparticles surface plays a crucial role in applications of nanoparticles in biomedicine. The surface protein conformation depends on several factors, namely, nature of protein-nanoparticles interaction, chemical composition of the surface of nanoparticles etc. A model of the electrostatic binding of proteins on charged surface nanoparticles has been proposed earlier (Ghosh et al 2013 Colloids Surf. B 103 267). Also, the irreversible denaturation of the protein conformation due to binding of counterions was reported. In this paper, we have used this model, involving reverse charge parity, to show selective binding of proteins on charged surface iron oxide nanoparticles (IONPs). IONPs were surface functionalized with cetylpyridinium chloride (CPC), cetyl(trimethyl)ammonium bromide (CTAB) and cetylpyridinium iodide (CPI). The effect of counterions (Cl-, Br- and I-) on protein conformation has also been investigated. Several proteins such as ?-lactalbumin (ALA), ?-lactoglobulin (BLG), ovalbumin (OVA), bovin serum albumin (BSA) and HEWL were chosen for this investigation.

Ghosh, Goutam; Panicker, Lata; Barick, K. C.

2014-03-01

162

Protein Model Database  

Microsoft Academic Search

The phenomenal success of the genome sequencing projects reveals the power of completeness in revolutionizing biological science. Currently it is possible to sequence entire organisms at a time, allowing for a systemic rather than fractional view of their organization and the various genome-encoded functions. There is an international plan to move towards a similar goal in the area of protein

K Fidelis; A Adzhubej; A Kryshtafovych; P Daniluk

2005-01-01

163

Random Analysis of Presence and Absence of Twoand Three-Amino-Acid Sequences and Distributions of Amino Acids, Two- and Three-Amino-Acid Sequences in Bovine p53 Protein  

E-print Network

In this study we use five probabilistic procedures to analyse the bovine p53 protein. (1) We count each kind of two-, three- and multi-amino-acid sequences along bovine p53 protein from one terminal to the other and calculate their frequencies and probabilities. (2) We compare the amino-acid sequences in bovine p53 protein with the theoretical amino-acid sequences and determine which theoretical amino-acid sequences are present and absent. (3) We use the random principle to predict the frequencies of presence and absence of amino-acid sequences in bovine p53 protein from its amino acid composition and compare the predicted frequencies with the counted frequencies. (4) We use the random principle to predict the probability that an amino acid follows a preceding amino acid and compare the predicted probabilities with the probabilities occurred in bovine p53 protein. (5) We use the random principle to predict the distributions of amino acids, two- and three-amino-acid sequences in bovine p53 protein and compare the predicted distributions with the measured distributions.

Guang Wu; Shaomin Yan

164

Mapping the calcification of bovine pericardium in rat model by enhanced micro-computed tomography.  

PubMed

The calcification initiation and progression of bioprosthetic heart valve were investigated in a rat model by enhanced micro-computed tomography, together with histologic study and scanning electron microscope analysis. The implantation data at early stage showed apparent dendritic patterns in the radiographic images for the glutaraldehyde-treated bovine pericardium and this dendritic pattern was verified to be associated with the vessel distribution in the tissue. Histologic study and scanning electron microscope analysis both indicated that the calcium deposits in the pericardium vessels regions were more grievous than those scattered in the collagen fibers in the first two weeks after implantation. Subsequently, calcification spreaded and the entire sample was severely calcified in 60 days. PMID:24973299

Liu, Jing; Zhong, Shengping; Lan, Hualin; Meng, Xu; Zhang, Haibo; Fan, Yubo; Wang, Yuxing; Wang, Chunren; Wang, Zhaoxu

2014-09-01

165

Molecular characterization of RNA and protein synthesis during a one-step growth curve of bovine viral diarrhoea virus in ovine (SFT-R) cells  

Microsoft Academic Search

The aim of this study was to determine the kinetics of noncytopathic bovine viral diarrhoea virus (BVDV) multiplication and synthesis of BVDV specific RNA and proteins in ovine cells (SFT-R) during a one-step growth curve. The virus titre and RNA level were determined by focus-forming assay and real time RT-PCR. The RNA synthesis was detected by Northern blot while synthesis

N. Mishra; B. S. Mathapati; K. Rajukumar; R. K. Nema; S. P. Behera; S. C. Dubey

2010-01-01

166

Immunohistochemical study of seminiferous epithelium in adult bovine testis using monoclonal antibodies against Ki67 protein and proliferating cell nuclear antigen (PCNA)  

Microsoft Academic Search

The distribution pattern of proliferating cell nuclear antigen (PCNA) and Ki-67 protein was studied in adult bovine seminiferous epithelium by means of immunohistochemistry using monoclonal antibodies. Tailoring the methodological protocol for each of the two proliferation markers was a necessary prerequisite for obtaining optimal results in tubular sections and whole-mounts. A-, I- and B-spermatogonia displayed PCNA-positive nuclei, except during meta-,

Karl-Heinz Wrobel; Daniela Bickel; Richard Kujat

1996-01-01

167

Evidence of a humoral immune response against the prokaryotic expressed N-terminal autoprotease (N pro ) protein of bovine viral diarrhoea virus  

Microsoft Academic Search

Bovine viral diarrhoea virus (BVDV) is an economically important pathogen of cattle and sheep belonging to the genus Pestivirus of the family Flaviviridae. Although the BVDV non-structural N-terminal protease (Npro) acts as an interferon antagonist and subverts the host innate immunity, little is known about its immunogenicity. Hence,\\u000a we expressed a recombinant BVDV Npro-His fusion protein (28 kDa) in E.

Niranjan Mishra; Katherukamem Rajukumar; Shruti Shrikant Pitale; Anil Prakash; Ram Kumar Nema; Sthita Pragnya Behera; Shiv Chandra Dubey

2010-01-01

168

The bovine fatty acid binding protein 4 gene is significantly associated with marbling and subcutaneous fat depth in Wagyu x Limousin F2 crosses  

Microsoft Academic Search

Fatty acid binding protein 4 (FABP4), which is expressed in adipose tissue, interacts with peroxisome proliferator-activated receptors and binds to hormone-sensitive lipase and therefore, plays an important role in lipid metabolism and homeostasis in adipocytes. The objective of this study was to investigate associations of the bovine FABP4 gene with fat deposition. Both cDNA and genomic DNA sequences of the

J J Michal; Z W Zhang; C T Gaskins; Z Jiang

2006-01-01

169

The Ca2+-binding sequence in bovine brain S100b protein beta-subunit. A spectroscopic study.  

PubMed Central

Conformational changes in the beta-subunit of the bovine brain Ca2+-binding protein S100b (S100-beta) accompanying Ca2+ binding were investigated by analysis of the spectroscopic properties of the single tyrosine residue (Tyr17 beta) and flow-dialysis binding experiments. S100-beta binds Ca2+ sequentially at two sites to change the conformation of the protein. The first Ca2+ ion binds to site II beta, a typical Ca2+-binding site in the C-terminal region, and it does not significantly perturb the proximal environment of Tyr17 beta. After the first site is occupied, another Ca2+ ion binds to the N-terminal Ca2+-binding site, I beta, and strengthens a hydrogen bond between Tyr17 beta and a neighbouring carboxylate acceptor group, which results in a large increase in the Tyr17 beta fluorescence spectrum half-width and a positive absorption and c.d. signal between 290 and 275 nm. Ca2+ binding to the S100b.Zn2+6 complex, studied by flow-dialysis and fluorescence measurements showed that, although Zn2+ ions increase the affinity of S100b protein for Ca2+, the Ca2+-binding sequence was not changed. Tb3+ (terbium ion) binding studies on the S100b.Zn2+6 complex proved that Tb3+ antagonizes only Ca2+ binding site II beta and confirmed the sequential occupation of Ca2+-binding sites on the S100b.Zn2+6 complex. PMID:2604719

Baudier, J; Cole, R D

1989-01-01

170

Antithrombin III and its interaction with heparin. Comparison of the human, bovine, and porcine proteins by /sup 1/H NMR spectroscopy  

SciTech Connect

/sup 1/H NMR has been used to characterize and compare the structures of antithrombin III from human, bovine, and porcine plasma as well as to investigate the interactions of each of these proteins with heparin fragments of defined length. The amino acid compositions of the three proteins are very similar, which is reflected in the gross features of their /sup 1/H NMR spectra. Human antithrombin III has five histidine residues, bovine has six, and porcine has five. The C(2) proton from each of these residues gives a narrow resonance and titrates with pH; the pK/sub a/'s are in the range 5.15-7.25. It is concluded that all histidines in each protein are surface residues with considerable independent mobility. The carbohydrate chains in each protein also give sharp resonances consistent with a surface location and motional flexibility. The /sup 1/H spectra are sensitive to heparin binding. Although heparin resonances obscure protein resonances in the region 3.2-6.0 ppm, difference spectra between antithrombin III with and without heparin show clear perturbation of a small number of aromatic and aliphatic protein protons. For human antithrombin III, it was shown that heparin fragments 8, 10, and 16 sugar residues in length result in almost identical perturbations to the protein. In contrast, tetrasaccharide results in fewer perturbations. Significantly, intact high molecular weight heparin causes the same spectral perturbations as the 16-residue fragment. These data are discussed in terms of requirements for heparin binding.

Gettins, P.

1987-03-10

171

Microtubule-associated protein tau in bovine retinal photoreceptor rod outer segments: comparison with brain tau  

PubMed Central

Recent studies have suggested a possible involvement of abnormal tau in some retinal degenerative diseases. The common view in these studies is that these retinal diseases share the mechanism of tau-mediated degenerative diseases in brain and that information about these brain diseases may be directly applied to explain these retinal diseases. Here we collectively examine this view by revealing three basic characteristics of tau in the rod outer segment (ROS) of bovine retinal photoreceptors, i.e., its isoforms, its phosphorylation mode and its interaction with microtubules, and by comparing them with those of brain tau. We find that ROS contains at least four isoforms: three are identical to those in brain and one is unique in ROS. All ROS isoforms, like brain isoforms, are modified with multiple phosphate molecules; however, ROS isoforms show their own specific phosphorylation pattern, and these phosphorylation patterns appear not to be identical to those of brain tau. Interestingly, some ROS isoforms, under the normal conditions, are phosphorylated at the sites identical to those in Alzheimers patient isoforms. Surprisingly, a large portion of ROS isoforms tightly associates with a membranous component(s) other than microtubules, and this association is independent of their phosphorylation states. These observations strongly suggest that tau plays various roles in ROS and that some of these functions may not be comparable to those of brain tau. We believe that knowledge about tau in the entire retinal network and/or its individual cells are also essential for elucidation of tau-mediated retinal diseases, if any. PMID:23712071

Yamazaki, Akio; Nishizawa, Yuji; Matsuura, Isao; Hayashi, Fumio; Usukura, Jiro; Bondarenko, Vladimir A.

2013-01-01

172

Bovine filensin possesses primary and secondary structure similarity to intermediate filament proteins  

PubMed Central

The cDNA coding for calf filensin, a membrane-associated protein of the lens fiber cells, has been cloned and sequenced. The predicted 755- amino acid-long open reading frame shows primary and secondary structure similarity to intermediate filament (IF) proteins. Filensin can be divided into an NH2-terminal domain (head) of 38 amino acids, a middle domain (rod) of 279 amino acids, and a COOH-terminal domain (tail) of 438 amino acids. The head domain contains a di- arginine/aromatic amino acid motif which is also found in the head domains of various intermediate filament proteins and includes a potential protein kinase A phosphorylation site. By multiple alignment to all known IF protein sequences, the filensin rod, which is the shortest among IF proteins, can be subdivided into three subdomains (coils 1a, 1b, and 2). A 29 amino acid truncation in the coil 2 region accounts for the smaller size of this domain. The filensin tail contains 6 1/2 tandem repeats which match analogous motifs of mammalian neurofilament M and H proteins. We suggest that filensin is a novel IF protein which does not conform to any of the previously described classes. Purified filensin fails to form regular filaments in vitro (Merdes, A., M. Brunkener, H. Horstmann, and S. D. Georgatos. 1991. J. Cell Biol. 115:397-410), probably due to the missing segment in the coil 2 region. Participation of filensin in a filamentous network in vivo may be facilitated by an assembly partner. PMID:8491777

1993-01-01

173

DNA sequence polymorphisms within the bovine guanine nucleotide-binding protein Gs subunit alpha (Gs?)-encoding (GNAS) genomic imprinting domain are associated with performance traits  

PubMed Central

Background Genes which are epigenetically regulated via genomic imprinting can be potential targets for artificial selection during animal breeding. Indeed, imprinted loci have been shown to underlie some important quantitative traits in domestic mammals, most notably muscle mass and fat deposition. In this candidate gene study, we have identified novel associations between six validated single nucleotide polymorphisms (SNPs) spanning a 97.6 kb region within the bovine guanine nucleotide-binding protein Gs subunit alpha gene (GNAS) domain on bovine chromosome 13 and genetic merit for a range of performance traits in 848 progeny-tested Holstein-Friesian sires. The mammalian GNAS domain consists of a number of reciprocally-imprinted, alternatively-spliced genes which can play a major role in growth, development and disease in mice and humans. Based on the current annotation of the bovine GNAS domain, four of the SNPs analysed (rs43101491, rs43101493, rs43101485 and rs43101486) were located upstream of the GNAS gene, while one SNP (rs41694646) was located in the second intron of the GNAS gene. The final SNP (rs41694656) was located in the first exon of transcripts encoding the putative bovine neuroendocrine-specific protein NESP55, resulting in an aspartic acid-to-asparagine amino acid substitution at amino acid position 192. Results SNP genotype-phenotype association analyses indicate that the single intronic GNAS SNP (rs41694646) is associated (P ? 0.05) with a range of performance traits including milk yield, milk protein yield, the content of fat and protein in milk, culled cow carcass weight and progeny carcass conformation, measures of animal body size, direct calving difficulty (i.e. difficulty in calving due to the size of the calf) and gestation length. Association (P ? 0.01) with direct calving difficulty (i.e. due to calf size) and maternal calving difficulty (i.e. due to the maternal pelvic width size) was also observed at the rs43101491 SNP. Following adjustment for multiple-testing, significant association (q ? 0.05) remained between the rs41694646 SNP and four traits (animal stature, body depth, direct calving difficulty and milk yield) only. Notably, the single SNP in the bovine NESP55 gene (rs41694656) was associated (P ? 0.01) with somatic cell count--an often-cited indicator of resistance to mastitis and overall health status of the mammary system--and previous studies have demonstrated that the chromosomal region to where the GNAS domain maps underlies an important quantitative trait locus for this trait. This association, however, was not significant after adjustment for multiple testing. The three remaining SNPs assayed were not associated with any of the performance traits analysed in this study. Analysis of all pairwise linkage disequilibrium (r2) values suggests that most allele substitution effects for the assayed SNPs observed are independent. Finally, the polymorphic coding SNP in the putative bovine NESP55 gene was used to test the imprinting status of this gene across a range of foetal bovine tissues. Conclusions Previous studies in other mammalian species have shown that DNA sequence variation within the imprinted GNAS gene cluster contributes to several physiological and metabolic disorders, including obesity in humans and mice. Similarly, the results presented here indicate an important role for the imprinted GNAS cluster in underlying complex performance traits in cattle such as animal growth, calving, fertility and health. These findings suggest that GNAS domain-associated polymorphisms may serve as important genetic markers for future livestock breeding programs and support previous studies that candidate imprinted loci may act as molecular targets for the genetic improvement of agricultural populations. In addition, we present new evidence that the bovine NESP55 gene is epigenetically regulated as a maternally expressed imprinted gene in placental and intestinal tissues from 8-10 week old bovine foetuses. PMID:21214909

2011-01-01

174

Calculation of protein conformation as an assembly of stable overlapping segments: application to bovine pancreatic trypsin inhibitor.  

PubMed Central

Conformations of bovine pancreatic trypsin inhibitor were calculated by assuming that the final structure as well as properly chosen overlapping segments thereof are simultaneously in low-energy (not necessarily the lowest-energy) conformational states. Therefore, the whole chain can be built up from building blocks whose conformations are determined primarily by short-range interactions. Our earlier buildup procedure was modified by taking account of a statistical analysis of known amino acid sequences that indicates that there is nonrandom pairing of amino acid residues in short segments along the chain, and by carrying out energy minimization on only these segments and on the whole chain [without minimizing the energies of intermediate-size segments (20-30 residues long)]. Results of this statistical analysis were used to determine the variable sizes of the overlapping oligopeptide building blocks used in the calculations; these varied from tripeptides to octapeptides, depending on the amino acid sequence. Successive stages of approximations were used to combine the low-energy conformations of these building blocks in order to keep the number of variables in the computations to a manageable size. The calculations led to a limited number of conformations of the protein (only two different groups, with very similar structure within each group), most residues of which were in the same conformational state as in the native structure. PMID:2023916

Simon, I; Glasser, L; Scheraga, H A

1991-01-01

175

Preparation, characterization, and localization of antisera against bovine MP26, an integral protein from lens fiber plasma membrane  

PubMed Central

Polyclonal antisera were prepared in rabbits using both native and chymotrypsin-digested bovine lens fiber plasma membranes. MP26, the principal protein of lens fiber plasma membranes, and CT20, a chymotryptic fragment of MP26, were isolated electrophoretically and used to purify anti-MP26 and anti-CT20 activity from the respective antisera by affinity chromatography. These affinity-purified antisera were characterized by immunoreplica. Immunofluorescence microscopy localized MP26 on sections of methacrylate-embedded lenses in the lens fiber plasma membranes, but not the lens epithelium. Immunocytochemistry of isolated native or chymotrypsin-digested lens fiber plasma membranes localized both the MP26 and the CT20 only in the nonjunctional plasma membranes, with no detectable activity in the lens fiber junctions themselves. Electron microscopy revealed a second set of pentalaminar profiles, thinner by 4 nm than the lens fiber junctions, which contained demonstrable anti-MP26 and anti-CT20 activity following immunocytochemistry. These results indicate either that MP26 is not a component of the lens fiber junctions, or that significant conformational changes accompany assembly of MP26 into lens fiber junctions, resulting in the masking of MP26 antigenic determinants. PMID:6339520

1983-01-01

176

Synthesis of nano-bioactive glass-ceramic powders and its in vitro bioactivity study in bovine serum albumin protein  

NASA Astrophysics Data System (ADS)

Bioactive glasses and ceramics have proved to be able to chemically bond to living bone due to the formation of an apatite-like layer on its surface. The aim of this work was preparation and characterization of bioactive glass-ceramic by sol-gel method. Nano-bioglass-ceramic material was crushed into powder and its bioactivity was examined in vitro with respect to the ability of hydroxyapatite layer to form on the surface as a result of contact with bovine serum albumin (BSA) protein. The obtained nano-bioactive glass-ceramic was analyzed before and after contact with BSA solution. This study used scanning electron microscope (SEM), transmission electron microscope (TEM), X-ray powder diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR) analysis to examine its morphology, crystallinity and composition. The TEM images showed that the NBG particles size were 10-40 nm. Bioactivity of nanopowder was confirmed by SEM and XRD due to the presence of a rich bone-like apatite layer. Therefore, this nano-BSA-bioglass-ceramic composite material is promising for medical applications such as bone substitutes and drug carriers.

Nabian, Nima; Jahanshahi, Mohsen; Rabiee, Sayed Mahmood

2011-07-01

177

Binding of a substrate analog to a domain swapping protein: X-ray structure of the complex of bovine seminal ribonuclease with uridylyl(2',5')adenosine.  

PubMed Central

Bovine seminal ribonuclease (BS-RNase) is a unique member of the pancreatic-like ribonuclease superfamily. The native enzyme is a mixture of two dimeric forms with distinct structural features. The most abundant form is characterized by the swapping of N-terminal fragments. In this paper, the crystal structure of the complex between the swapping dimer and uridylyl(2',5')adenosine is reported at 2.06 A resolution. The refined model has a crystallographic R-factor of 0.184 and good stereochemistry. The quality of the electron density maps enables the structure of both the inhibitor and active site residues to be unambiguously determined. The overall architecture of the active site is similar to that of RNase A. The dinucleotide adopts an extended conformation with the pyrimidine and purine base interacting with Thr45 and Asn71, respectively. Several residues (Gln11, His12, Lys41, His119, and Phe120) bind the oxygens of the phosphate group. The structural similarity of the active sites of BS-RNase and RNase A includes some specific water molecules believed to be relevant to catalytic activity. Upon binding of the dinucleotide, small but significant modifications of the tertiary and quaternary structure of the protein are observed. The ensuing correlation of these modifications with the catalytic activity of the enzyme is discussed. PMID:10082366

Vitagliano, L.; Adinolfi, S.; Riccio, A.; Sica, F.; Zagari, A.; Mazzarella, L.

1998-01-01

178

Bovine colostrum increases pore-forming claudin-2 protein expression but paradoxically not ion permeability possibly by a change of the intestinal cytokine milieu.  

PubMed

An impaired intestinal barrier function is involved in the pathogenesis of inflammatory bowel disease (IBD). Several nutritional factors are supposed to be effective in IBD treatment but scientific data about the effects on the intestinal integrity remain scarce. Bovine colostrum was shown to exert beneficial effects in DSS-induced murine colitis, and the present study was undertaken to explore the underlying molecular mechanisms. Western blot revealed increased claudin-2 expression in the distal ileum of healthy mice after feeding with colostrum for 14 days, whereas other tight junction proteins (claudin-3, 4, 10, 15) remained unchanged. The colostrum-induced claudin-2 induction was confirmed in differentiated Caco-2 cells after culture with colostrum for 48 h. Paradoxically, the elevation of claudin-2, which forms a cation-selective pore, was neither accompanied by increased ion permeability nor impaired barrier function. In an in situ perfusion model, 1 h exposure of the colonic mucosa to colostrum induced significantly increased mRNA levels of barrier-strengthening cytokine transforming growth factor-?, while interleukine-2, interleukine-6, interleukine-10, interleukine-13, and tumor-necrosis factor-? remained unchanged. Thus, modulation of the intestinal transforming growth factor-? expression might have compensated the claudin-2 increase and contributed to the observed barrier strengthening effects of colostrum in vivo and in vitro. PMID:23717570

Bodammer, Peggy; Kerkhoff, Claus; Maletzki, Claudia; Lamprecht, Georg

2013-01-01

179

Microwave Ablation Compared with Radiofrequency Ablation for Breast Tissue in an Ex Vivo Bovine Udder Model  

SciTech Connect

Purpose: To compare the effectiveness of microwave (MW) ablation with radiofrequency (RF) ablation for treating breast tissue in a nonperfused ex vivo model of healthy bovine udder tissue. Materials and Methods: MW ablations were performed at power outputs of 25W, 35W, and 45W using a 915-MHz frequency generator and a 2-cm active tip antenna. RF ablations were performed with a bipolar RF system with 2- and 3-cm active tip electrodes. Tissue temperatures were continuously monitored during ablation. Results: The mean short-axis diameters of the coagulation zones were 1.34 {+-} 0.14, 1.45 {+-} 0.13, and 1.74 {+-} 0.11 cm for MW ablation at outputs of 25W, 35W, and 45W. For RF ablation, the corresponding values were 1.16 {+-} 0.09 and 1.26 {+-} 0.14 cm with electrodes having 2- and 3-cm active tips, respectively. The mean coagulation volumes were 2.27 {+-} 0.65, 2.85 {+-} 0.72, and 4.45 {+-} 0.47 cm{sup 3} for MW ablation at outputs of 25W, 35W, and 45W and 1.18 {+-} 0.30 and 2.29 {+-} 0.55 cm{sup 3} got RF ablation with 2- and 3-cm electrodes, respectively. MW ablations at 35W and 45W achieved significantly longer short-axis diameters than RF ablations (P < 0.05). The highest tissue temperature was achieved with MW ablation at 45W (P < 0.05). On histological examination, the extent of the ablation zone in MW ablations was less affected by tissue heterogeneity than that in RF ablations. Conclusion: MW ablation appears to be advantageous with respect to the volume of ablation and the shape of the margin of necrosis compared with RF ablation in an ex vivo bovine udder.

Tanaka, Toshihiro, E-mail: toshihir@bf6.so-net.ne.jp [RWTH Aachen University, Applied Medical Engineering, Helmholtz-Institute Aachen (Germany); Westphal, Saskia, E-mail: swestphal@ukaachen.de [RWTH Aachen University, Department of Pathology Aachen University Hospital (Germany); Isfort, Peter, E-mail: isfort@hia.rwth-aachen.de [RWTH Aachen University, Applied Medical Engineering, Helmholtz-Institute Aachen (Germany); Braunschweig, Till, E-mail: tbraunschweig@ukaachen.de [RWTH Aachen University, Department of Pathology Aachen University Hospital (Germany); Penzkofer, Tobias, E-mail: penzkofer@hia.rwth-aachen.de; Bruners, Philipp, E-mail: bruners@rad.rwth-aachen.de [RWTH Aachen University, Applied Medical Engineering, Helmholtz-Institute Aachen (Germany); Kichikawa, Kimihiko, E-mail: kkichika@naramed-u.ac.jp [Nara Medical University, Department of Radiology (Japan); Schmitz-Rode, Thomas, E-mail: smiro@hia.rwth-aachen.de; Mahnken, Andreas H., E-mail: mahnken@rad.rwth-aachen.de [RWTH Aachen University, Applied Medical Engineering, Helmholtz-Institute Aachen (Germany)

2012-08-15

180

Polymorphic behavior in protein-surfactant mixtures: the water-bovine serum albumin-sodium taurodeoxycholate system.  

PubMed

Mixtures containing water, bovine serum albumin (BSA), and sodium taurodeoxycholate (NaTDC), a component of the bile in mammals, have been investigated in a wide range of composition and pH. Depending on the concentration of both solutes and the pH, solutions, precipitates, and gels are formed. Under spontaneous pH conditions, the transport properties in dilute solutions indicate the occurrence of significant interactions between BSA and the surfactant. Conversely, acidic media favor the formation of nonsoluble protein-surfactant complexes, with subsequent precipitation. The nucleation kinetics of the protein-surfactant complexes in solid form and the related precipitation processes can be slow or fast, depending on the overall solute content and the mole ratio. At high concentrations, a gel, extending on both sides of the charge neutralization line, and two-phase regions are observed. Gels shrink in open air and swell in the presence of excess water. Depending on concentration and temperature, the gels transform from an essentially liquidlike behavior to that peculiar to true gels (when G' > or = G''). The thermal gelation threshold, the temperature above which G' > or = G'', depends on BSA and NaTDC content and is concomitant to moderate heat effects, inferred by differential scanning calorimetry (DSC). The above data also indicate that the protein thermal denaturation in the gel is shifted to higher temperatures compared to water. Such a stabilizing effect is presumably related to the occurrence of both electrostatic and hydrophobic interactions with NaTDC. Water self-diffusion in the gels is slightly slower than that in the bulk and poorly sensitive to composition: it is about 65% the value of neat H2O in a wide concentration range, irrespective of the BSA, or NaTDC, concentration. A peculiar behavior is also observed in 23Na longitudinal and transverse relaxation rates. The T1 and T2 values, measured at 105.75 MHz on BSA-NaTDC gels, indicate that the motions determining the NMR relaxation of the sodium ions in the hydration layer of the protein-surfactant aggregates are not slow, having frequencies comparable with the Larmor one. The above properties, especially the rheological and the spectroscopic ones, are important for understanding the behavior of gels based on protein-surfactant mixtures. PMID:16800527

Orioni, Barbara; Roversi, Mauro; La Mesa, Camillo; Asaro, Fioretta; Pellizer, Giorgio; D'Errico, Gerardino

2006-06-22

181

Gene expression analysis of protein synthesis pathways in bovine mammary epithelial cells purified from milk during lactation and short-term restricted feeding.  

PubMed

The objective of the study was to investigate selected key regulatory pathways of milk protein biosynthesis in primary bovine mammary epithelial cells (MECs) of dairy cows during the first 155days of lactation. In addition, cows were exposed to feed restriction for a short period (FR) during different stages of lactation (week 4 and 21pp) to study adjustment processes of molecular protein biosynthesis to metabolic challenge. Morning milk samples from twenty-four Holstein-Friesian cows were collected throughout the experimental period (n=10 per animal). MEC from raw milk were purified using an immunomagnetic separation technique and used for real-time quantitative PCR analyses. As was seen in transcript abundances of all major milk proteins, mRNA levels of E74-like factor 5 (ELF5), an enhancer of signal transducer and activator of transcription (STAT) action, concomitantly decreased towards mid-lactation. Expression of ELF5 as well as of all milk protein genes showed a similar increase during FR in early lactation. Occasional changes in expression could be seen in other Janus kinase (JAK)/STAT factors and in mammalian target of rapamycin (mTOR) pathway elements. Amino acid transfer and glucose transporter and the ?-casein expression were also partially affected. In conclusion, our findings suggest a pivotal role of the transcription factor ELF5 in milk protein mRNA expression with complementary JAK/STAT and mTOR signalling for the regulation of protein biosynthesis in the bovine mammary gland. PMID:23402545

Sigl, T; Meyer, H H D; Wiedemann, S

2014-02-01

182

Effect of salt addition on the thermal behavior of proteins of bovine meat from Argentina.  

PubMed

Research was undertaken to investigate how the addition of sodium chloride (NaCl) and/or sodium tripolyphosphate (TPP) to sous vide cooked meat pieces produces an increase in water holding capacity (WHC). Semitendinosus muscles were injected to obtain tissue final concentrations of 0.70% NaCl, 0.25% TPP, 0.70% NaCl+0.25% TPP, and 1.20% NaCl+0.25% TPP. SDS-PAGE analysis showed increased protein solubilization in those treatments which included NaCl. Thermal analysis of whole muscles and isolated myofibrils showed the destabilizing effect of NaCl and a global stabilizing effect of TPP. Both salts together induced a destabilizing global effect, where TPP assisted NaCl in breaking the meat structure. It is suggested that the WHC increments are related to conformational changes in myofibrillar proteins and to the weakening of myofibrillar structure by the removal of myofibrillar proteins. PMID:22062916

Pighin, D G; Sancho, A M; Gonzalez, C B

2008-07-01

183

Functional characterization of bovine viral diarrhea virus nonstructural protein 5A by reverse genetic analysis and live cell imaging.  

PubMed

Nonstructural protein 5A (NS5A) of bovine viral diarrhea virus (BVDV) is a hydrophilic phosphoprotein with RNA binding activity and a critical component of the viral replicase. In silico analysis suggests that NS5A encompasses three domains interconnected by two low-complexity sequences (LCSs). While domain I harbors two functional determinants, an N-terminal amphipathic helix important for membrane association, and a Zn-binding site essential for RNA replication, the structure and function of the C-terminal half of NS5A are still ill defined. In this study, we introduced a panel of 10 amino acid deletions covering the C-terminal half of NS5A. In the context of a highly efficient monocistronic replicon, deletions in LCS I and the N-terminal part of domain II, as well as in domain III, were tolerated with regard to RNA replication. When introduced into a bicistronic replicon, only deletions in LCS I and the N-terminal part of domain II were tolerated. In the context of the viral full-length genome, these mutations allowed residual virion morphogenesis. Based on these data, a functional monocistronic BVDV replicon coding for an NS5A variant with an insertion of the fluorescent protein mCherry was constructed. Live cell imaging demonstrated that a fraction of NS5A-mCherry localizes to the surface of lipid droplets. Taken together, this study provides novel insights into the functions of BVDV NS5A. Moreover, we established the first pestiviral replicon expressing fluorescent NS5A-mCherry to directly visualize functional viral replication complexes by live cell imaging. PMID:24131714

Isken, Olaf; Langerwisch, Ulrike; Schnherr, Robert; Lamp, Benjamin; Schrder, Kristin; Duden, Rainer; Rmenapf, Tillmann H; Tautz, Norbert

2014-01-01

184

Presence of ecto-protein tyrosine phosphatase activity is vital for survival of Setaria cervi, a bovine filarial parasite.  

PubMed

The ecto protein tyrosine phosphatases (PTP) are known to play a crucial role in the pathogenesis and survival of the intracellular parasites. However, their presence and role in filarial parasites is still unknown. We found a significant amount of tyrosine phosphatase activity in the surface antigen fraction extracted from Setaria cervi (S. cervi), a bovine filarial parasite. An antibody designed against the conserved catalytic core of human protein tyrosine phosphatases, PTP1B cross reacted with a 63 kDa band in the surface antigen. We detected a significant amount of PTP activity in the intact S. cervi adult parasites as well as microfilariae in this study for the first time. This PTP may be localized on the surface of the parasite with an exposed active site available for the external substrates. The PTP activity was also inhibited by sodium orthovanadate and phenyl arsine oxide, specific inhibitors of PTP in both the life stages. The Km and Vmax for PTP in the adult parasites and microfilariae were determined to be 2.574??0.14 mM; 206.3??2.75 ?M Pi/h/two parasites and 5.510??0.59 mM; 62.27??2.27 ?M Pi/h/10(6) parasites respectively using O-P-L-Tyrosine as substrate. Interestingly, a positive correlation was observed between the inhibition in PTP activity and reduction in the motility/ viability of the parasites when they were subjected to the specific PTP inhibitors (Orthovanadate and Phenyl arsine oxide) for 4 h in the KRB maintenance medium. The activity was also significantly inhibited in the parasites exposed to antifilarial drug/compounds for e.g. Diethylcarbamazine, Acetylsalicylic Acid and SK7, a methyl chalcone. Therefore suggesting a possible role played by PTP in the survival of the parasite, its interaction with the host as well as in the screening of newly synthesized antifilarials/drugs. PMID:25028209

Singh, Neetu; Heneberg, Petr; Rathaur, Sushma

2014-10-01

185

Modelling transmission of bovine tuberculosis in red deer and wild boar in Normandy, France.  

PubMed

In early 2001, Mycobacterium bovis infection was confirmed in red deer (RD) (Cervus elaphus) shot in Normandy region, France. An epidemiological survey conducted during the following hunting season in two connected forests confirmed the occurrence of the disease in both free-ranging RD and wild boar (WB) (Sus scrofa). This was the first detected bovine tuberculosis outbreak in wildlife in France. We present a simple deterministic age-structured model of the within- and between-species M.bovis transmission in RD and WB populations that distinguishes direct transmission (horizontal and pseudo-vertical) and indirect transmission through contaminated offal left behind by hunters. Results issued from the epidemiological surveys conducted in Normandy forests were used to estimate transmission parameters. Because data for RD and WB populations were not available, population sizes at demographic equilibrium were estimated and used to run the model. We qualitatively tested different control measure scenarios with our model, considering different mortality rates and offal harvesting, to determine which ones affect the success of infection control. The most realistic control scenario would combine the total depopulation of RD and good compliance with offal harvesting, because the model suggests that infected offal left by hunters represents the main transmission source of M.bovis in the field. PMID:22958262

Zanella, G; Bar-Hen, A; Boschiroli, M-L; Hars, J; Moutou, F; Garin-Bastuji, B; Durand, B

2012-09-01

186

Comparative study of modifications produced by x rays in bovine serum proteins  

Microsoft Academic Search

Serum albumin and gamma globulin appear to be more radiosensitive than ; alpha and BETA globulins. Small irradiation doses are sufficient to ; chemically modify certain sites in these proteins without producing very serious ; modifications in the secondary and tertiary structures. Such modifications ; contribute to the understanding of the differences in the physiological, and in ; particular antigen

J. L. Azanza; A. Ducastaing; J. Raymond; P. Creach

1972-01-01

187

Crystal Structure of Bovine Coronavirus Spike Protein Lectin Received for publication,September 10, 2012, and in revised form, October 19, 2012 Published, JBC Papers in Press,October 22, 2012, DOI 10.1074/jbc.M112.418210  

E-print Network

Crystal Structure of Bovine Coronavirus Spike Protein Lectin Domain*S Received for publication of Medicine, Aurora, Colorado 80045 Background: Coronavirus spike protein N-terminal domains (NTDs) bind sugar or protein receptors. Results: We determined crystal structure of bovine coronavirus NTD and located its

Li, Fang

188

Enantioselectivity of bovine serum albumin-bonded columns produced with isolated protein fragments. II. Characterization of protein fragments and chiral binding sites.  

PubMed

Enantioselectivity of bovine serum albumin (BSA)-bonded columns produced with isolated protein fragments has been investigated. The BSA fragment, BSA-FG75, was isolated by size exclusion chromatography following peptic digest of BSA. The isolated BSA-FG75 was further fractionated to two fractions, BSA-F1 and BSA-F2, by anion-exchange chromatography. BSA-F1 and BSA-F2 had molecular mass of about 35000 daltons, estimated by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry, BSA-F1 has amino acid residues 1-307 estimated by electrospray ionization (ESI) mass spectrometry, while BSA-F2 is an N-terminal half BSA fragment. The BSA, BSA-FG75, BSA-F1 and BSA-F2 proteins were bound to aminopropyl-silica gels activated by N,N'-disuccinimidyl carbonate. The bound amounts of the BSA fragments were 2.2-2.7 times more than that of the intact BSA. Chiral recognition of 2-arylpropionic acid derivatives, benzodiazepines, warfarin and benzoin was obtained with the BSA fragment-bonded columns. The non-enantioselective interactions of benzoin and benzodiazepines except for clorazepate with BSA fragments were increased with protein surface coverages, while those of 2-arylpropionic acid, clorazepate and warfarin were decreased. The BSA fragment columns gave higher enantioselectivity for lorazepam and benzoin, and lower enantioselectivity for other compounds tested, compared with the BSA column. These results might be due to changes in the globular structure of the BSA fragment and/or changes in the local environment around the binding sites. PMID:9188181

Haginaka, J; Kanasugi, N

1997-05-01

189

The protection of bovine skeletal myofibrils from proteolytic damage post mortem by small heat shock proteins.  

PubMed

This study aimed to determine how small heat shock proteins (sHSPs) protect myofibrillar proteins from ?-calpain degradation during ageing. Immunoprecipitation experiments with M. longissimus dorsi (LD) from Angus heifers (n = 14) examined the interaction between ??-crystallin, desmin, titin, HSP20, HSP27 and ?-calpain. Results showed that ??-crystallin associated with desmin, titin, HSP20, HSP27 and ?-calpain. Exogenous ??-crystallin reduced desmin and titin degradations in myofibrillar extracts and attenuated ?-calpain activity. In a second experiment, bull LD (n = 94) were aged at -1.5C for up to 28 days post mortem. ?-Calpain autolysed faster in high ultimate pH (pH(u)) meat (pH(u)?6.2) and this was concomitant with the more rapid degradation of titin and filamin in this pH(u) group. Desmin stability in intermediate pH(u) meat (pH(u) 5.8 to 6.19) may be due to the protection of myofibril-bound sHSPs combined with the competitive inhibition of ?-calpain by sHSPs. PMID:24769876

Lomiwes, D; Hurst, S M; Dobbie, P; Frost, D A; Hurst, R D; Young, O A; Farouk, M M

2014-08-01

190

Cloning and expression of a cDNA encoding a bovine brain brefeldin A-sensitive guanine nucleotide-exchange protein for?ADP-ribosylation?factor  

PubMed Central

A 200-kDa guanine nucleotide-exchange protein (p200 or GEP) for ADP-ribosylation factors 1 and 3 (ARF1 and ARF3) that was inhibited by brefeldin A (BFA) was purified earlier from cytosol of bovine brain cortex. Amino acid sequences of four tryptic peptides were 47% identical to that of Sec7 from Saccharomyces cerevisiae, which is involved in vesicular trafficking in the Golgi. By using a PCR-based procedure with two degenerate primers representing sequences of these peptides, a product similar in size to Sec7 that contained the peptide sequences was generated. Two oligonucleotides based on this product were used to screen a bovine brain library, which yielded one clone that was a partial cDNA for p200. The remainder of the cDNA was obtained by 5? and 3? rapid amplification of cDNA ends (RACE). The ORF of the cDNA encodes a protein of 1,849 amino acids (?208 kDa) that is 33% identical to yeast Sec7 and 50% identical in the Sec7 domain region. On Northern blot analysis of bovine tissues, a ?7.4-kb mRNA was identified that hybridized with a p200 probe; it was abundant in kidney, somewhat less abundant in lung, spleen, and brain, and still less abundant in heart. A six-His-tagged fusion protein synthesized in baculovirus-infected Sf9 cells demonstrated BFA-inhibited GEP activity, confirming that BFA sensitivity is an intrinsic property of this ARF GEP and not conferred by another protein component of the complex from which p200 was originally purified. PMID:9371777

Morinaga, Naoko; Moss, Joel; Vaughan, Martha

1997-01-01

191

Ischemia reperfusion injury in the isolated hemoperfused bovine uterus--a model for the investigation of anti-inflammatory substances?  

PubMed

The inflammation model of the isolated hemoperfused bovine uterus was used to introduce a new in vitro model for the investigation of anti-inflammatory substances. As previous studies demonstrated both an increase in PGE2 synthesis and an up-regulation of COX-2 and iNOS mRNA by ischemia-reperfusion injury in the model (Braun and Kietzmann, 2004), inhibitory effects of the glucocorticoid dexamethasone, the NSAID flunixin and the selective COX-2 inhibitor DFU (5,5-dimethyl-3-(3-fluorophenyl)-4-(4-methylsulphonyl)-phenyl-2-(5H)-furanone) were studied. All substances caused a significant decrease in tissue PGE2 production, while none induced down-regulation of COX-2 mRNA. A slight decrease in the mRNA level of iNOS was observed after 300 minutes of perfusion with dexamethasone-supplemented perfusion medium. In conclusion, the suitability of the isolated hemoperfused bovine uterus for the investigation of anti-inflammatory substances, especially regarding their COX-2 selectivity, was demonstrated. Use of the isolated hemoperfused bovine uterus in pharmacological research and drug screening may contribute to a reduction of animal testing. PMID:15057408

Braun, Michael; Kietzmann, Manfred

2004-01-01

192

Blocking ELISA Using Recombinant NcSRS2 Protein for Diagnosing Bovine Neosporosis.  

PubMed

Neospora caninum is the etiologic agent of neosporosis, which leads to economic impacts on cattle industry. The reference method for serodiagnosis of neosporosis is the indirect fluorescent antibody test (IFAT). However, IFAT is laborious, expensive, and is not practicable in high throughput screening. In order to facilitate the serological diagnosis of neosporosis, we developed a blocking enzyme-linked immunosorbent assay (b-ELISA) based on NcSRS2 recombinant protein (rNcSRS2) and polyclonal antibodies against rNcSRS2 (b-ELISA/rNcSRS2). Compared to IFAT, b-ELISA/rNcSRS2 showed 93.7% accuracy (98.7% sensitivity and 88.7% specificity), suggesting its potential as diagnostic assay to detect N. caninum antibodies in cattle sera. PMID:25432863

Sinnott, Francine A; Monte, Leonardo G; Collares, Thais F; De Matos, Bruno M; Pacheco, Diene B; Borsuk, Sibele; Andreotti, Renato; Hartleben, Cludia P

2014-11-29

193

Jumonji domain-containing protein 3 regulates histone 3 lysine 27 methylation during bovine preimplantation development.  

PubMed

Understanding the mechanisms of epigenetic remodeling that follow fertilization is a fundamental step toward understanding the bases of early embryonic development and pluripotency. Extensive and dynamic chromatin remodeling is observed after fertilization, including DNA methylation and histone modifications. These changes underlie the transition from gametic to embryonic chromatin and are thought to facilitate embryonic genome activation. In particular, trimethylation of histone 3 lysine 27 (H3K27me3) is associated with gene-specific transcription repression. Global levels of this epigenetic mark are high in oocyte chromatin and decrease to minimal levels at the time of embryonic genome activation. We provide evidence that the decrease in H3K27me3 observed during early development is cell-cycle independent, suggesting an active mechanism for removal of this epigenetic mark. Among H3K27me3-specific demethylases, Jumonji domain-containing protein 3 (JMJD3), but not ubiquitously transcribed tetratricopeptide repeat X (UTX), present high transcript levels in oocytes. Soon after fertilization JMJD3 protein levels increase, concurrent with a decrease in mRNA levels. This pattern of expression suggests maternal inheritance of JMJD3. Knockdown of JMJD3 by siRNA injection in parthenogenetically activated metaphase II oocytes resulted in inhibition of the H3K27me3 decrease normally observed in preimplantation embryos. Moreover, knockdown of JMJD3 in oocytes reduced the rate of blastocyst development. Overall, these results indicate that JMJD3 is involved in active demethylation of H3K27me3 during early embryo development and that this mark plays an important role during the progression of embryos to blastocysts. PMID:22308433

Canovas, Sebastian; Cibelli, Jose B; Ross, Pablo J

2012-02-14

194

Coarse-grained protein model, cooperativity of folding and subdomain structure  

NASA Astrophysics Data System (ADS)

We investigate how does the range of attraction of a coarse-grained protein model affect cooperativity of folding transition. Free-energy landscapes of chymotrypsin inhibitor 2 (CI2) and bovine pancreatic trypsin inhibitor (BPTI) are obtained by a lattice protein model with G?-like interaction. With the range of attraction being varied as a parameter, we find that a short-range nature of interaction is important for cooperativity. BPTI exhibits a folding intermediate whose structure is similar to that observed experimentally, when the range of attractions is appropriately set. Thus subdomain structure is determined mainly by the native topology.

Kenzaki, Hiroo; Kikuchi, Macoto

2006-05-01

195

The Importance of Protein-Protein Interactions on the pH-Induced Conformational Changes of Bovine Serum Albumin: A Small-Angle X-Ray Scattering Study  

PubMed Central

Abstract The combined effects of concentration and pH on the conformational states of bovine serum albumin (BSA) are investigated by small-angle x-ray scattering. Serum albumins, at physiological conditions, are found at concentrations of ?3545 mg/mL (42 mg/mL in the case of humans). In this work, BSA at three different concentrations (10, 25, and 50 mg/mL) and pH values (2.09.0) have been studied. Data were analyzed by means of the Global Fitting procedure, with the protein form factor calculated from human serum albumin (HSA) crystallographic structure and the interference function described, considering repulsive and attractive interaction potentials within a random phase approximation. Small-angle x-ray scattering data show that BSA maintains its native state from pH 4.0 up to 9.0 at all investigated concentrations. A pH-dependence of the absolutenet protein charge is shown and the charge number per BSA is quantified to 10(2), 8(1), 13(2), 20(2), and 26(2) for pH values 4.0, 5.4, 7.0, 8.0, and 9.0, respectively. The attractive potential diminishes as BSA concentration increases. The coexistence of monomers and dimers is observed at 50 mg/mL and pH 5.4, near the BSA isoelectric point. Samples at pH 2.0 show a different behavior, because BSA overall shape changes as a function of concentration. At 10 mg/mL, BSA is partially unfolded and a strong repulsive protein-protein interaction occurs due to the high amount of exposed charge. At 25 and 50 mg/mL, BSA undergoes some re-folding, which likely results in a molten-globule state. This work concludes by confirming that the protein concentration plays an important role on the pH-unfolded BSA state, due to a delicate compromise between interaction forces and crowding effects. PMID:20085727

Barbosa, Leandro R.S.; Ortore, Maria Grazia; Spinozzi, Francesco; Mariani, Paolo; Bernstorff, Sigrid; Itri, Rosangela

2010-01-01

196

Identity elements in bovine tRNA(Trp) required for the specific stimulation of gelonin, a plant ribosome-inactivating protein.  

PubMed Central

Ribosome-inactivating proteins (RIPs) are RNA-N-glycosidases widely present in plants that depurinate RNA in ribosomes at a specific universally conserved position, A4324, in the rat 28S rRNA. A small group of RIPs (cofactor-dependent RIPs) require ATP and tRNA to reach maximal activity on isolated ribosomes. Among cofactor-dependent RIPs, gelonin is specifically and uniquely stimulated by tRNA(Trp). The active species are avian (chicken) and mammalian (beef, rat, and rabbit) tRNA(Trp), whereas yeast tRNA(Trp) is completely devoid of stimulating activity. In the present article, bovine and yeast tRNA(Trp) with unmodified bases were prepared by assembly of the corresponding genes from synthetic oligonucleotides followed by PCR and T7 RNA polymerase transcription of the amplified products. The two synthetic tRNAs were fully active (bovine) or inactive (yeast) as the wild-type tRNAs. Construction of chimeric tRNA(Trp) transcripts identified the following bovine nucleotides as recognition elements for gelonin-stimulating activity: G26 and bp G12-C23 in the D arm and G57, A59, and bp G51-C63 and U52-A62 in the T arm. Among single-stranded nucleotides, A59 has a prominent role, but full expression of the gelonin-stimulating activity requires an extensive cooperation between nucleotides in both arms. PMID:10573126

Brigotti, M; Carnicelli, D; Pallanca, A; Rizzi, S; Accorsi, P; Montanaro, L; Sperti, S

1999-01-01

197

Effect of bovine lactoferrin in a therapeutic hamster model of hepatic amoebiasis.  

PubMed

Entamoeba histolytica is the causative agent of amoebiasis, a disease that produces dysentery as a result of the perforation of the large intestine. This parasite often invades other organs, primarily the liver, leading to an amoebic liver abscess (ALA), which can cause death. Metronidazole is the drug of choice for the treatment of ALA; however, it produces toxic side effects in patients. Lactoferrin (Lf) is a glycoprotein of the innate immune response that sequesters iron in the mucosae. Lf possesses immune-regulatory properties, such as antiinflammatory and antioxidant activities. Moreover, the microbicidal activity of apoLf, which lacks bound iron, has been shown. In this study, we evaluated the therapeutic effect of bovine Lf (bLf) against ALA in a model of hepatic amoebiasis in hamsters. Interestingly, hamsters treated intragastrically with Lf (2.5 mg/100 g mass) over a period of 8 days showed no clinical signs of disease and ALA was effectively decreased, with only 0.63% detectable lesion, compared with 63% in untreated animals. Furthermore, liver function and blood cells approached normal levels among those receiving bLf treatment. These results suggest that bLf may aid in the therapy of amoebiasis, likely without producing undesirable effects in patients. PMID:22332957

Ordaz-Pichardo, Cynthia; Len-Sicairos, Nidia; Hernndez-Ramrez, Vernica Ivonne; Talams-Rohana, Patricia; de la Garza, Mireya

2012-06-01

198

Spatio-temporal expression patterns of aurora kinases a, B, and C and cytoplasmic polyadenylation-element-binding protein in bovine oocytes during meiotic maturation.  

PubMed

Maturation of immature bovine oocytes requires cytoplasmic polyadenylation and synthesis of a number of proteins involved in meiotic progression and metaphase-II arrest. Aurora serine-threonine kinases--localized in centrosomes, chromosomes, and midbody--regulate chromosome segregation and cytokinesis in somatic cells. In frog and mouse oocytes, Aurora A regulates polyadenylation-dependent translation of several mRNAs such as MOS and CCNB1, presumably by phosphorylating CPEB, and Aurora B phosphorylates histone H3 during meiosis. We analyzed the expression of three Aurora kinase genes--AURKA, AURKB, and AURKC--in bovine oocytes during meiosis by reverse transcription followed by quantitative real-time PCR and immunodetection. Aurora A was the most abundant form in oocytes, both at mRNA and protein levels. AURKA protein progressively accumulated in the oocyte cytoplasm during antral follicle growth and in vitro maturation. AURKB associated with metaphase chromosomes. AURKB, AURKC, and Thr-phosphorylated AURKA were detected at a contractile ring/midbody during the first polar body extrusion. CPEB, localized in oocyte cytoplasm, was hyperphosphorylated during prophase/metaphase-I transition. Most CPEB degraded in metaphase-II oocytes and remnants remained localized in a contractile ring. Roscovitine, U0126, and metformin inhibited meiotic divisions; they all induced a decrease of CCNB1 and phospho-MAPK3/1 levels and prevented CPEB degradation. However, only metformin depleted AURKA. The Aurora kinase inhibitor VX680 at 100 nmol/L did not inhibit meiosis but led to multinuclear oocytes due to the failure of the polar body extrusion. Thus, in bovine oocyte meiosis, massive destruction of CPEB accompanies metaphase-I/II transition, and Aurora kinases participate in regulating segregation of the chromosomes, maintenance of metaphase-II, and formation of the first polar body. PMID:17687118

Uzbekova, Svetlana; Arlot-Bonnemains, Yannick; Dupont, Jolle; Dalbis-Tran, Rozenn; Papillier, Pascal; Pennetier, Sophie; Thlie, Aurore; Perreau, Christine; Mermillod, Pascal; Prigent, Claude; Uzbekov, Rustem

2008-02-01

199

Stochastic simulation modeling to determine time to detect Bovine Viral Diarrhea antibodies in bulk tank milk.  

PubMed

A stochastic simulation model was developed to estimate the time from introduction of Bovine Viral Diarrhea Virus (BVDV) in a herd to detection of antibodies in bulk tank milk (BTM) samples using three ELISAs. We assumed that antibodies could be detected, after a fixed threshold prevalence of seroconverted milking cows was reached in the herd. Different thresholds were set for each ELISA, according to previous studies. For each test, antibody detection was simulated in small (70 cows), medium (150 cows) and large (320 cows) herds. The assays included were: (1) the Danish blocking ELISA, (2) the SVANOVIR()BVDV-Ab ELISA, and (3) the ELISA BVD/MD p80 Institute Pourquier. The validation of the model was mainly carried out by comparing the predicted incidence of persistently infected (PI) calves and the predicted detection time, with records from a BVD infected herd. Results showed that the SVANOVIR, which was the most efficient ELISA, could detect antibodies in the BTM of a large herd 280 days (95% prediction interval: 218; 568) after a transiently infected (TI) milking cow has been introduced into the herd. The estimated time to detection after introduction of one PI calf was 111 days (44; 605). With SVANOVIR ELISA the incidence of PIs and dead born calves could be limited and the impact of the disease on the animal welfare and income of farmers (before detection) could be minimized. The results from the simulation modeling can be used to improve the current Danish BVD surveillance program in detecting early infected herds. PMID:25081944

Foddai, Alessandro; Ene, Claes; Krogh, Kaspar; Stockmarr, Anders; Halasa, Tariq

2014-11-01

200

Herbal adaptogens combined with protein fractions from bovine colostrum and hen egg yolk reduce liver TNF-? expression and protein carbonylation in Western diet feeding in rats  

PubMed Central

Background We examined if a purported anti-inflammatory supplement (AF) abrogated Western-diet (WD)-induced liver pathology in rats. AF contained: 1) protein concentrates from bovine colostrum and avian egg yolk; 2) herbal adaptogens and antioxidants; and 3) acetyl-L-carnitine. Methods Nine month-old male Brown Norway rats were allowed ad libitum access to WD for 4143 days and randomly assigned to WD?+?AF feeding twice daily for the last 3133 days (n?=?8), or WD and water-placebo feeding twice daily for the last 3133 days (n?=?8). Rats fed a low-fat/low-sucrose diet (CTL, n?=?6) for 4143 days and administered a water-placebo twice daily for the last 3133 days were also studied. Twenty-four hours following the last gavage-feed, liver samples were analyzed for: a) select mRNAs (via RT-PCR) as well as genome-wide mRNA expression patterns (via RNA-seq); b) lipid deposition; and, c) protein carbonyl and total antioxidant capacity (TAC). Serum was also examined for TAC, 8-isoprostane and clinical chemistry markers. Results WD?+?AF rats experienced a reduction in liver Tnf-? mRNA (-2.8-fold, p?protein carbonyl content differed between WD?+?AF versus WD rats, although liver protein carbonyls tended to be lower in WD?+?AF versus CTL rats (p?=?0.08). RNA-seq revealed that 19 liver mRNAs differed between WD?+?AF versus WD when both groups were compared with CTL rats (+/- 1.5-fold, p?

2014-01-01

201

[Experimental study of composites of bovine bone morphogenetic protein and bio-active glass ceramic implanted into surgically produced periodontal bony defects in dogs].  

PubMed

Bovine bone morphogenetic protein (bBMP) was incorporated with bio-active glass ceramic (BGC). The composite of bBMP-BGC and BGC were implanted into the surgically produced periodontal osseous defects in dogs. Observations at 10, 16, 20, and 24 weeks show that the implants of BMP-BGC have the ability of bone induction and enhance the regeneration of periodontal bony defects in a relatively short time, but the implants of BGC alone only have the ability of bone-conduction, these is no bone-induction ability, and made a more long time in repairing the periodontal bony defects. PMID:2517825

Jin, Y

1989-11-01

202

A phenomenological model of protein folding  

E-print Network

We construct a phenomenological effective field theory model that describes the universality class of biologically active single-strand proteins. The model allows both for an explicit construction of native state protein conformations, and a dynamical description of protein folding and unfolding processes. The model reveals a connection between homochirality and protein collapse, and enables the theoretical investigation of various other aspects of protein folding even in the case of very long polypeptide chains where other methods are not available.

Danielsson, Ulf H; Niemi, Antti J

2009-01-01

203

Tyrosine, phenylalanine, and disulfide contributions to the circular dichroism of proteins: circular dichroism spectra of wild-type and mutant bovine pancreatic trypsin inhibitor.  

PubMed

Improved descriptions of the lowest energy excited states of tyrosine and phenylalanine side chains have been developed in order to extend the capabilities of calculating the circular dichroism (CD) spectra of proteins. Four transitions (Lb, La, Bb, and Ba) for each of the side-chain chromophores were considered, and the transition monopole charges were obtained from a CNDO/S calculation on models representing the individual groups. Monopole charges at midpoints of the bonds, corresponding to the maximum transition charge densities in the Lb band, and monopole charges representing the vibronic coupling with the B transitions for the La transition were also included. The aromatic transitions were combined with the peptide transitions (npi, pi0pi n'pi, and pi+pi) and disulfide transitions (n1sigma and n4sigma) in the framework of the origin-independent matrix method to compute the CD spectra of different crystal forms and Y --> L and F --> L mutants of bovine pancreatic trypsin inhibitor (BPTI). The structures of the mutants were obtained by replacing the appropriate tyrosine or phenylalanine residue by leucine in the wild-type crystal structure. The CD calculations were performed on the energy-minimized structures. The CD spectrum calculated for the form II crystal structure of BPTI showed the best agreement with experiment. In the far UV, the calculated and experimental CD spectra agree to various extents for the wild-type and mutant BPTI. Among the mutants, the calculated CD spectra of Y4L, Y10L, Y23L, and F45L showed reasonable agreement with experiment, while those of Y21L and F22L, the two residues interacting with most aromatic groups, showed poor agreement. In the near UV, the negative bands predicted for the wild-type and mutant BPTI have much less intensity than observed experimentally. PMID:10451378

Sreerama, N; Manning, M C; Powers, M E; Zhang, J X; Goldenberg, D P; Woody, R W

1999-08-17

204

Combining a polarizable force-field and a coarse-grained polarizable solvent model: application to long dynamics simulations of bovine pancreatic trypsin inhibitor.  

PubMed

The dynamic coupling between a polarizable protein force field and a particle-based implicit solvent model is described. The polarizable force field, TCPEp, developed recently to simulate protein systems, is characterized by a reduced number of polarizable sites, with a substantial gain in efficiency for an equal chemical accuracy. The Polarizable Pseudo-Particle (PPP) solvent model represents the macroscopic solvent polarization by induced dipoles placed on mobile Lennard-Jones pseudo-particles. The solvent-induced dipoles are sensitive to the solute electric field, but not to each other, so that the computational cost of solvent-solvent interactions is basically negligible. The solute and solvent induced dipoles are determined self-consistently and the equations of motion are solved using an efficient iterative multiple time step procedure. The solvation cost with respect to vacuum simulations is shown to decrease with solute size: the estimated multiplicative factor is 2.5 for a protein containing about 1000 atoms, and as low as 1.15 for 8000 atoms. The model is tested for six 20 ns molecular dynamics trajectories of a traditional benchmark system: the hydrated Bovine Pancreatic Trypsin Inhibitor (BPTI). Even though the TCPEp parameters have not been refined to be used with the solvent PPP model, we observe a good conservation of the BPTI structure along the trajectories. Moreover, our approach is able to provide a description of the protein solvation thermodynamic at the same accuracy as the standard Poisson-Boltzman continuum methods. It provides in addition a good description of the microscopic structural aspects concerning the solute/solvent interaction. PMID:18351600

Masella, Michel; Borgis, Daniel; Cuniasse, Philippe

2008-08-01

205

Assessment of a Protein Cocktail-Based Skin Test for Bovine Tuberculosis in a Double-Blind Field Test in Cattle  

PubMed Central

Bovine tuberculosis (bTB) is a worldwide zoonosis caused mainly by Mycobacterium bovis. The traditional diagnostic method used often is the tuberculin skin test, which uses bovine purified protein derivatives (PPD-B). However, it is difficult to maintain uniformity of PPD-B from batch to batch, and it shares common antigens with nonpathogenic environmental mycobacteria. To overcome these problems, M. bovis-specific antigens that showed good T cell stimulation, such as CFP-10, ESAT-6, Rv3615c, etc., have been used in the skin test, but there have been no large-scale clinical studies on these antigens. In this study, two combinations (CFP-10/ESAT-6/TB10.4 protein cocktail and CFP-10/ESAT-6/Rv3872/MPT63 protein cocktail) were developed and used as stimuli in the skin test. Cattle were double-blind tested to assess the efficiency of the protein cocktail-based skin tests. The results showed that the CFP-10/ESAT-6/TB10.4 protein cocktail-based skin test can differentiate TB-infected cattle from Mycobacterium avium-infected ones and that it shows a high degree of agreement with the traditional tuberculin skin test (? = 0.8536) and gamma interferon (IFN-?) release assay (? = 0.8154). Compared to the tuberculin skin test, the relative sensitivity and relative specificity of the CFP-10/ESAT-6/TB10.4-based skin test were 87% and 97%, respectively., The relative sensitivity and relative specificity of the CFP-10/ESAT-6/TB10.4-based skin test were 93% and 92%, respectively, on comparison with the IFN-? release assay. The correlation between the increases in skin thickness observed after the inoculation of stimuli was high (PPD-B versus CFP-10/ESAT-6/TB10.4, Spearman r of 0.8435). The correlation between the optical density at 450 nm (OD450) obtained after blood stimulation with PPD-B and the increase in skin thickness observed after inoculation of the CFP-10/ESAT-6/TB10.4 protein cocktail was high (Spearman r = 0.7335). Therefore, the CFP-10/ESAT-6/TB10.4-based skin test responses correlate to traditional measures of bovine TB evaluation, including skin test and gamma interferon release assay. PMID:23365203

Xin, Ting; Jia, Hong; Ding, Jiabo; Li, Pingjun; Yang, Hongjun; Hou, Shaohua; Yuan, Weifeng; Guo, Xiaoyu; Wang, Haichun; Liang, Qianqian; Li, Ming

2013-01-01

206

Effects of butyrate on the expression of insulin-like growth factor binding proteins in bovine kidney epithelial cells  

Technology Transfer Automated Retrieval System (TEKTRAN)

Sodium butyrate induces cell cycle arrest and apoptosis in bovine kidney epithelial cells primarily via down-regulating cell cycle-related gene expression and enhancing expression of pro-apoptotic genes. The insulin-like growth factor (IGF) system plays an essential role in these processes as well a...

207

Species-specific anti-apoptotic activity of cellular prion protein in a mouse PrP-deficient neuronal cell line transfected with mouse, hamster, and bovine Prnp.  

PubMed

The neuroprotective function of prion protein (PrP) was revealed first by the fact that reintroduction of the mouse prion protein gene (Prnp) into a mouse Prnp(-/-) neuronal cell line, HpL3-4, could prevent apoptosis induced by serum deprivation. In the present study, the anti-apoptotic activities of mouse, hamster, and bovine PrP were compared by expressing mouse PrP (MoPrP), hamster PrP (HaPrP), and bovine PrP (BoPrP) in HpL3-4 cells, respectively. Morphological analysis and DNA fragmentation assays demonstrated that HpL3-4 cells expressing HaPrP, BoPrP, and empty vector (EM) showed the typical features of apoptosis with DNA laddering and apoptotic bodies after serum deprivation, whereas HpL3-4 cells expressing MoPrP showed decreased levels of apoptosis in comparison. The levels of histone-associated DNA fragments (mono- and oligonucleosomes) in the cytosol fractions of the cells correlated with the levels of DNA laddering. These results indicate a species-specific anti-apoptotic function of PrP exists, suggesting that the interaction of the mouse PrP with mouse host factors is required for its anti-apoptotic activity. PMID:18809465

Wu, Guoying; Nakajima, Kenta; Takeyama, Natsumi; Yukawa, Masayoshi; Taniuchi, Yojiro; Sakudo, Akikazu; Onodera, Takashi

2008-11-28

208

Modeling Enzymatic Reactions in Proteins.  

NASA Astrophysics Data System (ADS)

We will discuss application of our density functional (DFT)-based QM/MM methodology to modeling a variety of protein active sites, including methane monooxygenase, myoglobin, and cytochrome P450. In addition to the calculation of intermediates, transition states, and rate constants, we will discuss modeling of reactions requiring protein conformational changes. Our methodology reliably achieves small errors as a result of imposition of the QM/MM boundary. However, the accuracy of DFT methods can vary significantly with the type of system under study. We will discuss a novel approach to the reduction of errors in gradient corrected and hybrid DFT functionals, using empirical localized orbital corrections (DFT-LOC), which addresses this problem effectively. For example, the mean unsigned error in atomization energies for the G3 data set using the B3LYP-LOC model is 0.8 kcal/mole, as compared with 4.8 kcal/mole for B3LYP and 1.0 kcal/mole for G3 theory.

Friesner, Richard

2007-03-01

209

The bovine viral diarrhea virus E2 protein formulated with a novel adjuvant induces strong, balanced immune responses and provides protection from viral challenge in cattle.  

PubMed

Bovine viral diarrhea virus (BVDV) is still one of the most serious pathogens in cattle, meriting the development of improved vaccines. Recently, we developed a new adjuvant consisting of poly[di(sodium carboxylatoethylphenoxy)]-phosphazene (PCEP), either CpG ODN or poly(I:C), and an immune defense regulator (IDR) peptide. As this adjuvant has been shown to mediate the induction of robust, balanced immune responses, it was evaluated in an E2 subunit vaccine against BVDV in lambs and calves. The BVDV type 2 E2 protein was produced at high levels in a mammalian expression system and purified. When formulated with either CpG ODN or poly(I:C), together with IDR and PCEP, the E2 protein elicited high antibody titers and production of IFN-? secreting cells in lambs. As the immune responses were stronger when poly(I:C) was used, the E2 protein with poly(I:C), IDR and PCEP was subsequently tested in cattle. Robust virus neutralizing antibodies as well as cell-mediated immune responses, including CD8(+) cytotoxic T cell (CTL) responses, were induced. The fact that CTL responses were demonstrated in calves vaccinated with an E2 protein subunit vaccine indicates that this adjuvant formulation promotes cross-presentation. Furthermore, upon challenge with a high dose of virulent BVDV-2, the vaccinated calves showed almost no temperature response, weight loss, leukopenia or virus replication, in contrast to the control animals, which had severe clinical disease. These data suggest that this E2 subunit formulation induces significant protection from BVDV-2 challenge, and thus is a promising BVDV vaccine candidate; in addition, the adjuvant platform has applications in bovine vaccines in general. PMID:25454860

Snider, Marlene; Garg, Ravendra; Brownlie, Robert; van den Hurk, Jan V; van Drunen Littel-van den Hurk, Sylvia

2014-11-28

210

Adipogenesis of bovine perimuscular preadipocytes  

SciTech Connect

In this study, non-transformed progeny adipofibroblasts, derived from mature adipocyte dedifferentiation, was used as a novel in vitro model to study adipogenic gene expression in cattle. Adipofibroblasts from dedifferentiated mature perimuscular fat (PMF) tissue were cultured with differentiation stimulants until the cells exhibited morphological differentiation. Treated cells were harvested from day 2 to 16 for RNA extraction, whereas control cells were cultured without addition of stimulants. Results from time course gene expression assays by quantitative real-time PCR revealed that peroxisome proliferator-activated receptor gamma (PPAR-{gamma}), sterol regulatory element binding protein 1 (SREBP-1) and their six down-stream genes were co-expressed at day 2 post-differentiation induction. When compared to other adipogenesis culture systems, the adipogenic gene expression of bovine PMF adipofibroblasts culture was different, especially to the rodent model. Collectively, these results demonstrated PPAR-{gamma} and SREBP-1 cooperatively play a key role to regulate the re-differentiation of bovine adipofibroblasts, during early conversion stages in vitro.

Taniguchi, Masaaki; Le Luo Guan; Zhang Bing [Department of Agricultural, Food and Nutritional Science, University of Alberta, 410 Ag-For Centre, Edmonton, Alta., T6G 2P5 (Canada); Dodson, Michael V. [Department of Animal Sciences, Washington State University, P.O. Box 646310, Pullman, WA 99164 (United States); Okine, Erasmus [Department of Agricultural, Food and Nutritional Science, University of Alberta, 410 Ag-For Centre, Edmonton, Alta., T6G 2P5 (Canada); Moore, Stephen S. [Department of Agricultural, Food and Nutritional Science, University of Alberta, 410 Ag-For Centre, Edmonton, Alta., T6G 2P5 (Canada)], E-mail: Stephen.moore@ualberta.ca

2008-02-01

211

Impact of external sources of infection on the dynamics of bovine tuberculosis in modelled badger populations  

PubMed Central

Background The persistence of bovine TB (bTB) in various countries throughout the world is enhanced by the existence of wildlife hosts for the infection. In Britain and Ireland, the principal wildlife host for bTB is the badger (Meles meles). The objective of our study was to examine the dynamics of bTB in badgers in relation to both badger-derived infection from within the population and externally-derived, trickle-type, infection, such as could occur from other species or environmental sources, using a spatial stochastic simulation model. Results The presence of external sources of infection can increase mean prevalence and reduce the threshold group size for disease persistence. Above the threshold equilibrium group size of 68 individuals predicted by the model for bTB persistence in badgers based on internal infection alone, external sources of infection have relatively little impact on the persistence or level of disease. However, within a critical range of group sizes just below this threshold level, external infection becomes much more important in determining disease dynamics. Within this critical range, external infection increases the ratio of intra- to inter-group infections due to the greater probability of external infections entering fully-susceptible groups. The effect is to enable bTB persistence and increase bTB prevalence in badger populations which would not be able to maintain bTB based on internal infection alone. Conclusions External sources of bTB infection can contribute to the persistence of bTB in badger populations. In high-density badger populations, internal badger-derived infections occur at a sufficient rate that the additional effect of external sources in exacerbating disease is minimal. However, in lower-density populations, external sources of infection are much more important in enhancing bTB prevalence and persistence. In such circumstances, it is particularly important that control strategies to reduce bTB in badgers include efforts to minimise such external sources of infection. PMID:22738118

2012-01-01

212

Characterization of aggregation and protein expression of bovine corneal endothelial cells as microcarrier cultures in a rotating-wall vessel  

Microsoft Academic Search

Rotating-wall vessels are beneficial to tissue engineering in that the reconstituted tissue formed in these low-shear bioreactors undergoes extensive three-dimensional growth and differentiation. In the present study, bovine corneal endothelial (BCE) cells were grown in a high-aspect rotating-wall vessel (HARV) attached to collagen-coated Cytodex-3 beads as a representative monolayer culture to investigate factors during HARV cultivation which affect three-dimensional growth

James W. Muhitch; Kim C. O'Connor; Diane A. Blake; Daniel J. Lacks; Nitsa Rosenzweig; Glenn F. Spaulding

2000-01-01

213

Bovine TWINKLE and mitochondrial ribosomal protein L43 genes are regulated by an evolutionary conserved bidirectional promoter.  

PubMed

TWINKLE is a mitochondrial DNA helicase playing an important role in mitochondrial DNA replication. In human, mutations in this gene cause progressive external ophtalmoplegia and mitochondrial DNA depletion syndrome-7. TWINKLE is well conserved among multicellular eukaryotes and is believed to be a key regulator of mitochondrial DNA copy number in mammals. Despite its involvement in several diseases and its important function in mitochondrial DNA metabolism, nothing is known about the regulation of the expression of TWINKLE. We have analysed the 5'-flanking genomic region of the bovine TWINKLE gene and found it was localised adjacent to the MRPL43 gene in a head-to-head orientation, suggesting that both genes are regulated by a shared bidirectional promoter. The bovine 75-bp long intergenic region shows substantial homology across different species and contains several conserved putative transcription factor binding sites. A TATA box, however, was lacking. Using a dual fluorescent reporter system and transient transfection assays, we have analysed the bovine intergenic region between TWINKLE and MRPL43. This small genomic fragment showed a bidirectional promoter activity. As the TWINKLE/MRPL43 bidirectional promoter tested was highly conserved, it is likely that the results we obtained here in cattle may be extended to the other species. PMID:24361965

Meersseman, Cdric; Ljard, Vronique; Rebours, Emmanuelle; Boussaha, Mekki; Maftah, Abderrahman; Petit, Daniel; Rocha, Dominique

2014-03-01

214

Both foot-and-mouth disease virus and bovine viral diarrhea virus replication are inhibited by Mx1 protein originated from porcine.  

PubMed

Mx1 protein is I type interferons (IFNs)-induced 76-kDa guanosine triphosphatases (GTPases) that belong to the dynamin superfamily of large GTPases. Mx1 proteins have attracted attention because some display antiviral activity against pathogenic RNA and DNA viruses. Meanwhile, Mx1 gene generally exists in organisms or cells of mammalian, fish and chicken. Blocking a wide range of RNA virus replication by inhibiting nuclear viral mRNA synthesis is a unique property of Mx1 protein. In order to investigate a novel prevention measure against foot-and-mouth disease virus (FMDV) and bovine viral diarrhea virus (BVDV), which frequently break out in Xinjiang Uygur Autonomous Region of China, we investigated the effects of porcine Mx1 protein on FMDV and BVDV replication by measuring viral reverse transcriptase activity at various time intervals. In our study, Mx1 protein was overexpressed in BHK-21 and MDBK cells mediated by lentivirus prior to infect with FMDV and BVDV. FMDV and BVDV replication levels were monitored by quantitative real-Time PCR. The results showed porcine Mx1 overexpression significantly inhibited both FMDV and BVDV replication within 12 and 36 hours post-infection (pi). The finding may provide a new therapeutic approach for preventing from FDMV and BVDV infection. PMID:25153459

Shi, Huijun; Fu, Qiang; Ren, Yan; Wang, Dawei; Qiao, Jun; Wang, Pengyan; Zhang, Hui; Chen, Chuangfu

2015-01-01

215

Effects of Saturated Long-chain Fatty Acid on mRNA Expression of Genes Associated with Milk Fat and Protein Biosynthesis in Bovine Mammary Epithelial Cells  

PubMed Central

This study was conducted to determine the effects of saturated long-chain fatty acids (LCFA) on cell proliferation and triacylglycerol (TAG) content, as well as mRNA expression of ?s1-casein (CSN1S1) and genes associated with lipid and protein synthesis in bovine mammary epithelial cells (BMECs). Primary cells were isolated from the mammary glands of Holstein dairy cows, and were passaged twice. Then cells were cultured with different levels of palmitate or stearate (0, 200, 300, 400, 500, and 600 ?M) for 48 h and fetal bovine serum in the culture solution was replaced with fatty acid-free BSA (1 g/L). The results showed that cell proliferation tended to be increased quadratically with increasing addition of stearate. Treatments with palmitate or stearate induced an increase in TAG contents at 0 to 600 ?M in a concentration-dependent manner, and the addition of 600 ?M was less effective in improving TAG accumulation. The expression of acetyl-coenzyme A carboxylase alpha, fatty acid synthase and fatty acid-binding protein 3 was inhibited when palmitate or stearate were added in culture medium, whereas cluster of differentiation 36 and CSN1S1 mRNA abundance was increased in a concentration-dependent manner. The mRNA expressions of peroxisome proliferator-activated receptor gamma, mammalian target of rapamycin and signal transducer and activator of transcription 5 with palmitate or stearate had no significant differences relative to the control. These results implied that certain concentrations of saturated LCFA could stimulate cell proliferation and the accumulation of TAG, whereas a reduction may occur with the addition of an overdose of saturated LCFA. Saturated LCFA could up-regulate CSN1S1 mRNA abundance, but further studies are necessary to elucidate the mechanism for regulating milk fat and protein synthesis. PMID:25049969

Qi, Lizhi; Yan, Sumei; Sheng, Ran; Zhao, Yanli; Guo, Xiaoyu

2014-01-01

216

The use of bovine screws to promote bone formation using a tibia model in dogs  

PubMed Central

The objective of this study was to evaluate the use of a unique resorbable bovine bone screw, to stimulate bone formation. Bovine bone screws were inserted in the tibia beagle dogs. Each animal received 8 screws, divided into Groups A (screws + no membranes), B (screws + titanium reinforced membranes) and C (bone defects treated with autogenous bone grafts). Animals were sacrificed at 2, 4 and 6 months. New bone was measured with a periodontal probe and reported an average of 7.4 mm in vertical bone gain for Group B, 3.6 mm for Group A and 1.7 mm for Group C. Submission to Kruskal-Wallis test showed statistical differences between groups (p<0,05). Histological examination revealed an intimate contact between the newly formed bone and the resorbing bone screws. Conclusion: Bovine bone screws provide environment for new bone formation and thus may provide an alternative therapy for enhancing bone formation vertically, including for regenerative procedures as well as prior to implant therapy. PMID:23058228

Bianchini, Marco Aurlio; Pontual, Marco Antnio B; Bez, Leonardo; Benfatti, Csar Augusto M; Boabaid, Fernanda; Somerman, Martha J; Magini, Ricardo S

2013-01-01

217

Modeling protein binding and elution over a chromatographic surface probed by surface plasmon resonance.  

PubMed

Surface plasmon resonance (SPR) spectroscopy is used as a scaled-down, analytical, pseudo-chromatography tool for analyzing protein binding and elution over an ion-exchange surface under cyclic sorption conditions. A micrometric-scale adsorption surface was produced by immobilizing a typical ion exchange ligand--diethylaminoethyl (DEAE)--onto commercially available planar gold sensor chip surfaces pre-derivatized with a self-assembled monolayer of 11-mercaptoundecanoic acid with known density. An explicit mathematical formulation is provided for the deconvolution and interpretation of the SPR sensorgrams. An adsorption rate model is proposed to describe the SPR sensorgrams for bovine serum albumin, used here as model protein, when the DEAE surface is subjected to a cyclic series of binding and elution steps. Overall, we demonstrate that the adsorption rate model is capable of quantitatively describing BSA binding and elution for protein titers from dilute conditions up to overloaded conditions and a broad range of salt concentrations. PMID:20171645

Vicente, Tiago; Mota, Jos P B; Peixoto, Cristina; Alves, Paula M; Carrondo, Manuel J T

2010-03-26

218

Moving-Shot versus Fixed Electrode Techniques for Radiofrequency Ablation: Comparison in an Ex-Vivo Bovine Liver Tissue Model  

PubMed Central

Objective To compare the ablation characteristics of the moving-shot technique (MST) and the fixed electrode technique (FET) for radiofrequency (RF) ablation in an ex-vivo bovine liver tissue model. Materials and Methods We performed RF ablation using FET in 110 bovine liver blocks using 11 different ablation times ranging from 5 seconds to 5 minutes (10 blocks per each time duration). Ten bovine liver blocks at each ablation time of 1- or 2-minute, were ablated with MST, which treated conceptual ablation units by moving the electrode tip. We evaluated the ablation volume obtained with FET across ablation time lengths. The results of FET and MST performed with the same ablation time lengths, i.e., 1- and 2-minute ablation time were also compared. Results The ablation volume achieved with FET gradually increased with increasing ablation time; however, the pair-wise statistical comparison between 2 neighboring ablation time lengths was not significant after 30 seconds. MST with either 1- or 2-minute ablation time achieved larger ablation volumes (1.1 0.2 mL vs. 2.7 0.3 mL, p < 0.001; and 1.4 0.2 mL vs. 5.6 0.4 mL, p < 0.001, respectively), longer true RF times (46.7 4.6 seconds vs. 60 seconds, p < 0.001; and 64.8 4.6 seconds vs. 120 seconds, p < 0.001, respectively), fewer numbers of RF cut-offs (1.6 0.5 vs. 0, p < 0.001; and 5.5 0.5 vs. 0, p < 0.001, respectively), and greater energy deposition (2050.16 209.2 J vs. 2677.76 83.68 J, p < 0.001; and 2970.64 376.56 J vs. 5564.72 5439.2 J, p < 0.001, respectively), than FET. Conclusion The MST can achieve a larger ablation volume by preventing RF cut-off, compared with the FET in an ex-vivo bovine liver model. PMID:25469097

Ha, Eun Ju; Lee, Jeong Hyun

2014-01-01

219

Technical note: A pilot study using a mouse mastitis model to study differences between bovine associated coagulase-negative staphylococci.  

PubMed

Coagulase-negative staphylococci (CNS) are a group of bacteria classified as either minor mastitis pathogens or commensal microbiota. Recent research suggests species- and even strain-related epidemiological and genetic differences within the large CNS group. The current pilot study investigated in 2 experiments whether a mouse mastitis model validated for bovine Staphylococcus aureus can be used to explore further differences between CNS species and strains. In a first dose titration experiment, a low inoculum dose of S. aureus Newbould 305 (positive control) was compared with increasing inoculum doses of a Staphylococcus chromogenes strain originating from a chronic bovine intramammary infection to a sham-inoculated mammary glands (negative control). In contrast to the high bacterial growth following inoculation with S. aureus, S. chromogenes was retrieved in very low levels at 24 h postinduction (p.i.). In a second experiment, the inflammation inflicted by 3 CNS strains was studied in mice. The host immune response induced by the S. chromogenes intramammary strain was compared with the one induced by a Staphylococcus fleurettii strain originating from cow bedding sawdust and by a S. chromogenes strain originating from a teat apex of a heifer. As expected, at 28 and 48 h p.i., low bacterial growth and local neutrophil influx in the mammary gland were induced by all CNS strains. As hypothesized, bacterial growth p.i. was the lowest for S. fleurettii compared with that induced by the 2 S. chromogenes strains, and the overall immune response established by the 3 CNS strains was less pronounced compared with the one induced by S. aureus. Proinflammatory cytokine profiling revealed that S. aureus locally induced IL-6 and IL-1? but not TNF-?, whereas, overall, CNS-inoculated glands lacked a strong cytokine host response but also induced IL-1? locally. Compared with both other CNS strains, S. chromogenes from the teat apex inflicted a more variable IL-1? response characterized by a more intense local reaction in several mice. This pilot study suggests that an intraductal mouse model can mimic bovine CNS mastitis and has potential as a complementary in vivo tool for future CNS mastitis research. Furthermore, it indicates that epidemiologically different bovine CNS species or strains induce a differential host innate immune response in the murine mammary gland. PMID:25497801

Breyne, K; De Vliegher, S; De Visscher, A; Piepers, S; Meyer, E

2015-02-01

220

The effect of the number of observations used for Fourier transform infrared model calibration for bovine milk fat composition on the estimated genetic parameters of the predicted data  

Microsoft Academic Search

Fourier transform infrared spectroscopy is a suitable method to determine bovine milk fat composition. However, the determination of fat composition by gas chromatography, required for calibration of the infrared prediction model, is expensive and labor intensive. It has recently been shown that the number of calibration samples is strongly related to the model's validation r2 (i.e., accuracy of prediction). However,

M. J. M. Rutten; H. Bovenhuis; Arendonk van J. A. M

2010-01-01

221

Protein crystal growth in microgravity review of large scale temperature induction method: Bovine insulin, human insulin and human {alpha}-interferon  

SciTech Connect

The Protein Crystal Growth Facility (PCF) is space-flight hardware that accommodates large scale protein crystal growth experiments using temperature change as the inductive step. Recent modifications include specialized instrumentation for monitoring crystal nucleation with laser light scattering. This paper reviews results from its first seven flights on the Space Shuttle, the last with laser light scattering instrumentation in place. The PCF's objective is twofold: (1) the production of high quality protein crystals for x-ray analysis and subsequent structure-based drug design and (2) preparation of a large quantity of relatively contaminant free crystals for use as time-release protein pharmaceuticals. The first three Shuttle flights with bovine insulin constituted the PCF's proof of concept, demonstrating that the space-grown crystals were larger and diffracted to higher resolution than their earth-grown counterparts. The later four PCF missions were used to grow recombinant human insulin crystals for x-ray analysis and continue productions trials aimed at the development of a processing facility for crystalline recombinant a-interferon.

Long, Marianna M.; Bishop, John Bradford; DeLucas, Lawrence J.; Nagabhushan, Tattanhalli L.; Reichert, Paul; Smith, G. David [Center for Macromolecular Crystallography University of Alabama at Birmingham, Birmingham, Alabama (United States); Schering Plough Research Institute Kenilworth, New Jersey (United States); Hauptman-Woodward Medical Research Institute Buffalo, New York and Roswell Park Cancer Institute Buffalo, New York (United States)

1997-01-10

222

Antibody responses against non-structural protein 3 of bovine viral diarrhoea virus in milk and serum samples from animals immunised with an inactivated vaccine.  

PubMed

Antibodies against non-structural protein 3 (NS3, p80) of bovine viral diarrhoea virus (BVDV) were determined in milk from cows vaccinated with an inactivated BVDV vaccine and compared to serum antibody levels. Animals in one herd were vaccinated with an inactivated BVDV vaccine according to the standard protocol and animals from a second herd with an intensive schedule. Serum and milk samples were tested for BVDV NS3 antibodies using five commercial ELISAs. With a few exceptions, vaccination according to the standard schedule did not induce BVDV NS3-specific antibodies in serum or milk. However, after vaccination according to the intensive schedule, anti-NS3 antibodies were detected for a short time in serum and, to a lesser extent, in milk. Bulk milk was a suitable substrate for BVDV monitoring of herds vaccinated with the inactivated BVD vaccine. PMID:21482158

Alvarez, Marcelino; Donate, Jorge; Makoschey, Birgit

2012-03-01

223

Modeling Intrinsically Disordered Proteins with Bayesian Statistics  

E-print Network

The characterization of intrinsically disordered proteins is challenging because accurate models of these systems require a description of both their thermally accessible conformers and the associated relative stabilities ...

Fisher, Charles K.

224

An economic model to evaluate the mitigation programme for bovine viral diarrhoea in Switzerland.  

PubMed

Economic analyses are indispensable as sources of information to help policy makers make decisions about mitigation resource use. The aim of this study was to conduct an economic evaluation of the Swiss national mitigation programme for bovine viral diarrhoea virus (BVDV), which was implemented in 2008 and concludes in 2017. The eradication phase of the mitigation programme comprised testing and slaughtering of all persistently infected (PI) animals found. First, the whole population was antigen tested and all PI cattle removed. Since October 2008, all newborn calves have been subject to antigen testing to identify and slaughter PI calves. All mothers of PI calves were retested and slaughtered if the test was positive. Antigen testing in calves and elimination of virus-carriers was envisaged to be conducted until the end of 2011. Subsequently, a surveillance programme will document disease freedom or detect disease if it recurs. Four alternative surveillance strategies based on antibody testing in blood from newborn calves and/or milk from primiparous cows were proposed by Federal Veterinary Office servants in charge of the BVDV mitigation programme. A simple economic spreadsheet model was developed to estimate and compare the costs and benefits of the BVDV mitigation programme. In an independent project, the impact of the mitigation programme on the disease dynamics in the population was simulated using a stochastic compartment model. Mitigation costs accrued from materials, labour, and processes such as handling and testing samples, and recording results. Benefits were disease costs avoided by having the mitigation programme in place compared to a baseline of endemic disease equilibrium. Cumulative eradication costs and benefits were estimated to determine the break-even point for the eradication component of the programme. The margin over eradication cost therefore equalled the maximum expenditure potentially available for surveillance without the net benefit from the mitigation programme overall becoming zero. Costs of the four surveillance strategies and the net benefit of the mitigation programme were estimated. Simulations were run for the years 2008-2017 with 20,000 iterations in @Risk for Excel. The mean baseline disease costs were estimated to be 16.04 m CHF (1 Swiss Franc, CHF=0.73 at the time of analysis) (90% central range, CR: 14.71-17.39 m CHF) in 2008 and 14.89 m CHF (90% CR: 13.72-16.08 m CHF) in 2009. The break-even point was estimated to be reached in 2012 and the margin over eradication cost 63.15m CHF (90% CR: 53.72-72.82 m CHF). The discounted cost for each surveillance strategy was found to be smaller than the margin, so the mitigation programme overall is expected to have a positive net economic benefit irrespective of the strategy adopted. For economic efficiency, the least cost surveillance alternative must be selected. PMID:22402180

Hsler, B; Howe, K S; Presi, P; Strk, K D C

2012-09-15

225

Protein Structure Prediction with Lattice Models  

E-print Network

that catalyze most cellular biochemical reactions. Amino acids are joined end-to-end during protein synthesis1 Protein Structure Prediction with Lattice Models William E. Hart Sandia National Laboratories ............................................ 1-21 1.1 Introduction A protein is a complex biological macromolecule composed of a sequence

Newman, Alantha

226

Bovine Pericardium Patch Wrapping Intestinal Anastomosis Improves Healing Process and Prevents Leakage in a Pig Model  

PubMed Central

Failure of intestinal anastomosis is a major complication following abdominal surgery. Biological materials have been introduced as reinforcement of abdominal wall hernia in contaminated setting. An innovative application of biological patch is its use as reinforcement of gastrointestinal anastomosis. The aim of study was to verify whether the bovine pericardium patch improves the healing of anastomosis, when in vivo wrapping the suture line of pig intestinal anastomosis, avoiding leakage in the event of deliberately incomplete suture. Forty-three pigs were randomly divided: Group 1 (control, n?=?14): hand-sewn ileo-ileal and colo-colic anastomosis; Group 2 (n?=?14): standard anastomosis wrapped by pericardium bovine patch; Group 3 (n?=?1) and 4 (n?=?14): one suture was deliberately incomplete and also wrapped by patch in the last one. Intraoperative evaluation, histological, biochemical, tensiometric and electrophysiological studies of intestinal specimens were performed at 48 h, 7 and 90 days after. In groups 2 and 4, no leak, stenosis, abscess, peritonitis, mesh displacement or shrinkage were found and adhesion rate decreased compared to control. Biochemical studies showed mitochondrial function improvement in colic wrapped anastomosis. Tensiometric evaluations suggested that the patch preserves the colic contractility similar to the controls. Electrophysiological results demonstrated that the patch also improves the mucosal function restoring almost normal transport properties. Use of pericardium bovine patch as reinforcement of intestinal anastomosis is safe and effective, significantly improving the healing process. Data of prevention of acute peritonitis and leakage in cases of iatrogenic perforation of anastomoses, covered with patch, is unpublished. PMID:24489752

Testini, Mario; Gurrado, Angela; Portincasa, Piero; Scacco, Salvatore; Marzullo, Andrea; Piccinni, Giuseppe; Lissidini, Germana; Greco, Luigi; De Salvia, Maria Antonietta; Bonfrate, Leonilde; Debellis, Lucantonio; Sardaro, Nicola; Staffieri, Francesco; Carrat, Maria Rosaria; Crovace, Antonio

2014-01-01

227

Bovine pericardium patch wrapping intestinal anastomosis improves healing process and prevents leakage in a pig model.  

PubMed

Failure of intestinal anastomosis is a major complication following abdominal surgery. Biological materials have been introduced as reinforcement of abdominal wall hernia in contaminated setting. An innovative application of biological patch is its use as reinforcement of gastrointestinal anastomosis. The aim of study was to verify whether the bovine pericardium patch improves the healing of anastomosis, when in vivo wrapping the suture line of pig intestinal anastomosis, avoiding leakage in the event of deliberately incomplete suture. Forty-three pigs were randomly divided: Group 1 (control, n = 14): hand-sewn ileo-ileal and colo-colic anastomosis; Group 2 (n = 14): standard anastomosis wrapped by pericardium bovine patch; Group 3 (n = 1) and 4 (n = 14): one suture was deliberately incomplete and also wrapped by patch in the last one. Intraoperative evaluation, histological, biochemical, tensiometric and electrophysiological studies of intestinal specimens were performed at 48 h, 7 and 90 days after. In groups 2 and 4, no leak, stenosis, abscess, peritonitis, mesh displacement or shrinkage were found and adhesion rate decreased compared to control. Biochemical studies showed mitochondrial function improvement in colic wrapped anastomosis. Tensiometric evaluations suggested that the patch preserves the colic contractility similar to the controls. Electrophysiological results demonstrated that the patch also improves the mucosal function restoring almost normal transport properties. Use of pericardium bovine patch as reinforcement of intestinal anastomosis is safe and effective, significantly improving the healing process. Data of prevention of acute peritonitis and leakage in cases of iatrogenic perforation of anastomoses, covered with patch, is unpublished. PMID:24489752

Testini, Mario; Gurrado, Angela; Portincasa, Piero; Scacco, Salvatore; Marzullo, Andrea; Piccinni, Giuseppe; Lissidini, Germana; Greco, Luigi; De Salvia, Maria Antonietta; Bonfrate, Leonilde; Debellis, Lucantonio; Sardaro, Nicola; Staffieri, Francesco; Carrat, Maria Rosaria; Crovace, Antonio

2014-01-01

228

Stochastic model for protein flexibility analysis  

NASA Astrophysics Data System (ADS)

Protein flexibility is an intrinsic property and plays a fundamental role in protein functions. Computational analysis of protein flexibility is crucial to protein function prediction, macromolecular flexible docking, and rational drug design. Most current approaches for protein flexibility analysis are based on Hamiltonian mechanics. We introduce a stochastic model to study protein flexibility. The essential idea is to analyze the free induction decay of a perturbed protein structural probability, which satisfies the master equation. The transition probability matrix is constructed by using probability density estimators including monotonically decreasing radial basis functions. We show that the proposed stochastic model gives rise to some of the best predictions of Debye-Waller factors or B factors for three sets of protein data introduced in the literature.

Xia, Kelin; Wei, Guo-Wei

2013-12-01

229

Physical interaction between bovine viral diarrhea virus nonstructural protein 4A and adenosine deaminase acting on RNA (ADAR).  

PubMed

Bovine viral diarrhea virus (BVDV) is a positive-sense RNA virus known to produce double-stranded RNA (dsRNA) during its replication in the cytoplasm. Extended dsRNA duplexes can be hyperedited by adenosine deaminase acting on RNA (ADAR), which catalyzes adenosine (A)-to-inosine (I) editing. A-to-I editing has been reported for various viruses. A number of cellular antiviral defense strategies are stimulated by dsRNA, and this may involve hyperediting of dsRNA by ADARs, followed by targeted cleavage by cytoplasmic endonucleases. Here, we identify ADAR as a binding partner of BVDV NS4A in vitro and in vivo and show that the N-terminal domain of NS4A is the ADAR-binding domain. We also show that ADAR has an inhibitory effect on BVDV replication when overexpressed in BVDV-infected bovine cells. Our findings suggest a role of NS4A in the interaction of BVDV with ADAR that favors virus replication. PMID:24500065

Mohamed, Yassir Mahgoub; Bangphoomi, Norasuthi; Yamane, Daisuke; Suda, Yuto; Kato, Kentaro; Horimoto, Taisuke; Akashi, Hiroomi

2014-07-01

230

Efficacy of a Novel Whey Protein Gel Complex to Increase the Unsaturated Fatty Acid Composition of Bovine Milk Fat  

Microsoft Academic Search

A novel whey protein emulsion gel (WPEG) complex was developed to protect dietary unsaturated fatty acids from rumen biohydrogenation with the goal of modifying the fatty acid composition of milk fat. Three experiments were conducted with WPEG complexes made from either whey protein concentrate containing 80% crude protein, whey protein isolate, or whey pro- tein concentrate high-gel capacity. Each experiment

S. M. Carroll; E. J. DePeters; M. Rosenberg

2006-01-01

231

Phosphoproteome analysis of sarcoplasmic and myofibrillar proteins in bovine longissimus muscle in response to postmortem electrical stimulation.  

PubMed

Protein phosphorylation changes of the sarcoplasmic and myofibrillar proteins in beef longissimus muscle in response to electrical stimulation (ES) was investigated. Sarcoplasmic and myofibrillar proteins purified from muscle samples taken at 0, 3 and 10h after ES were separated on SDS-PAGE and stained with phosphorous and protein specific stains. There was a significant effect of ES on phosphorylation of total sarcoplasmic and myofibrillar proteins (P<0.05). However, although there an instant effect of ES on the phosphorylation level of the myofibrillar proteins, the ES effect on the sarcoplasmic proteins (P<0.05) was first observed after 3h. Several protein bands were analyzed by LC-MS/MS, revealing that the major glycolytic proteins, including glycogen debranching enzyme, glycogen phosphorylase and 6-phosphofructokinase probably are affected by ES together with different heat shock proteins. This work gives an insight into the regulation of the glycolytic enzymes and muscle contraction on application of electrical stimulation. PMID:25577070

Li, Chunbao; Zhou, Guanghong; Xu, Xinglian; Lundstrm, Kerstin; Karlsson, Anders; Lametsch, Ren

2015-05-15

232

Conserved Cysteine Residue in the DNA-Binding Domain of the Bovine Papillomavirus Type 1 E2 Protein Confers Redox Regulation of the DNA- Binding Activity in Vitro  

NASA Astrophysics Data System (ADS)

The bovine papillomavirus type 1 E2 open reading frame encodes three proteins involved in viral DNA replication and transcriptional regulation. These polypeptides share a carboxyl-terminal domain with a specific DNA-binding activity; through this domain the E2 polypeptides form dimers. In this study, we demonstrate the inhibition of E2 DNA binding in vitro by reagents that oxidize or otherwise chemically modify the free sulfydryl groups of reactive cysteine residues. However, these reagents had no effect on DNA-binding activity when the E2 polypeptide was first bound to DNA, suggesting that the free sulfydryl group(s) may be protected by DNA binding. Sensitivity to sulfydryl modification was mapped to a cysteine residue at position 340 in the E2 DNA-binding domain, an amino acid that is highly conserved among the E2 proteins of different papillomaviruses. Replacement of this residue with other amino acids abrogated the sensitivity to oxidation-reduction changes but did not affect the DNA-binding property of the E2 protein. These results suggest that papillomavirus DNA replication and transcriptional regulation could be modulated through the E2 proteins by changes in the intracellular redox environment. Furthermore, a motif consisting of a reactive cysteine residue carboxyl-terminal to a lysine residue in a basic region of the DNA-binding domain is a feature common to a number of transcriptional regulatory proteins that, like E2, are subject to redox regulation. Thus, posttranslational regulation of the activity of these proteins by the intracellular redox environment may be a general phenomenon.

McBride, Alison A.; Klausner, Richard D.; Howley, Peter M.

1992-08-01

233

In bovine binucleate trophoblast giant cells, pregnancy-associated glycoproteins and placental prolactin-related protein-I are conjugated to asparagine-linked N-acetylgalactosaminyl glycans.  

PubMed

Bovine binucleate trophoblast giant cells (BNCs) produce large amounts of PAS-positive cytoplasmic granules. After fusion of BNCs with uterine epithelial cells, the contents of these granules are released into the maternal stroma which underlies the uterine epithelium. Histochemically, the granules can be labeled with N-acetylgalactosamine-specific lectins ( Dolichos biflorus, Vicia villosa, and Wisteria floribunda agglutinins) and with Phaseolus vulgaris leucoagglutinin. In this study, we used lectin western blot analysis of proteins from fetal cotyledons to characterize the lectin binding glycoproteins. Lectin western blots showed several bands. A main band of approximately 65 kDa was identified as pregnancy-associated glycoproteins (PAGs) and a double band at 34-35 kDa as prolactin-related protein-I (PRP-I) by their crossreactivity with specific antisera. Enzymatic cleavage of N-linked glycans with peptide- N-glycanase F abolished the lectin binding to PRP and PAGs in western blots, revealing that the lectins bound to asparagine-linked glycans. The high specificity of the lectins was used for the enrichment of PRP-I and PAGs from placental cotyledons with Vicia villosa lectin affinity chromatography. The occurrence of the relatively uncommon asparagine-linked N-acetylgalactosaminyl glycans on secretory proteins of the BNCs suggests a functional role of this specific glycosylation pattern. PMID:12649735

Klisch, Karl; Leiser, Rudolf

2003-03-01

234

Chlorpyrifos Alters Functional Integrity and Structure of an In Vitro BBB Model: Co-cultures of Bovine Endothelial Cells and Neonatal Rat Astrocytes  

Microsoft Academic Search

The bloodbrain barrier (BBB) is a structural and functional interface between the circulatory system and the brain. Organophosphorous compounds such as chlorpyrifos (CPF) may cross the BBB and disrupt BBB integrity and function. To determine events that may contribute to CPF toxicity, we used an in vitro BBB model in which bovine microvascular endothelial cells (BMEC) and neonatal rat astrocytes

Damani K. Parran; Geraldine Magnin; Wen Li; Bernard S. Jortner; Marion Ehrich

2005-01-01

235

Information-driven structural modelling of protein-protein interactions.  

PubMed

Protein-protein docking aims at predicting the three-dimensional structure of a protein complex starting from the free forms of the individual partners. As assessed in the CAPRI community-wide experiment, the most successful docking algorithms combine pure laws of physics with information derived from various experimental or bioinformatics sources. Of these so-called "information-driven" approaches, HADDOCK stands out as one of the most successful representatives. In this chapter, we briefly summarize which experimental information can be used to drive the docking prediction in HADDOCK, and then focus on the docking protocol itself. We discuss and illustrate with a tutorial example a "classical" protein-protein docking prediction, as well as more recent developments for modelling multi-body systems and large conformational changes. PMID:25330973

Rodrigues, Joo P G L M; Karaca, Ezgi; Bonvin, Alexandre M J J

2015-01-01

236

Hidden Markov Models in Computational Biology Applications to Protein Modeling  

Microsoft Academic Search

Ridden .Markov Models (HMMs) are applied t.0 the problems of statistical modeling, database searching and multiple sequence alignment of protein families and protein domains. These methods are demonstrated on the globin family, the protein kinase catalytic domain, and the EF-hand calcium binding motif. In each case the parameters of an HMM are estimated from a training set of unaligned sequences.

Anders Krogh; Michael Brown; I. Saira

1994-01-01

237

Hyperoxia-induced ciliary loss and oxidative damage in an in vitro bovine model: The protective role of antioxidant vitamins E and C  

SciTech Connect

Highlights: Black-Right-Pointing-Pointer A new bovine bronchial model for studying hyperoxia-induced cilia loss is presented. Black-Right-Pointing-Pointer Hyperoxia-induced cilia loss was associated with increased sloughing of cells. Black-Right-Pointing-Pointer Hyperoxia led to higher epithelial glutathione levels, evidence of oxidative stress. Black-Right-Pointing-Pointer Hyperoxia led to increased DNA damage (Comet), and lipid peroxidation (TBARS). Black-Right-Pointing-Pointer Vitamins C and E partially protected against hyperoxia-induced cilia loss. -- Abstract: Although elevated oxygen fraction is used in intensive care units around the world, pathological changes in pulmonary tissue have been shown to occur with prolonged exposure to hyperoxia. In this work a bovine bronchus culture model has been successfully used to evaluate the effects of hyperoxia on ciliated epithelium in vitro. Samples were cultured using an air interface method and exposed to normoxia, 21% O{sub 2} or hyperoxia, 95% O{sub 2}. Cilial coverage was assessed using scanning electron microscopy (SEM). Tissue damage (lactate dehydrogenase, LDH, in the medium), lipid peroxidation (thiobarbituric acid reactive substances, TBARS), DNA damage (comet assay), protein oxidation (OxyBlot kit) and antioxidant status (total glutathione) were used to assess whether the hyperoxia caused significant oxidative stress. Hyperoxia caused a time-dependent decline (t{sub Vulgar-Fraction-One-Half} = 3.4 d compared to 37.1 d under normoxia) in cilial coverage (P < 0.0001). This was associated with a significant increase in the number of cells (2.80 {+-} 0.27 Multiplication-Sign 10{sup 6} compared to 1.97 {+-} 0.23 Multiplication-Sign 10{sup 6} ml{sup -1} after 6 d), many apparently intact, in the medium (P < 0.05); LDH release (1.06 {+-} 0.29 compared to 0.83 {+-} 0.36 {mu}mol min{sup -1} g{sup -1} after 6 d; P < 0.001); lipid peroxidation (352 {+-} 16 versus 247 {+-} 11 {mu}mol MDA g{sup -1} for hyperoxia and normoxia, respectively); % tail DNA (18.7 {+-} 2.2 versus 11.1 {+-} 1.5); protein carbonyls (P < 0.05); and total glutathione (229 {+-} 20 {mu}mol g{sup -1} versus 189 {+-} 15 {mu}mol g{sup -1}). Vitamins E (10{sup -7} M) and C (10{sup -6} or 10{sup -7} M) alone or in combination (10{sup -7} M and 10{sup -6} M, respectively) had a significant protective effect on the hyperoxia-induced reduction in percentage cilial coverage (P < 0.05). In conclusion, hyperoxia caused damage to cultured bovine bronchial epithelium and denudation of cilia. The antioxidant vitamins E and C significantly protected against hyperoxia-induced cilia loss.

Al-Shmgani, Hanady S.; Moate, Roy M. [School of Biomedical and Biological Sciences, University of Plymouth (United Kingdom)] [School of Biomedical and Biological Sciences, University of Plymouth (United Kingdom); Sneyd, J. Robert [Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth (United Kingdom)] [Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth (United Kingdom); Macnaughton, Peter D. [Derriford Critical Care Unit, Plymouth (United Kingdom)] [Derriford Critical Care Unit, Plymouth (United Kingdom); Moody, A. John, E-mail: jmoody@plymouth.ac.uk [School of Biomedical and Biological Sciences, University of Plymouth (United Kingdom)

2012-12-14

238

An integrated probabilistic model for functional prediction of proteins  

Microsoft Academic Search

We develop an integrated probabilistic model to combine protein physical interactions, genetic interactions, highly correlated gene expression network, protein complex data, and domain structures of individual proteins to predict protein functions. The model is an extension of our previous model for protein function prediction based on Markovian random field theory. The model is flexible in that other protein pairwise relationship

Minghua Deng; Ting Chen; Fengzhu Sun

2003-01-01

239

A soft and transparent handleable protein model  

NASA Astrophysics Data System (ADS)

The field of structural biology currently relies on computer-generated graphical representations of three-dimensional (3D) structures to conceptualize biomolecules. As the size and complexity of the molecular structure increases, model generation and peer discussions become more difficult. It is even more problematic when discussing protein-protein interactions wherein large surface area contact is considered. This report demonstrates the viability of a new handleable protein molecular model with a soft and transparent silicone body similar to the molecule's surface. A full-color printed main chain structure embedded in the silicone body enables users to simultaneously feel the molecular surface, view through the main chain structure, and manually simulate molecular docking. The interactive, hands-on experience deepens the user's intuitive understanding of the complicated 3D protein structure and elucidates ligand binding and protein-protein interactions. This model would be an effective discussion tool for the classroom or laboratory that stimulates inspired learning in this study field.

Kawakami, Masaru

2012-08-01

240

Temporal regulation of mRNAs for select bone morphogenetic proteins (BMP), BMP receptors and their associated SMAD proteins during bovine early embryonic development: effects of exogenous BMP2 on embryo developmental progression  

PubMed Central

Background We previously demonstrated embryotrophic actions of maternal (oocyte-derived) follistatin during bovine early embryogenesis. Classical actions of follistatin are attributed to inhibition of activity of growth factors including activins and bone morphogenetic proteins (BMP). However, temporal changes in BMP mRNA in early bovine embryos and the effects of exogenous BMP on embryo developmental progression are not understood. The objectives of present studies were to characterize mRNA abundance for select BMP, BMP receptors and BMP receptor associated SMADs during bovine oocyte maturation and early embryogenesis and determine effects of addition of exogenous BMP protein on early development. Methods Relative abundance of mRNA for BMP2, BMP3, BMP7, BMP10, SMAD1, SMAD5, ALK3, ALK6, ALK2, BMPR2, ACVR2A and ACVR2B was determined by RT-qPCR analysis of germinal vesicle (GV) and in vitro matured metaphase II (MII) oocytes and in vitro produced embryos collected at pronuclear, 2-cell (C), 4C, 8C, 16C, morula and blastocyst stages. Effects of addition of recombinant human BMP2 (0, 1, 10 and 100ng/ml) during initial 72h of embryo culture on early cleavage (within 30h post insemination), total cleavage, development to 8C-16C and blastocyst stages and blastocyst mRNA abundance for markers of inner cell mass (NANOG) and trophectoderm (CDX2) were also determined. Results Abundance of mRNA for BMP2, BMP10, SMAD1, SMAD5, ALK3, ALK2, BMPR2 and ACVR2B was elevated in MII oocytes and/or pronuclear stage embryos (relative to GV) and remained elevated through the 8C -16C stages, whereas BMP3, BMP7 and ALK2 mRNAs were transiently elevated. Culture of embryos to the 8C stage in the presence of ?-amanitin resulted in increased abundance for all of above transcripts examined relative to untreated 8C embryos. Effects of addition of exogenous BMP2 on early cleavage rates and rates of development to 8C-16C and blastocyst stages were not observed, but BMP2 treatment increased blastocyst mRNA for CDX2 and NANOG. Conclusions Abundance of maternally derived mRNAs for above BMP system components are dynamically regulated during oocyte maturation and early embryogenesis. Exogenous BMP2 treatment does not influence progression to various developmental endpoints, but impacts characteristics of resulting blastocysts. Results support a potential role for BMPs in bovine early embryogenesis. PMID:25027287

2014-01-01

241

Removal of model proteins by means of low-pressure inductively coupled plasma discharge  

NASA Astrophysics Data System (ADS)

Surgical instruments are intended to come into direct contact with the patients' tissues and thus interact with their first immune defence system. Therefore they have to be cleaned, sterilized and decontaminated, in order to prevent any kind of infections and inflammations or to exclude the possibility of transmission of diseases. From this perspective, the removal of protein residues from their surfaces constitutes new challenges, since certain proteins exhibit high resistance to commonly used sterilization and decontamination techniques and hence are difficult to remove without inducing major damages to the object treated. Therefore new approaches must be developed for that purpose and the application of non-equilibrium plasma discharges represents an interesting option. The possibility to effectively remove model proteins (bovine serum albumin, lysozyme and ubiquitin) from surfaces of different materials (Si wafer, glass, polystyrene and gold) by means of inductively coupled plasma discharges sustained in different argon containing mixtures is demonstrated and discussed in this paper.

Kylin, O.; Rauscher, H.; Gilliland, D.; Brtagnol, F.; Rossi, F.

2008-05-01

242

SWISS-MODEL: an automated protein homology-modeling server  

Microsoft Academic Search

SWISS-MODEL (http:\\/\\/swissmodel.expasy.org) is a server for automated comparative modeling of three- dimensional (3D) protein structures. It pioneered the field of automated modeling starting in 1993 and is the most widely-used free web-based automated modeling facility today. In 2002 the server computed 120 000 user requests for 3D protein models. SWISS- MODEL provides several levels of user interaction through its World

Torsten Schwede; Jrgen Kopp; Nicolas Guex; Manuel C. Peitsch

2003-01-01

243

Models of globular proteins in aqueous solutions  

NASA Astrophysics Data System (ADS)

Protein crystallization is a continuing area of research. Currently, there is no universal theory for the conditions required to crystallize proteins. A better understanding of protein crystallization will be helpful in determining protein structure and preventing and treating certain diseases. In this thesis, we will extend the understanding of globular proteins in aqueous solutions by analyzing various models for protein interactions. Experiments have shown that the liquid-liquid phase separation curves for lysozyme in solution with salt depend on salt type and salt concentration. We analyze a simple square well model for this system whose well depth depends on salt type and salt concentration, to determine the phase coexistence surfaces from experimental data. The surfaces, calculated from a single Monte Carlo simulation and a simple scaling argument, are shown as a function of temperature, salt concentration and protein concentration for two typical salts. Urate Oxidase from Asperigillus flavus is a protein used for studying the effects of polymers on the crystallization of large proteins. Experiments have determined some aspects of the phase diagram. We use Monte Carlo techniques and perturbation theory to predict the phase diagram for a model of urate oxidase in solution with PEG. The model used includes an electrostatic interaction, van der Waals attraction, and a polymerinduced depletion interaction. The results agree quantitatively with experiments. Anisotropy plays a role in globular protein interactions, including the formation of hemoglobin fibers in sickle cell disease. Also, the solvent conditions have been shown to play a strong role in the phase behavior of some aqueous protein solutions. Each has previously been treated separately in theoretical studies. Here we propose and analyze a simple, combined model that treats both anisotropy and solvent effects. We find that this model qualitatively explains some phase behavior, including the existence of a lower critical point under certain conditions.

Wentzel, Nathaniel James

244

MicroRNA regulation of bovine monocyte inflammatory and metabolic networks in an in vivo infection model  

Technology Transfer Automated Retrieval System (TEKTRAN)

Bovine mastitis is an inflammation-driven disease of the bovine mammary gland that costs the global dairy industry several billion dollars per annum. Because disease susceptibility is a multi-factorial complex phenotype, a multi-omic integrative biology approach is required to dissect the multilayer...

245

Regeneration of bovine and octopus opsins in situ with natural and artificial retinals  

SciTech Connect

The authors consider the problem of color regulation in visual pigments for both bovine rhodopsin and octopus rhodopsin. Both pigments have 11-cis-retinal as their chromophore. These rhodopsins were bleached in their native membranes, and the opsins were regenerated with natural and artificial chromophores. Both bovine and octopus opsins were regenerated with the 9-cis- and 11-cis-retinal isomers, but the octopus opsin was additionally regenerated with the 13-cis and all-trans isomers. Titration of the octopus opsin with 11-cis-retinal gave an extinction coefficient for octopus rhodopsin of 27,000 {plus minus} 3,000 M{sup {minus}1} cm{sup {minus}1} at 475 nm. The absorption maxima of bovine artificial pigments formed by regenerating opsin with the 11-cis dihydro series of chromophores support a color regulation model for bovine rhodopsin in which the chromophore-binding site of the protein has two negative charges: one directly hydrogen bonded to the Schiff base nitrogen and another near carbon-13. Formation of octopus artificial pigments with both all-trans and 11-cis dihydro chromophores leads to a similar model for octopus rhodopsin and metarhodopsin: there are two negative charges in the chromophore-binding site, one directly hydrogen bonded to the Schiff base nitrogen and a second near carbon-13. The interaction of this second charge with the chromophore in octopus rhodopsin is weaker than in bovine, while in metarhodopsin it is as strong as in bovine.

Koutalos, Y.; Ebrey, T.G.; Tsuda, M.; Odashima, K.; Lien, T.; Park, M.H.; Shimizu, N.; Derguini, F.; Nakanishi, K.; Gilson, H.R.; Honig, B. (Univ. of Illinois, Urbana-Champaign (USA))

1989-03-21

246

Screening of Mycobacterium avium subsp. paratuberculosis mutants for attenuation in a bovine monocyte-derived macrophage model.  

PubMed

Vaccination remains a major tool for prevention and progression of Johne's disease, a chronic enteritis of ruminants worldwide. Currently there is only one licensed vaccine within the United States and two vaccines licensed internationally against Johne's disease. All licensed vaccines reduce fecal shedding of Mycobacterium avium subsp. paratuberculosis (MAP) and delay disease progression. However, there are no available vaccines that prevent disease onset. A joint effort by the Johne's Disease Integrated Program (JDIP), a USDA-funded consortium, and USDA-APHIS/VS sought to identify transposon insertion mutant strains as vaccine candidates in part of a three phase study. The focus of the Phase I study was to evaluate MAP mutant attenuation in a well-defined in vitro bovine monocyte-derived macrophage (MDM) model. Attenuation was determined by colony forming unit (CFUs) counts and slope estimates. Based on CFU counts alone, the MDM model did not identify any mutant that significantly differed from the wild-type control, MAP K-10. Slope estimates using mixed models approach identified six mutants as being attenuated. These were enrolled in protection studies involving murine and baby goat vaccination-challenge models. MDM based approach identified trends in attenuation but this did not correlate with protection in a natural host model. These results suggest the need for alternative strategies for Johne's disease vaccine candidate screening and evaluation. PMID:25072030

Lamont, Elise A; Talaat, Adel M; Coussens, Paul M; Bannantine, John P; Grohn, Yrjo T; Katani, Robab; Li, Ling-ling; Kapur, Vivek; Sreevatsan, Srinand

2014-01-01

247

Screening of Mycobacterium avium subsp. paratuberculosis mutants for attenuation in a bovine monocyte-derived macrophage model  

PubMed Central

Vaccination remains a major tool for prevention and progression of Johne's disease, a chronic enteritis of ruminants worldwide. Currently there is only one licensed vaccine within the United States and two vaccines licensed internationally against Johne's disease. All licensed vaccines reduce fecal shedding of Mycobacterium avium subsp. paratuberculosis (MAP) and delay disease progression. However, there are no available vaccines that prevent disease onset. A joint effort by the Johne's Disease Integrated Program (JDIP), a USDA-funded consortium, and USDAAPHIS/VS sought to identify transposon insertion mutant strains as vaccine candidates in part of a three phase study. The focus of the Phase I study was to evaluate MAP mutant attenuation in a well-defined in vitro bovine monocyte-derived macrophage (MDM) model. Attenuation was determined by colony forming unit (CFUs) counts and slope estimates. Based on CFU counts alone, the MDM model did not identify any mutant that significantly differed from the wild-type control, MAP K-10. Slope estimates using mixed models approach identified six mutants as being attenuated. These were enrolled in protection studies involving murine and baby goat vaccination-challenge models. MDM based approach identified trends in attenuation but this did not correlate with protection in a natural host model. These results suggest the need for alternative strategies for Johne's disease vaccine candidate screening and evaluation. PMID:25072030

Lamont, Elise A.; Talaat, Adel M.; Coussens, Paul M.; Bannantine, John P.; Grohn, Yrjo T.; Katani, Robab; Li, Ling-ling; Kapur, Vivek; Sreevatsan, Srinand

2014-01-01

248

Computational model for protein unfolding simulation  

NASA Astrophysics Data System (ADS)

The protein folding problem is one of the fundamental and important questions in molecular biology. However, the all-atom molecular dynamics studies of protein folding and unfolding are still computationally expensive and severely limited by the time scale of simulation. In this paper, a simple and fast protein unfolding method is proposed based on the conformational stability analyses and structure modeling. In this method, two structure-based conditions are considered to identify the unstable regions of proteins during the unfolding processes. The protein unfolding trajectories are mimicked through iterative structure modeling according to conformational stability analyses. Two proteins, chymotrypsin inhibitor 2 (CI2) and ? -spectrin SH3 domain (SH3) were simulated by this method. Their unfolding pathways are consistent with the previous molecular dynamics simulations. Furthermore, the transition states of the two proteins were identified in unfolding processes and the theoretical ? values of these transition states showed significant correlations with the experimental data (the correlation coefficients are >0.8). The results indicate that this method is effective in studying protein unfolding. Moreover, we analyzed and discussed the influence of parameters on the unfolding simulation. This simple coarse-grained model may provide a general and fast approach for the mechanism studies of protein folding.

Tian, Xu-Hong; Zheng, Ye-Han; Jiao, Xiong; Liu, Cai-Xing; Chang, Shan

2011-06-01

249

A network model to correlate conformational change and the impedance spectrum of single proteins  

NASA Astrophysics Data System (ADS)

Integrated nanodevices based on proteins or biomolecules are attracting increasing interest in today's research. In fact, it has been shown that proteins such as azurin and bacteriorhodopsin manifest some electrical properties that are promising for the development of active components of molecular electronic devices. Here we focus on two relevant kinds of protein: bovine rhodopsin, prototype of G-protein-coupled-receptor (GPCR) proteins, and the enzyme acetylcholinesterase (AChE), whose inhibition is one of the most qualified treatments of Alzheimer's disease. Both these proteins exert their function starting with a conformational change of their native structure. Our guess is that such a change should be accompanied with a detectable variation of their electrical properties. To investigate this conjecture, we present an impedance network model of proteins, able to estimate the different impedance spectra associated with the different configurations. The distinct types of conformational change of rhodopsin and AChE agree with their dissimilar electrical responses. In particular, for rhodopsin the model predicts variations of the impedance spectra up to about 30%, while for AChE the same variations are limited to about 10%, which supports the existence of a dynamical equilibrium between its native and complexed states.

Alfinito, Eleonora; Pennetta, Cecilia; Reggiani, Lino

2008-02-01

250

Protein hydrogen exchange: Testing current models  

E-print Network

Protein hydrogen exchange: Testing current models John J. Skinner,1 * Woon K. Lim,2 Sabrina Bedard,1 Ben E. Black,1 and S. Walter Englander1 1 Johnson Research Foundation, Department of Biochemistry of protein hydrogen exchange (HX), HX rates of most of the backbone amide hydrogens of Staphylococcal

Englander, S. Walter

251

Relationship between stearoyl-CoA desaturase 1 gene expression, relative protein abundance, and its fatty acid products in bovine tissues.  

PubMed

Stearoyl-CoA desaturase 1 (SCD1) greatly contributes to the unsaturated fatty acids present in milk and meat of cattle. The SCD1 enzyme introduces a double bond into certain saturated fatty acyl-CoAs producing monounsaturated fatty acids (MUFA). The SCD1 enzyme also has been shown to be active in the bovine mammary gland converting t11 18:1 (vaccenic acid) to c9 t11 conjugated linoleic acid (CLA). The objective of this study was to determine any association between the gene expression of SCD1 and occurrence of its products (c9 14:1, c9 16:1, c9 18:1, and c9 t11 18:2) in various bovine tissues. Tissue samples were obtained from lactating Holstein cows (n=28) at slaughter, frozen in liquid nitrogen and stored at -80 C. Total RNA was extracted and converted to complementary DNA for quantitative real time polymerase chain reaction (PCR) analysis of the SCD1 gene. Extracted lipid was converted to fatty acid methyl esters and analysed by GC. Tissues varied in expression of SCD1 gene with mammary, cardiac, intestinal adipose, and skeletal muscle expressing greater copy number as compared with lung, large intestine, small intestine and liver (371, 369, 328, 286, 257, 145, 73, and 21 copies/ng RNA, respectively). Tissues with high mRNA expression of SCD1 contained greater SCD1 protein whereas detection of SCD1 protein in tissues with low SCD1 mRNA expression was very faint or absent. Across tissues, the desaturase indices for c9 18:1 (r=0.24) and sum of SCD products (r=0.20) were positively correlated with SCD1 gene expression (P<0.01 for both). Within each tissue, the relationship between SCD1 gene expression and the desaturase indices varied. No correlation was detected between SCD1 expression and desaturase indices in the liver, large and small intestines, lung, cardiac or skeletal muscles. Positive correlations, however, were detected between SCD1 expression and the desaturase indices in intestinal adipose tissue (P<0.02 for all) except 14:1, whereas only c9 18:1, c9 t11 18:2 and sum of all desaturase indices were positively correlated with SCD1 expression in mammary tissue (P < or = 0.03). Overall, the relationship between SCD1 gene expression and occurrence of its products seems to be tissue specific. PMID:24904960

Rezamand, Pedram; Watts, Jason S; Yavah, Katherine M; Mosley, Erin E; Ma, Liying; Corl, Benjamin A; McGuire, Mark A

2014-08-01

252

Mathematical Modelling of the Transmission Dynamics of Contagious Bovine Pleuropneumonia Reveals Minimal Target Profiles for Improved Vaccines and Diagnostic Assays  

PubMed Central

Contagious bovine pleuropneumonia (CBPP) is a cattle disease that has hampered the development of the livestock sector in sub-Saharan Africa. Currently, vaccination with a live vaccine strain is its recommended control measure although unofficial antimicrobial use is widely practiced. Here, modelling techniques are used to assess the potential impact of early elimination of infected cattle via accurate diagnosis on CBPP dynamics. A herd-level stochastic epidemiological model explicitly incorporating test sensitivity and specificity is developed. Interventions by annual vaccination, annual testing and elimination and a combination of both are implemented in a stepwise manner and their effectiveness compared by running 1000 simulations per intervention over ten years. The model predicts that among the simulated interventions, the ones likely to eliminate the disease from an isolated herd all involved annual vaccination of more than 75% of the animals with a vaccine that protects for at least 18 months combined with annual testing (and elimination of positive reactors) of 75% of the animals every six months after vaccination. The highest probability of disease elimination was 97.5% and this could occur within a median of 2.3 years. Generally, our model predicts that regular testing and elimination of positive reactors using improved tests will play a significant role in minimizing CBPP burden especially in the current situation where improved vaccines are yet to be developed. PMID:25668725

Ssematimba, Amos; Jores, Joerg; Mariner, Jeffrey C.

2015-01-01

253

Mathematical analysis of a model for the growth of the bovine corpus luteum.  

PubMed

The corpus luteum (CL) is an ovarian tissue that grows in the wound space created by follicular rupture. It produces the progesterone needed in the uterus to maintain pregnancy. Rapid growth of the CL and progesterone transport to the uterus require angiogenesis, the creation of new blood vessels from pre-existing ones, a process which is regulated by proteins that include fibroblast growth factor 2 (FGF2). In this paper we develop a system of time-dependent ordinary differential equations to model CL growth. The dependent variables represent FGF2, endothelial cells (ECs), luteal cells, and stromal cells (like pericytes), by assuming that the CL volume is a continuum of the three cell types. We assume that if the CL volume exceeds that of the ovulated follicle, then growth is inhibited. This threshold volume partitions the system dynamics into two regimes, so that the model may be classified as a Filippov (piecewise smooth) system. We show that normal CL growth requires an appropriate balance between the growth rates of luteal and stromal cells. We investigate how angiogenesis influences CL growth by considering how the system dynamics depend on the dimensionless EC proliferation rate, [Formula: see text]. We find that weak (low [Formula: see text]) or strong (high [Formula: see text]) angiogenesis leads to 'pathological' CL growth, since the loss of CL constituents compromises progesterone production or delivery. However, for intermediate values of [Formula: see text], normal CL growth is predicted. The implications of these results for cow fertility are also discussed. For example, inadequate angiogenesis has been linked to infertility in dairy cows. PMID:24337679

Prokopiou, Sotiris A; Byrne, Helen M; Jeffrey, Mike R; Robinson, Robert S; Mann, George E; Owen, Markus R

2014-12-01

254

Mitochondrial integrity in a neonatal bovine model of right ventricular dysfunction.  

PubMed

Right ventricular (RV) function is a key determinant of survival in patients with both RV and left ventricular (LV) failure, yet the mechanisms of RV failure are poorly understood. Recent studies suggest cardiac metabolism is altered in RV failure in pulmonary hypertension (PH). Accordingly, we assessed mitochondrial content, dynamics, and function in hearts from neonatal calves exposed to hypobaric hypoxia (HH). This model develops severe PH with concomitant RV hypertrophy, dilation, and dysfunction. After 2 wk of HH, pieces of RV and LV were obtained along with samples from age-matched controls. Comparison with control assesses the effect of hypoxia, whereas comparison between the LV and RV in HH assesses the additional impact of RV overload. Mitochondrial DNA was unchanged in HH, as was mitochondrial content as assessed by electron microscopy. Immunoblotting for electron transport chain subunits revealed a small increase in mitochondrial content in HH in both ventricles. Mitochondrial dynamics were largely unchanged. Activity of individual respiratory chain complexes was reduced (complex I) or unchanged (complex V) in HH. Key enzymes in the glycolysis pathway were upregulated in both HH ventricles, alongside upregulation of hypoxia-inducible factor-1? protein. Importantly, none of the changes in expression or activity were different between ventricles, suggesting the changes are in response to HH and not RV overload. Upregulation of glycolytic modulators without chamber-specific mitochondrial dysfunction suggests that mitochondrial capacity and activity are maintained at the onset of PH, and the early RV dysfunction in this model results from mechanisms independent of the mitochondria. PMID:25416385

Bruns, Danielle R; Brown, R Dale; Stenmark, Kurt R; Buttrick, Peter M; Walker, Lori A

2015-01-15

255

Interaction of serum proteins with CYP isoforms in human liver microsomes: inhibitory effects of human and bovine albumin, alpha-globulins, alpha-1-acid glycoproteins and gamma-globulins on CYP2C19 and CYP2D6  

Microsoft Academic Search

The effects of serum proteins on the in vitro hydroxylation pathways of mephenytoin (CYP2C19) and debrisoquine (CYP2D6) were studied to enhance the predictability of in vivo drug metabolism from in vitro assays. Both CYP substrates are known to be weakly bound to albumin and the applicability of the free drug hypothesis was further appraised. Since bovine serum albumin (BSA) is

Bang Qian Xu; Mikio Ishii; Li Rong Ding; Nancy E Fischer; Tadanobu Inaba

2003-01-01

256

Quantitative thermodynamic model for globular protein folding  

NASA Astrophysics Data System (ADS)

We present a statistical mechanics formalism for theoretical description of the process of protein folding ? unfolding transition in water environment. The formalism is based on the construction of the partition function of a protein obeying two-stage-like folding kinetics. Using the statistical mechanics model of solvation of hydrophobic hydrocarbons we obtain the partition function of infinitely diluted solution of proteins in water environment. The calculated dependencies of the protein heat capacities upon temperature are compared with the corresponding results of experimental measurements for staphylococcal nuclease and metmyoglobin.

Yakubovich, Alexander V.; Solov'yov, Andrey V.

2014-06-01

257

Role of mitogen-activated protein kinases and tyrosine kinases on IL-1-Induced NF-kappaB activation and iNOS expression in bovine articular chondrocytes.  

PubMed

Nitric oxide (NO), produced by the inducible isoform of the NO synthase (iNOS), plays an important role in the pathophysiology of arthritic diseases. This work aimed at elucidating the role of the mitogen-activated protein kinases (MAPK), p38MAPK and p42/44MAPK, and of protein tyrosine kinases (PTK) on interleukin-1beta (IL-1)-induced iNOS expression in bovine articular chondrocytes. The specific inhibitor of the p38MAPK, SB 203580, effectively inhibited IL-1-induced iNOS mRNA and protein synthesis, as well as NO production, while the specific inhibitor of the p42/44MAPK, PD 98059, had no effect. These responses to IL-1 were also inhibited by treatment of the cells with the tyrosine kinase inhibitors, genistein and tyrphostin B42, which also prevented IL-1-induced NF-kappaB activation. The p38MAPK inhibitor, SB 203580, had no effect on IL-1-induced NF-kappaB activation. Finally, the p42/44MAPK inhibitor, PD 98059, prevented IL-1-induced AP-1 activation in a concentration that did not inhibit iNOS expression. In conclusion, this study shows that (1) PTK are part of the signaling pathway that leads to IL-1-induced NF-kappaB activation and iNOS expression; (2) the p38MAPK cascade is required for IL-1-induced iNOS expression; (3) the p42/44MAPK and AP-1 are not involved in IL-1-induced iNOS expression; and (4) NF-kappaB and the p38MAPK lie on two distinct pathways that seem to be independently required for IL-1-induced iNOS expression. Hence, inhibition of any of these two signaling cascades is sufficient to prevent iNOS expression and the subsequent production of NO in articular chondrocytes. PMID:11829533

Mendes, A Ferreira; Caramona, M Margarida; Carvalho, A Pato; Lopes, M Celeste

2002-02-01

258

Effect of polyelectrolyte structure on protein-polyelectrolyte coacervates: coacervates of bovine serum albumin with poly(diallyldimethylammonium chloride) versus chitosan.  

PubMed

Electrostatic interactions between synthetic polyelectrolytes and proteins can lead to the formation of dense, macroion-rich liquid phases, with equilibrium microheterogeneities on length scales up to hundreds of nanometers. The effects of pH and ionic strength on the rheological and optical properties of these coacervates indicate microstructures sensitive to protein-polyelectrolyte interactions. We report here on the properties of coacervates obtained for bovine serum albumin (BSA) with the biopolyelectrolyte chitosan and find remarkable differences relative to coacervates obtained for BSA with poly(diallyldimethylammonium chloride) (PDADMAC). Coacervation with chitosan occurs more readily than with PDADMAC. Viscosities of coacervates obtained with chitosan are more than an order of magnitude larger and, unlike those with PDADMAC, show temperature and shear rate dependence. For the coacervates with chitosan, a fast relaxation time in dynamic light scattering, attributable to relatively unrestricted protein diffusion in both systems, is diminished in intensity by a factor of 3-4, and the consequent dominance by slow modes is accompanied by a more heterogeneous array of slow apparent diffusivities. In place of a small-angle neutron scattering Guinier region in the vicinity of 0.004 A-1, a 10-fold increase in scattering intensity is observed at lower q. Taken together, these results confirm the presence of dense domains on length scales of hundreds of nanometers to micrometers, which in coacervates prepared with chitosan are less solidlike, more interconnected, and occupy a larger volume fraction. The differences in properties are thus correlated with differences in mesophase structure. PMID:17892297

Kayitmazer, A Basak; Strand, Sabina P; Tribet, Christophe; Jaeger, Werner; Dubin, Paul L

2007-11-01

259

Transcriptional and replicational activation functions in the bovine papillomavirus type 1 E2 protein are encoded by different structural determinants.  

PubMed Central

A set of E2 proteins with mutations in the amino-terminal transactivation domain was made by a scheme called clustered charged-to-alanine scan. These mutant E2 proteins were tested for expression, stability, and compartmentalization in cells and for sequence-specific DNA binding, as well as in functional assays for transcriptional and replicational activation. We identified four groups of mutants. First, mutants K111A, K112A, and E176A were unable to activate replication and transcription because of oligomerization-induced retention of oligomers in the cytoplasm. Second, although fractions of the mutant proteins E74A and D143A/ R172C existed in the oligomeric form, they were localized in the nucleus. Certain fractions of these proteins existed as a dimer able to form a specific complex and activate replication; however, these proteins were inactive in transcriptional activation. Third, mutants R37A and D122A were localized in the nucleus, existed in the dimeric form, supported replication efficiently, and were severely crippled in transcriptional activation. The fourth group of mutants did not differ considerably from the wild-type protein. The activation of transcription by the wild type as well as mutant E2 proteins was dependent on the concentration of input E2 expression vector DNA and had a bell-like shape. We suggest that the reduction of transcriptional activation at higher E2 concentrations, the self-squelching activity, is caused by oligomerization of the E2 transactivator and is one of the mechanisms for the regulation of E2 activity. Our results also show that transcriptional and replicational activation activities are encoded by different determinants in the E2 protein. PMID:8709243

Abroi, A; Kurg, R; Ustav, M

1996-01-01

260

High antibody titres against predicted Mycoplasma surface proteins do not prevent sequestration in infected lung tissue in the course of experimental contagious bovine pleuropneumonia.  

PubMed

Contagious bovine pleuropneumonia (CBPP), a severe respiratory disease of cattle caused by Mycoplasma mycoides subsp. mycoides (Mmm) is endemic in many African countries due to fragmented veterinary services and the lack of an efficient vaccine and sensitive diagnostics. More efficient tools to control the disease are needed, but to develop the tools, a better understanding of host-pathogen interactions is necessary. The aim of this study was to characterize the kinetics of the humoral immune response against 65 Mmm surface antigens for an extended period in cattle that survived a primary infection with Mmm. We describe clinical and haematological outcomes, and dissect the humoral immune response over time, to specific antigens and compared the antibody responses between different pathomorphological outcomes. No antigen-specific antibodies correlating with protection were identified. Interestingly we found that animals that developed Mycoplasma-containing sequestra had significantly higher antibody levels against proteins comprising the surface proteome than the animals that cleared Mycoplasma from their lungs. Based on these data we suggest that high antibody titres might play a role in the establishment of pathomorphological changes, such as vasculitis, which should be investigated in future studies. Beneficial antibody specificities and cellular immune responses need to be identified in order to foster the development of an improved vaccine in the future. PMID:24880898

Schieck, Elise; Liljander, Anne; Hamsten, Carl; Gicheru, Nimmo; Scacchia, Massimo; Sacchini, Flavio; Heller, Martin; Schnee, Christiane; Sterner-Kock, Anja; Hlinak, Andreas; Naessens, Jan; Poole, Jane; Persson, Anja; Jores, Joerg

2014-08-01

261

Identification and isolation of a platelet GPIb-like protein in human umbilical vein endothelial cells and bovine aortic smooth muscle cells.  

PubMed Central

Glycoprotein Ib (GPIb) is an intrinsic platelet membrane protein that plays a major role in platelet adherence and mediates ristocetin-dependent platelet von Willebrand factor binding. Recent reports that the platelet membrane glycoprotein complex IIb/IIIa is expressed in several cell types prompted us to look for GPIb expression in other vascular cells. Immunoperoxidase staining of human stomach and skin histologic sections with polyclonal as well as monoclonal anti-GPIb antibody revealed the presence of GPIb in the endothelial cell and smooth muscle cell layers. Western blotting using monospecific polyclonal anti-GPIb antibodies confirmed the presence of immunoreactive GPIb in human umbilical vein endothelial and bovine aortic smooth muscle cell cultures. Fab fragments of a monoclonal anti-GPIb antibody were used to immunoprecipitate [3H]leucine labeled GPIb from metabolically labeled cells. The GPIb in these cells was functional as measured by ristocetin-dependent cell agglutination and by vWF binding. Endothelial cells as well as smooth muscle cells bound 125I-labeled vWF in a ristocetin-dependent manner, with a Kd of 7.9 nM. Images PMID:3284916

Asch, A S; Adelman, B; Fujimoto, M; Nachman, R L

1988-01-01

262

Distinct composition of bovine milk from Jersey and Holstein-Friesian cows with good, poor, or noncoagulation properties as reflected in protein genetic variants and isoforms.  

PubMed

The objective of this study was to examine variation in overall milk, protein, and mineral composition of bovine milk in relation to rennet-induced coagulation, with the aim of elucidating the underlying causes of milk with impaired coagulation abilities. On the basis of an initial screening of 892 milk samples from 42 herds with Danish Jersey and Holstein-Friesian cows, a subset of 102 samples was selected to represent milk with good, poor, or noncoagulating properties (i.e., samples that within each breed represented the most extremes in regard to coagulation properties). Milk with good coagulation characteristics was defined as milk forming a strong coagulum based on oscillatory rheology, as indicated by high values for maximum coagulum strength (G'(max)) and curd firming rate (CFR) and a short rennet coagulation time. Poorly coagulating milk formed a weak coagulum, with a low G'(max) and CFR and a long rennet coagulation time. Noncoagulating milk was defined as milk that failed to form a coagulum, having G'(max) and CFR values of zero at measurements taken within 1h after addition of rennet. For both breeds, a lower content of total protein, total casein (CN) and ?-CN, and lower levels of minerals (Ca, P, Mg) were identified in poorly coagulating and noncoagulating milk in comparison with milk with good coagulation properties. Liquid chromatography/electrospray ionization-mass spectrometry revealed the presence of a great variety of genetic variants of the major milk proteins, namely, ?(S1)-CN (variants B and C), ?(S2)-CN (A), ?-CN (A(1), A(2), B, I, and F), ?-CN (A, B, and E), ?-lactalbumin (B), and ?-lactoglobulin (A, B, and C). In poorly coagulating and noncoagulating milk samples of both breeds, the predominant composite genotype of ?(S1)-, ?-, and ?-CN was BB-A(2)A(2)-AA, which confirmed a genetic contribution to impaired milk coagulation. Interestingly, subtle variations in posttranslational modification of CN were observed between the coagulation classes in both breeds. Poorly coagulating and noncoagulating milk contained a lower fraction of the least phosphorylated ?(S1)-CN form, ?(S1)-CN 8P, relative to total ?(S1)-CN, along with a lower fraction of glycosylated ?-CN relative to total ?-CN. Thus, apparent variation was observed in the milk and protein composition, in the genetic makeup of the major milk proteins, and in the posttranslational modification level of CN between milk samples with either good or impaired coagulation ability, whereas the composition of poorly coagulating and noncoagulating milk was similar. PMID:23040012

Jensen, H B; Poulsen, N A; Andersen, K K; Hammershj, M; Poulsen, H D; Larsen, L B

2012-12-01

263

Bovine leukemia virus, an animal model for the study of intrastrain variability.  

PubMed Central

Intradermal injection of a cloned bovine leukemia virus (BLV) provirus (pV344) into sheep allowed direct evaluation of intrastrain variability. A sheep was injected with pV344 DNA mixed with DEAE-dextran and became persistently infected with BLV strain 344. After 18 months, DNA was extracted from peripheral blood leukocytes from a single 0.5-ml blood sample. The long terminal repeat (LTR) and the env gene were amplified by using the polymerase chain reaction, cloned, and sequenced. Nineteen independent LTR clones (0.6-kb inserts) and 16 env clones (1-kb inserts) were analyzed. The in vivo rate of nucleotide change was 0.009%/year (two mutations out of 14,464 bp in 1.5 years), corresponding to only one amino acid change in the env gene. Five point mutations (all transitions), corresponding to a modification rate of 0.034%/year (five mutations out of 9,709 bp in 1.5 years), were identified in the LTR. As a control for Taq DNA polymerase errors, the same procedure using pV344 plasmid DNA was carried out. Out of 9,944 bp sequenced, three point mutations were found (i.e., one misincorporation in 3,315 nucleotides). These data demonstrate the extremely low level (or absence) of intrastrain variability of BLV in vivo. Consequently, BLV persistence in the infected host does not seem to result from an escape mutant strategy, in sharp contrast with the high mutation rates observed in the lentivirus family. The lack of genetic variation supports the possibility of successful vaccine against BLV and probably against the related human T-cell leukemia viruses. PMID:8380455

Willems, L; Thienpont, E; Kerkhofs, P; Burny, A; Mammerickx, M; Kettmann, R

1993-01-01

264

Modeling protein synthesis from a physicist's perspective: a toy model  

E-print Network

Proteins are polymers of amino acids. These macromolecules are synthesized by intracellular machines called ribosomes. Although the experimental investigation of protein synthesis has been a traditional area of research in molecular cell biology, important quantitative models of protein synthesis have been reported in research journals devoted to statistical physics and related interdisciplinary topics. From the perspective of a physicist, protein synthesis is the classical transport of interacting ribosomes on a messenger RNA (mRNA) template that dictates the sequence of the amino acids on the protein. We discuss appropriate simplification of the models and methods. In particular, we develop and analyze a simple toy model using some elementary techniques of non-equilibrium statistical mechanics and predict the average rate of protein synthesis and the spatial organization of the ribosomes in the steady state.

Aakash Basu; Debashish Chowdhury

2007-02-17

265

Simple Hydrophobic/Hydrophilic Protein Folding Model  

NSDL National Science Digital Library

the Simple Hydrophobic/Hydrophilic Protein Folding Model implements a 2-Dimensional hydrophobic/hydrophilic (HP) folding protein to test the energetics of protein folding, the change in size of a protein relative to energy, and the computation time for complex protein problems. A Metropolis Monte-Carlo algorithm is used to determine if randomly guided movements are carried out by monomers (non-specific amino acids) within the polymer (protein tertiary structure). The Monte-Carlo steps are run in a worker task (separate to EJS) while size and energy are periodically updated according to the Frames Per Second (FPS). A worker task isolates a single thread from the operating computer and uses that to cycle through a block of code as quickly as possible. In this case, one cycle constitutes one Monte-Carlo time step, the time unit. To accurately update data from a thread that runs outside of the EJS module, atomic variables are used. Every time the program updates the evolution page, the atomic variables for size and energy are recorded and added to the view (i.e. plots) for the polymer structure that occurred in the nearest worker task cycle to that evolution update. The Simple Hydrophobic/Hydrophilic Protein Folding Model was created using the Easy Java/JavaScript Simulations (EjsS) version 5 modeling tool. It is distributed as a ready-to-run (compiled) Java archive.

Kozlowski, Ryan

2014-06-01

266

in silico protein recombination applied to Comparative Modelling  

E-print Network

·definition of fitness ·design of the algorithm #12;proteins models are implicitly coded solutions · linearin silico protein recombination applied to Comparative Modelling Bruno Contreras-Moreira, Paul W template + 1alignment) #12;genetic operators recombinant protein modelmutant protein model model A + model

Moreira, Bruno Contreras

267

The effect of lutein, sesamol, ellagic acid and olive leaf extract on lipid oxidation and oxymyoglobin oxidation in bovine and porcine muscle model systems  

Microsoft Academic Search

The effect of lutein (100, 200, 300?g\\/ml), sesamol (500, 1000, 2000?g\\/ml), ellagic acid (300, 600, 900?g\\/ml) and olive leaf extract (100, 200, 300?g\\/ml) on oxymyoglobin oxidation and lipid oxidation in bovine and porcine muscle model systems (25% M. longissimus thoracis et lumborum homogenates) was examined. Radical scavenging activity, using the DPPH assay, and iron-chelating activities of lutein, sesamol, ellagic acid

J. E. Hayes; V. Stepanyan; P. Allen; M. N. OGrady; N. M. OBrien; J. P. Kerry

2009-01-01

268

Insulin-like growth factor-I and insulin-like growth factor binding proteins in the bovine mammary gland: Receptors, endogenous secretion, and appearance in milk  

SciTech Connect

This is the first study to characterize both insulin-like growth factor-I (IGF-I) and insulin-like growth factor binding proteins (IGFBPs) in bovine milk, to characterize the IGF-I receptor in the dry and lactating mammary gland, and to report de novo synthesis and secretion of IGF-I and IGFBP from normal mammary tissue. Immunoreactive IGF-I was principally associated with 45 kDa IGFBP in milk. Multiparous cows had a higher IGF-I concentration of 307 ng/ml than primiparous cows at 147 ng/ml. IGF-I concentration on day 56 of lactation was 34 ng/ml for combined parity groups. At parturition, IGF-I mass in blood and milk pools was 1.4 and 1.2 mg, respectively. Binding of {sup 125}I-IGF-I was specific for IGF-I with anIC{sub 50} of 2.2 ng which was a 10- and 1273-fold greater affinity than IGF-II and insulin, respectively. Association constants, as determined by Scatchard analysis, were similar for both pregnant and lactating cows at 3.5 and 4.0 L/nM, respectively. In addition, estimated mean receptor concentration was 0.25 and 0.23 pM/mg protein for pregnant and lactating cows, respectively. In a survey of mammary microscomes prepared from 48 cows, {sup 125}I-IGF-I binding declined with progressing lactation and a similar trend was observed during pregnancy.

Campbell, P.G.

1988-01-01

269

Comment on Critical micellar concentration and protein-surfactant interaction (Comment to Destructive and protective action of sodium dodecyl sulphate micelles on the native conformation of Bovine Serum Albumin: A study by extrinsic fluorescence probe 1-hydroxy-2-naphthaldehyde)  

NASA Astrophysics Data System (ADS)

Commenting on the Letter entitled 'Destructive and protective action of sodium dodecyl sulphate micelles on the native conformation of Bovine Serum Albumin: A study by extrinsic fluorescence probe 1-hydroxy-2-naphthaldehyde' [Chem. Phys. Lett. 463 (2008) 183], this short contribution aims to clarify that the critical micellar concentration (CMC) of a charged surfactant strongly depends on the ionic strength. Main features of fluorimetric determinations of the CMC are also briefly discussed. In general, the study of surfactant-induced protein transitions will greatly benefit from independent 'blank' experiments to evaluate the CMC of the surfactant under the conditions of the protein assays.

Ragone, Raffaele

2009-11-01

270

Crystal structure of the cytochrome bc complex from bovine heart mitochondria  

Microsoft Academic Search

On the basis of x-ray diffraction data to a resolution of 2.9 angstroms, atomic models of most protein components of the bovine cytochrome bc complex were built, including core 1, core 2, cytochrome b, subunit 6, and subunit 7, a carboxyl-terminal fragment of cytochrome c, and an amino-terminal fragment of the iron-sulfur protein. The positions of the four iron centers

Di Xia; Hoeon Kim; J. Deisenhofer; Li Zhang

1997-01-01

271

Assignment of the Multifunctional NS3 Protein of Bovine Viral Diarrhea Virus during RNA Replication: an In Vivo and In Vitro Study  

PubMed Central

Studies on the replication of the pestivirus bovine viral diarrhea virus (BVDV) were considerably facilitated by the recent discovery of an autonomous subgenomic BVDV RNA replicon (DI9c). DI9c comprises mainly the untranslated regions of the viral genome and the coding region of the nonstructural proteins NS3, NS4A, NS4B, NS5A, and NS5B. To assess the significance of the NS3-associated nucleoside triphosphatase/helicase activity during RNA replication and to explore other functional features of NS3, we generated a repertoire of DI9c derivatives bearing in-frame mutations in different parts of the NS3 coding unit. Most alterations resulted in deficient replicons, several of which encoded an NS3 protein with an inhibited protease function. Three lesions permitted replication, though at a lower level than that of the wild-type RNA, i.e., replacement of the third position of the DEYH helicase motif II by either T or F and an insertion of four amino acid residues in the C-terminal part of NS3. While polyprotein proteolysis was found to be almost unaffected in these latter replicons, in vitro studies with the purified mutant NS3 proteins revealed a significantly impaired helicase activity for the motif II substitutions. NS3 with a DEFH motif, moreover, showed a significantly lower ATPase activity. In contrast, the C-terminal insertion had no negative impact on the ATPase/RNA helicase activity of NS3. All three mutations affected the synthesis of both replication productsnegative-strand intermediate and progeny positive-strand RNAin a symmetric manner. Unexpectedly, various attempts to rescue or enhance the replication capability of nonfunctional or less functional DI9c NS3 derivatives, respectively, by providing intact NS3 in trans failed. Our experimental data thus demonstrate that the diverse enzymatic activities of the NS3 proteinin particular the ATPase/RNA helicaseplay a pivotal role even during early steps of the viral replication pathway. They may further indicate the C-terminal part of NS3 to be an important functional determinant of the RNA replication process. PMID:10516027

Grassmann, Claus W.; Isken, Olaf; Behrens, Sven-Erik

1999-01-01

272

Modeling protein cores with Markov random fields.  

PubMed

A mathematical formalism is introduced that has general applicability to many protein structure models used in the various approaches to the "inverse protein folding problem." The inverse nature of the problem arises from the fact that one begins with a set of assumed tertiary structures and searches for those most compatible with a new sequence, rather than attempting to predict the structure directly from the new sequence. The formalism is based on the well-known theory of Markov random fields (MRFs). Our MRF formulation provides explicit representations for the relevant amino acid position environments and the physical topologies of the structural contacts. In particular, MRF models can readily be constructed for the secondary structure packing topologies found in protein domain cores, or other structural motifs, that are anticipated to be common among large sets of both homologous and nonhomologous proteins. MRF models are probabilistic and can exploit the statistical data from the limited number of proteins having known domain structures. The MRF approach leads to a new scoring function for comparing different threadings (placements) of a sequence through different structure models. The scoring function is very important, because comparing alternative structure models with each other is a key step in the inverse folding problem. Unlike previously published scoring functions, the one derived in this paper is based on a comprehensive probabilistic formulation of the threading problem. PMID:7833593

White, J V; Muchnik, I; Smith, T F

1994-12-01

273

Estradiol and Progesterone Exhibit Similar Patterns of Hepatic Gene Expression Regulation in the Bovine Model  

PubMed Central

Female sex steroid hormones, estradiol-17? (E2-17?) and progesterone (P4) regulate reproductive function and gene expression in a broad range of tissues. Given the central role of the liver in regulating homeostasis including steroid hormone metabolism, we sought to understand how E2-17? and P4 interact to affect global gene expression in liver. Ovariectomized cows (n?=?8) were randomly assigned to 4 treatment groups applied in a replicated Latin Square design: 1) No hormone supplementation, 2) E2-17? treatment (ear implant), 3) P4 treatment (intravaginal inserts), and 4) E2-17? combined with P4. After 14 d of treatment, liver biopsies were collected, allowing 28 d intervals between periods. Changes in gene expression in the liver biopsies were monitored using bovine-specific arrays. Treatment with E2-17? altered expression of 479 genes, P4 472 genes, and combined treatment significantly altered expression of 468 genes. In total, 578 genes exhibited altered expression including a remarkable number (346 genes) that responded similarly to E2-17?, P4, or combined treatment. Additional evidence for similar gene expression actions of E2-17 and/or P4 were: principal component analysis placed almost every treatment array at a substantial distance from controls; Venn diagrams indicated overall treatment effects for most regulated genes; clustering analysis indicated the two major clusters had all treatments up-regulating (172 genes) or down-regulating (173 genes) expression. Thus, unexpectedly, common biological pathways were regulated by E2-17? and/or P4 in liver. This indicates that the mechanism of action of these steroid hormones in the liver might be either indirect or might occur through non-genomic pathways. This unusual pattern of gene expression in response to steroid hormones is consistent with the idea that there are classical and non-classical tissue-specific responses to steroid hormone actions. Future studies are needed to elucidate putative mechanism(s) responsible for overlapping actions of E2-17? and P4 on the liver transcriptome. PMID:24069207

Piccinato, Carla A.; Rosa, Guilherme J. M.; NJai, Alhaji U.; Jefcoate, Colin R.; Wiltbank, Milo C.

2013-01-01

274

Locus Characterization and Gene Expression of Bovine FNDC5: Is the Myokine Irisin Relevant in Cattle?  

PubMed Central

The transmembrane protein FNDC5 was recently characterized as precursor of an exercise induced myokine named irisin. Previous studies found a relationship between circulating irisin levels and muscle mass in humans. Consequently, we tested the hypothesis whether FNDC5/irisin is involved in the modulation of body composition in cattle. Since information on the bovine FNDC5 locus was scarce, we characterized the gene experimentally as prerequisite for these investigations. We provide here a revised and extended gene model for bovine FNDC5. Although similarly organized like the human and murine loci, a higher variability was observed at transcript level in the bovine locus. FNDC5 mRNA was abundant in bovine skeletal muscle and was detected at lower levels in adipose tissue and liver. There were no expression differences between two groups of bulls highly different in muscularity and adiposity. Full-length FNDC5 protein (25 kDa) was present in bovine skeletal muscle independent of muscularity. Neither FNDC5 nor its putatively secreted peptide irisin were found in circulation of bulls. In contrast, we demonstrated that FNDC5 (25 kDa) and irisin (12 kDa) were present in murine skeletal muscle and that irisin was circulating in murine serum. This indicates fundamental differences in the regulation of FNDC5 and irisin between rodents and cattle. PMID:24498244

Komolka, Katrin; Albrecht, Elke; Schering, Lisa; Brenmoehl, Julia; Hoeflich, Andreas; Maak, Steffen

2014-01-01

275

Locus characterization and gene expression of bovine FNDC5: is the myokine irisin relevant in cattle?  

PubMed

The transmembrane protein FNDC5 was recently characterized as precursor of an exercise induced myokine named irisin. Previous studies found a relationship between circulating irisin levels and muscle mass in humans. Consequently, we tested the hypothesis whether FNDC5/irisin is involved in the modulation of body composition in cattle. Since information on the bovine FNDC5 locus was scarce, we characterized the gene experimentally as prerequisite for these investigations. We provide here a revised and extended gene model for bovine FNDC5. Although similarly organized like the human and murine loci, a higher variability was observed at transcript level in the bovine locus. FNDC5 mRNA was abundant in bovine skeletal muscle and was detected at lower levels in adipose tissue and liver. There were no expression differences between two groups of bulls highly different in muscularity and adiposity. Full-length FNDC5 protein (25 kDa) was present in bovine skeletal muscle independent of muscularity. Neither FNDC5 nor its putatively secreted peptide irisin were found in circulation of bulls. In contrast, we demonstrated that FNDC5 (25 kDa) and irisin (12 kDa) were present in murine skeletal muscle and that irisin was circulating in murine serum. This indicates fundamental differences in the regulation of FNDC5 and irisin between rodents and cattle. PMID:24498244

Komolka, Katrin; Albrecht, Elke; Schering, Lisa; Brenmoehl, Julia; Hoeflich, Andreas; Maak, Steffen

2014-01-01

276

Generation of a Persistently Infected MDBK Cell Line with Natural Bovine Spongiform Encephalopathy (BSE)  

PubMed Central

Bovine spongiform encephalopathy (BSE) is a zoonotic transmissible spongiform encephalopathy (TSE) thought to be caused by the same prion strain as variant Creutzfeldt-Jakob disease (vCJD). Unlike scrapie and chronic wasting disease there is no cell culture model allowing the replication of proteinase K resistant BSE (PrPBSE) and the further in vitro study of this disease. We have generated a cell line based on the Madin-Darby Bovine Kidney (MDBK) cell line over-expressing the bovine prion protein. After exposure to naturally BSE-infected bovine brain homogenate this cell line has shown to replicate and accumulate PrPBSE and maintain infection up to passage 83 after initial challenge. Collectively, we demonstrate, for the first time, that the BSE agent can infect cell lines over-expressing the bovine prion protein similar to other prion diseases. These BSE infected cells will provide a useful tool to facilitate the study of potential therapeutic agents and the diagnosis of BSE. PMID:25647616

Tark, Dongseob; Kim, Hyojin; Neale, Michael H.; Kim, Minjeong; Sohn, Hyunjoo; Lee, Yoonhee; Cho, Insoo; Joo, Yiseok; Windl, Otto

2015-01-01

277

Structure of bovine adrenal dopamine beta-monooxygenase, as deduced from cDNA and protein sequencing: evidence that the membrane-bound form of the enzyme is anchored by an uncleaved signal peptide.  

PubMed

A full-length cDNA for dopamine beta-monooxygenase (D beta M) from bovine adrenal glands has been cloned and sequenced. The soluble and membrane-derived forms of D beta M have also been sequenced from their N-termini. While the observed sequences for the soluble protein correspond to those previously reported [Joh, T.H., & Hwang, O. (1986) Ann. N.Y. Acad. Sci. 493, 343-350], the heavy subunit of membrane-derived enzyme is found to contain a unique N-terminus. Alignment of this N-terminus with that deduced from cDNA cloning indicates identity at 22 (and possibly 26) out of 27 residues. This comparison leads us to conclude that the membranous form of bovine D beta M retains an uncleaved N-terminal signal peptide as the source of membrane anchoring. PMID:2620060

Taljanidisz, J; Stewart, L; Smith, A J; Klinman, J P

1989-12-26

278

Using Vorono fingerprints to rescore Hex protein-protein docking models T. Bourquard1  

E-print Network

processors Bioinformatics, 26(19):2398-405. 2. Hwang H et al (2008) Protein-protein docking Benchmark versionUsing Voronoï fingerprints to rescore Hex protein-protein docking models T. Bourquard1 , J. Azé2 Applications, France Introduction Protein-protein docking procedures normally consist of two successive steps

Ritchie, Dave

279

Evaluation of antimicrobial treatment in a bovine model of acute Chlamydia psittaci infection: tetracycline versus tetracycline plus rifampicin.  

PubMed

Antimicrobial treatment of chlamydial infections is known to be of limited efficacy. In this study, effects of doxycycline (D), usually the drug of choice, were compared with the combined therapy of doxycycline and rifampicin (R) in a bovine model of respiratory Chlamydia psittaci infection. After intrabronchial inoculation of the pathogen, 30 animals were assigned to five groups (n=6 per group): untreated controls, monotherapy with D (5mgkg(-1) day(-1) or 10mgkg(-1) day(-1) ), and combination therapy of D and R (600mgday(-1) ). Treatment continued until day 14 post inoculation (d.p.i.). Clinical signs, inflammatory markers, and pathological findings confirmed successful infection in all animals. Reisolation of the pathogen was possible in 4/6 untreated animals and in 4/12 animals treated with D alone until 4d.p.i., but in none of the calves of the two D+R groups. Pathogen detection was possible in all animals without significant differences among groups. Severity of disease and time course of its resolution, assessed by clinical and pathological findings as well as inflammatory parameters, were not significantly different between untreated controls and calves receiving D alone or in combination with R. Regardless of the treatment regimen, all groups recovered clinically and cleared the infection within 2weeks. PMID:25113145

Prohl, Annette; Lohr, Markus; Ostermann, Carola; Liebler-Tenorio, Elisabeth; Berndt, Angela; Schroedl, Wieland; Rothe, Michael; Schubert, Evelyn; Sachse, Konrad; Reinhold, Petra

2014-08-11

280

Probing the interaction of trans-resveratrol with bovine serum albumin: a fluorescence quenching study with Tachiya model.  

PubMed

The interaction of trans-resveratrol (TRES) and bovine serum albumin (BSA) was investigated using fluorescence spectroscopy (FS) with Tachiya model. The binding number maximum of TRES was determined to be 8.86 at 293.15 K, 23.42 at 303.15 K and 33.94 at 313.15 K and the binding mechanism analyzed in detail. The apparent binding constants (K (a)) between TRES and BSA were 5.02 x 10(4) (293.15 K), 8.89 x 10(4) (303.15 K) and 1.60 x 10(5) L mol(-1) (313.15 K), and the binding distances (r) between TRES and BSA were 2.44, 3.01, and 3.38 nm at 293.15, 303.15, and 313.15 K, respectively. The addition of TRES to BSA solution leads to the enhancement in RLS intensity, exhibiting the formation of the aggregate in solution. The negative entropy change and enthalpy change indicated that the interaction of TRES and BSA was driven mainly by van der Waals interactions and hydrogen bonds. The process of binding was a spontaneous process in which Gibbs free energy change was negative. PMID:18351302

Xiao, J B; Chen, X Q; Jiang, X Y; Hilczer, M; Tachiya, M

2008-01-01

281

Multiple model approach - dealing wtih alignment ambiguities in protein modeling  

SciTech Connect

Sequence alignments for distantly homologous proteins are often ambiguous, which creates a weak link in structure prediction by homology. We address this problem by using several plausible alignments in a modeling procedure, obtaining many models of the target. All are subsequently evaluated by a threading algorithm. It is shown that this approach can identify best alignments and produce reasonable models, whose quality is now limited only by the extent of the structural similarity between the known and predicted protein. Using a similar approach the structure prediction for the oxidized dimer of S100A1 protein, for which the structure is not known, is presented. 24 refs., 2 figs., 2 tabs.

Pawlowski, K.; Bierzynski, A. [Institute of Biochemistry & Biophysics, Warszawa (Poland); Jaroszewski, L. [Warsaw Univ. (Poland); Godzik, A. [Scripps Research Institute, La Jolla, CA (United States)

1996-12-31

282

Modeling protein synthesis from a physicist's perspective: a toy model  

E-print Network

Proteins are polymers of amino acids. These macromolecules are synthesized by intracellular machines called {\\it ribosome}. Although, traditionally, the experimental investigation of protein synthesis has been an active area of research in molecular cell biology, important quantitative models of this phenomenon have been reported mostly in the research journals devoted to statistical physics and related interdisciplinary topics. From the perspective of a physicist, protein synthesis is a phenomenon of {\\it classical transport of interacting ribosomes on a messenger RNA (mRNA) template} that dictates the sequence of the amino acids on the protein. Here we bring this frontier area of contemporary research into the classroom by appropriate simplification of the models and methods. In particular, we develope a simple toy model and analyze it by some elementary techniques of non-equilibrium statistical mechanics to predict the average rate of protein synthesis and their spatial organization in the steady-state.

Basu, A; Basu, Aakash; Chowdhury, Debashish

2007-01-01

283

Differential effects of SB 242235, a selective p38 mitogen-activated protein kinase inhibitor, on IL1 treated bovine and human cartilage\\/chondrocyte cultures  

Microsoft Academic Search

The p38 MAP kinase inhibitor, SB 242235, was evaluated for its effects on the metabolism of bovine and human cartilage and primary chondrocyte cultures. SB 242235 had no effect on proteoglycan synthesis (PG) in bovine articular cartilage explants (BAC), as measured by [35S]-sulfate incorporation into glycosaminoglycans (GAGs). In addition, the compound had no effect on IL-1?-induced GAG release from these

A. M Badger; A. K Roshak; M. N Cook; T. M Newman-Tarr; B. A Swift; K Carlson; J. R Connor; J. C Lee; M Gowen; M. W Lark; S Kumar

2000-01-01

284

Recombinant Lactococcus lactis fails to secrete bovine chymosine.  

PubMed

Bovine chymosin is an important milk-clotting agent used in the manufacturing of cheeses. Currently, the production of recombinant proteins by genetically modified organisms is widespread, leading to greatly reduced costs. Lactococcus (L.) lactis, the model lactic acid bacterium, was considered a good candidate for heterologous chymosin production for the following reasons: (1) it is considered to be a GRAS (generally regarded as safe) microorganism, (2) only one protease is present on its surface, (3) it can secrete proteins of different sizes, and (4) it allows for the direct production of protein in fermented food products. Thus, three genetically modified L. lactis strains were constructed to produce and target the three different forms of bovine chymosin, prochymosin B, chymosin A and chymosin B to the extracellular medium. Although all three proteins were stably produced in L. lactis, none of the forms were detected in the extracellular medium or showed clotting activity in milk. Our hypothesis is that this secretion deficiency and lack of clotting activity can be explained by the recombinant protein being attached to the cell envelope. Thus, the development of other strategies is necessary to achieve both production and targeting of chymosin in L. lactis, which could facilitate the downstream processing and recovery of this industrially important protein. PMID:25184638

Luerce, Tesslia Diniz; Azevedo, Marcela Santiago Pacheco; LeBlanc, Jean Guy; Azevedo, Vasco; Miyoshi, Anderson; Pontes, Daniela

2014-09-01

285

Recombinant Lactococcus lactis fails to secrete bovine chymosine.  

PubMed

Bovine chymosin is an important milk-clotting agent used in the manufacturing of cheeses. Currently, the production of recombinant proteins by genetically modified organisms is widespread, leading to greatly reduced costs. Lactococcus (L.) lactis, the model lactic acid bacterium, was considered a good candidate for heterologous chymosin production for the following reasons: (1) it is considered to be a GRAS (generally regarded as safe) microorganism, (2) only one protease is present on its surface, (3) it can secrete proteins of different sizes, and (4) it allows for the direct production of protein in fermented food products. Thus, three genetically modified L. lactis strains were constructed to produce and target the three different forms of bovine chymosin, prochymosin B, chymosin A and chymosin B to the extracellular medium. Although all three proteins were stably produced in L. lactis, none of the forms were detected in the extracellular medium or showed clotting activity in milk. Our hypothesis is that this secretion deficiency and lack of clotting activity can be explained by the recombinant protein being attached to the cell envelope. Thus, the development of other strategies is necessary to achieve both production and targeting of chymosin in L. lactis, which could facilitate the downstream processing and recovery of this industrially important protein. PMID:25482140

Luerce, Tesslia Diniz; Azevedo, Marcela Santiago Pacheco; LeBlanc, Jean Guy; Azevedo, Vasco; Miyoshi, Anderson; Pontes, Daniela

2014-09-01

286

Modelling of DNA-protein recognition  

NASA Technical Reports Server (NTRS)

Computer model-building procedures using stereochemical principles together with theoretical energy calculations appear to be, at this stage, the most promising route toward the elucidation of DNA-protein binding schemes and recognition principles. A review of models and bonding principles is conducted and approaches to modeling are considered, taking into account possible di-hydrogen-bonding schemes between a peptide and a base (or a base pair) of a double-stranded nucleic acid in the major groove, aspects of computer graphic modeling, and a search for isogeometric helices. The energetics of recognition complexes is discussed and several models for peptide DNA recognition are presented.

Rein, R.; Garduno, R.; Colombano, S.; Nir, S.; Haydock, K.; Macelroy, R. D.

1980-01-01

287

Inelastic neutron scattering analysis of low frequency motion in proteins: A normal mode study of the bovine pancreatic trypsin inhibitor  

NASA Astrophysics Data System (ADS)

An improved understanding of the function of macromolecules of biological interest requires the characterization of their low-frequency internal fluctuations (?w?kBT where kBT200 cm-1 at room temperature), which dominate the atomic displacements. To explore the potential or inelastic neutron scattering for supplying information about such motions, we employ the formalism of Zemach and Glauber [A. C. Zemach and R. J. Glauber, Phys. Rev. 101, 118 (1956)] to calculate the one-phonon vibrational incoherent scattering function, Svibinc (q,w), of a small protein, BPTI. An in vacuo normal mode analysis of BPTI [B. Brooks and M. Karplus, Proc. Natl. Acad. Sci. U.S.A. 80, 6571 (1983)], is used for the calculation of Svibinc (q,w). The dependence of Svibinc (q,w) on energy transfer and momentum transfer is investigated and the results are placed in the context of present instrumental capabilities. Although the overall energy dependence of Svibinc (q,w) has a simple form, the variations in the hydrogen atom displacements in the different modes have a significant effect on the scattering. Mode anisotropy is strongly manifested in oriented spectra calculated without instrumental resolution broadening. Contributions from individual atoms and residues to the unbroadened whole molecule scattering are examined in detail. They are found to depend significantly on the atom or residue examined. This suggests that inelastic neutron scattering has considerable potential for the investigation of local dynamic variations in proteins by use of a deuterated protein with specifically protonated residues. Orientational averaging and instrumental resolution broadening of Svibinc (q,w) indicate that the one-phonon scattering detectable on the most suitable current instrument would show strong features arising principally from the frequency distribution of the vibrational modes. Multiphonon scattering is small at low momentum transfers in the low frequency range of most interest (<30 cm-1) but increases rapidly with increasing energy and momentum transfers. It is shown to originate from the lowest frequency modes. The momentum transfer dependence of the one-phonon Svibinc (q,w) is investigated. An expression is found which can be used to extrapolate the calculated one-phonon scattering to zero momentum transfer using experimentally obtainable ranges of momentum transfer. This permits the extraction of an amplitude-weighted frequency distribution function. At current resolutions this function is similar in form to the unweighted frequency distribution function, knowledge of which would be very useful for analysis of protein thermodynamics and dynamics.

Smith, Jeremy; Cusack, Stephen; Pezzeca, Ulrik; Brooks, Bernard; Karplus, Martin

1986-09-01

288

Bovine Leukemia Virus SU Protein Interacts with Zinc, and Mutations within Two Interacting Regions Differently Affect Viral Fusion and Infectivity In Vivo  

PubMed Central

Bovine leukemia virus (BLV) and human T-cell lymphotropic virus type 1 (HTLV-1) belong to the genus of deltaretroviruses. Their entry into the host cell is supposed to be mediated by interactions of the extracellular (SU) envelope glycoproteins with cellular receptors. To gain insight into the mechanisms governing this process, we investigated the ability of SU proteins to interact with specific ligands. In particular, by affinity chromatography, we have shown that BLV SU protein specifically interacted with zinc ions. To identify the protein domains involved in binding, 16 peptides distributed along the sequence were tested. Two of them appeared to be able to interact with zinc. To unravel the role of these SU regions in the biology of the virus, mutations were introduced into the env gene of a BLV molecular clone in order to modify residues potentially interacting with zinc. The fusogenic capacity of envelope mutated within the first zinc-binding region (104 to 123) was completely abolished. Furthermore, the integrity of this domain was also required for in vivo infectivity. In contrast, mutations within the second zinc-binding region (218 to 237) did not hamper the fusogenic capacity; indeed, the syncytia were even larger. In sheep, mutations in region 218 to 237 did not alter infectivity or viral spread. Finally, we demonstrated that the envelope of the related HTLV-1 was also able to bind zinc. Interestingly, zinc ions were found to be associated with the receptor-binding domain (RBD) of Friend murine leukemia virus (Fr-MLV) SU glycoprotein, further supporting their relevance in SU structure. Based on the sequence similarities shared with the Fr-MLV RBD, whose three-dimensional structure has been experimentally determined, we located the BLV zinc-binding peptide 104-123 on the opposite side of the potential receptor-binding surface. This observation supports the hypothesis that zinc ions could mediate interactions of the SU RBD either with the C-terminal part of SU, thereby contributing to the SU structural integrity, or with a partner(s) different from the receptor. PMID:12134000

Gatot, Jean-Stphane; Callebaut, Isabelle; Van Lint, Carine; Demont, Dominique; Kerkhofs, Pierre; Portetelle, Daniel; Burny, Arsne; Willems, Luc; Kettmann, Richard

2002-01-01

289

Protein Modelling: What Happened to the Protein Structure Gap?  

PubMed Central

Computational modeling and prediction of three-dimensional macromolecular structures and complexes from their sequence has been a long standing vision in structural biology as it holds the promise to bypass part of the laborious process of experimental structure solution. Over the last two decades, a paradigm shift has occurred: starting from a situation where the structure knowledge gap between the huge number of protein sequences and small number of known structures has hampered the widespread use of structure-based approaches in life science research, today some form of structural information either experimental or computational is available for the majority of amino acids encoded by common model organism genomes. Template based homology modeling techniques have matured to a point where they are now routinely used to complement experimental techniques. With the scientific focus of interest moving towards larger macromolecular complexes and dynamic networks of interactions, the integration of computational modeling methods with low-resolution experimental techniques allows studying large and complex molecular machines. Computational modeling and prediction techniques are still facing a number of challenges which hamper the more widespread use by the non-expert scientist. For example, it is often difficult to convey the underlying assumptions of a computational technique, as well as the expected accuracy and structural variability of a specific model. However, these aspects are crucial to understand the limitations of a model, and to decide which interpretations and conclusions can be supported. PMID:24010712

Schwede, Torsten

2013-01-01

290

Population dynamics simulations of functional model proteins  

NASA Astrophysics Data System (ADS)

In order to probe the fundamental principles that govern protein evolution, we use a minimalist model of proteins to provide a mapping from genotype to phenotype. The model is based on physically realistic forces of protein folding and includes an explicit definition of protein function. Thus, we can find the fitness of a sequence from its ability to fold to a stable structure and perform a function. We study the fitness landscapes of these functional model proteins, that is, the set of all sequences mapped on to their corresponding fitnesses and connected to their one mutant neighbors. Through population dynamics simulations we directly study the influence of the nature of the fitness landscape on evolution. Populations are observed to move to a steady state, the distribution of which can often be predicted prior to the population dynamics simulations from the nature of the fitness landscape and a quantity analogous to a partition function. In this paper, we develop a scheme for predicting the steady-state population on a fitness landscape, based on the nature of the fitness landscape, thereby obviating the need for explicit population dynamics simulations and providing some insight into the impact on molecular evolution of the nature of fitness landscapes. Poor predictions are indicative of fitness landscapes that consist of a series of weakly connected sublandscapes.

Blackburne, Benjamin P.; Hirst, Jonathan D.

2005-10-01

291

Models of Crk Adaptor Proteins in Cancer  

PubMed Central

The Crk family of adaptor proteins (CrkI, CrkII, and CrkL), originally discovered as the oncogene fusion product, v-Crk, of the CT10 chicken retrovirus, lacks catalytic activity but engages with multiple signaling pathways through their SH2 and SH3 domains. Crk proteins link upstream tyrosine kinase and integrin-dependent signals to downstream effectors, acting as adaptors in diverse signaling pathways and cellular processes. Crk proteins are now recognized to play a role in the malignancy of many human cancers, stimulating renewed interest in their mechanism of action in cancer progression. The contribution of Crk signaling to malignancy has been predominantly studied in fibroblasts and in hematopoietic models and more recently in epithelial models. A mechanistic understanding of Crk proteins in cancer progression in vivo is still poorly understood in part due to the highly pleiotropic nature of Crk signaling. Recent advances in the structural organization of Crk domains, new roles in kinase regulation, and increased knowledge of the mechanisms and frequency of Crk overexpression in human cancers have provided an incentive for further study in in vivo models. An understanding of the mechanisms through which Crk proteins act as oncogenic drivers could have important implications in therapeutic targeting. PMID:23226572

Bell, Emily S.

2012-01-01

292

A Bovine Herpesvirus 1 Protein Expressed in Latently Infected Neurons (ORF2) Promotes Neurite Sprouting in the Presence of Activated Notch1 or Notch3  

PubMed Central

Bovine herpesvirus 1 (BHV-1) infection induces clinical symptoms in the upper respiratory tract, inhibits immune responses, and can lead to life-threatening secondary bacterial infections. Following acute infection, BHV-1 establishes latency in sensory neurons within trigeminal ganglia, but stress can induce reactivation from latency. The latency-related (LR) RNA is the only viral transcript abundantly expressed in latently infected sensory neurons. An LR mutant virus with stop codons at the amino terminus of the first open reading frame (ORF) in the LR gene (ORF2) is not reactivated from latency, in part because it induces higher levels of apoptosis in infected neurons. ORF2 inhibits apoptosis in transiently transfected cells, suggesting that it plays a crucial role in the latency-reactivation cycle. ORF2 also interacts with Notch1 or Notch3 and inhibits its ability to trans activate certain viral promoters. Notch3 RNA and protein levels are increased during reactivation from latency, suggesting that Notch may promote reactivation. Activated Notch signaling interferes with neuronal differentiation, in part because neurite and axon generation is blocked. In this study, we demonstrated that ORF2 promotes neurite formation in mouse neuroblastoma cells overexpressing Notch1 or Notch3. ORF2 also interfered with Notch-mediated trans activation of the promoter that regulates the expression of Hairy Enhancer of Split 5, an inhibitor of neurite formation. Additional studies provided evidence that ORF2 promotes the degradation of Notch3, but not that of Notch1, in a proteasome-dependent manner. In summary, these studies suggest that ORF2 promotes a mature neuronal phenotype that enhances the survival of infected neurons and consequently increases the pool of latently infected neurons. PMID:23152506

Sinani, Devis; Frizzo da Silva, Leticia

2013-01-01

293

The mitogenic signaling pathway but not the plasminogen activator- inducing pathway of basic fibroblast growth factor is mediated through protein kinase C in fetal bovine aortic endothelial cells  

PubMed Central

Basic fibroblast growth factor (bFGF) induces cell proliferation and plasminogen activator (PA) activity in transformed fetal bovine aortic endothelial (FBAE) GM 7373 cells. A similar response is observed after treatment with 12-O-tetradecanoylphorbol-13-acetate (TPA). In these cells, bFGF and TPA cause activation of protein kinase C (PKC), as demonstrated by the induction of the phosphorylation of an 87-kD PKC substrate in intact cells and by the increase in membrane-associated PKC activity. Activation of PKC by bFGF or TPA is inhibited in cells made PKC-deficient by pretreatment with high concentrations of TPA. The mitogenic activity of bFGF or of TPA is completely inhibited in PKC- deficient cells or in naive cells treated with the PKC inhibitor H-7. However, these cells proliferate in response to serum, epidermal growth factor, and dibutyryl cyclic AMP. Similar results are obtained in normal FBAE AG 7680 cells. These data indicate that activation of PKC is responsible for the mitogenic activity of bFGF in FBAE cells. On the contrary, the PA-inducing activity of bFGF is unaffected by down- regulation of PKC or by treatment with the PKC inhibitor H-7 in both transformed GM 7373 and normal AG 7680 cells. bFGF induces a rapid 45Ca influx in naive and in PKC-deprived GM 7373 cells. In these cells, addition of EGTA to the incubation medium prevents both the 45Ca influx and the increase in PA activity induced by bFGF, without affecting its mitogenic activity. Even though the involvement of PKC in the increase of cell-associated PA activity induced by bFGF can not be completely dismissed, the present results suggest a role of calcium entry in the modulation of the PA-inducing activity of bFGF. PMID:2551911

1989-01-01

294

Fold assessment for comparative protein structure modeling.  

PubMed

Accurate and automated assessment of both geometrical errors and incompleteness of comparative protein structure models is necessary for an adequate use of the models. Here, we describe a composite score for discriminating between models with the correct and incorrect fold. To find an accurate composite score, we designed and applied a genetic algorithm method that searched for a most informative subset of 21 input model features as well as their optimized nonlinear transformation into the composite score. The 21 input features included various statistical potential scores, stereochemistry quality descriptors, sequence alignment scores, geometrical descriptors, and measures of protein packing. The optimized composite score was found to depend on (1) a statistical potential z-score for residue accessibilities and distances, (2) model compactness, and (3) percentage sequence identity of the alignment used to build the model. The accuracy of the composite score was compared with the accuracy of assessment by single and combined features as well as by other commonly used assessment methods. The testing set was representative of models produced by automated comparative modeling on a genomic scale. The composite score performed better than any other tested score in terms of the maximum correct classification rate (i.e., 3.3% false positives and 2.5% false negatives) as well as the sensitivity and specificity across the whole range of thresholds. The composite score was implemented in our program MODELLER-8 and was used to assess models in the MODBASE database that contains comparative models for domains in approximately 1.3 million protein sequences. PMID:17905832

Melo, Francisco; Sali, Andrej

2007-11-01

295

Candidate mechanisms underlying atypical progesterone profiles as deduced from parameter perturbations in a mathematical model of the bovine estrous cycle.  

PubMed

The complex interplay of physiological factors that underlies fertility in dairy cows was investigated using a mechanistic mathematical model of the dynamics of the bovine estrous cycle. The model simulates the processes of follicle and corpus luteum development and its relations with key hormones that interact to control these processes. Several factors may perturb the regular oscillatory behavior of a normal estrous cycle, and such perturbations are likely the effect of simultaneous changes in multiple parameters. The objective of this paper was to investigate how multiple parameter perturbation changes the behavior of the estrous cycle model, so as to identify biological mechanisms that could play a role in the development of cystic ovaries. Cystic ovaries are a common reason for reproductive failure in dairy cows, but much about the causes of this disorder remains unknown. We investigated in which region of the parameter space the model predicts a normal cycle, and when a progesterone pattern occurred with delayed ovulation (indicating a cystic follicle) or delayed luteolysis (indicating a persistent corpus luteum). Perturbation of the initial values for all parameters simultaneously showed 2 specific parameter configurations leading to delayed ovulation or delayed luteolysis immediately. The most important parameter changes in these 2 configurations involve the regulation of corpus luteum functioning, luteolytic signals, and GnRH synthesis, suggesting that these mechanisms are likely involved in the development of cystic ovaries. In the multidimensional parameter space, areas exist in which the parameter configurations resulted in normal cycles. These areas may be separated by areas in which irregular cycle patterns occurred. These irregular patterns thus mark the transition from one stable (normal) situation to another. Interestingly, within a series, there were some cycles with delayed ovulation and some with delayed luteolysis in these patterns. This could represent a situation of resumption of normal cyclicity (e.g., after parturition). In conclusion, the method of parameter perturbation used in the present study is an effective tool to find parameter configurations that lead to progesterone profiles associated with delayed ovulation and delayed luteolysis. Thereby, the model helps to generate hypotheses regarding the underlying cause of the development of cystic ovaries, which could be investigated in future experiments. PMID:22720939

Boer, H M T; Apri, M; Molenaar, J; Sttzel, C; Veerkamp, R; Woelders, H

2012-07-01

296

Effect of low voltage electrical stimulation on protein and quality changes in bovine muscles during postmortem aging.  

PubMed

This experiment was conducted to determine the influence of low voltage electrical stimulation (ES) on the tenderness development of beef round muscles. Eight steers were slaughtered, and ES applied to one side of each carcass within 90 min of exsanguination. Steaks from M. longissimus dorsi, semimembranosus, adductor, and gracilis were vacuum packaged and aged at 4 C for 9 d. Star probe, sensory evaluation, Western blot assays of troponin-T and ?-calpain autolysis and 2D-DIGE were conducted. ES resulted in accelerated (P<0.05) pH decline of the longissimus in the first 24h postmortem. ES did not influence (P>0.05) proteolysis and tenderness, but did alter the predominance of metabolic proteins in the soluble fraction of muscle. Aging for 9 d improved tenderness (P<0.05). The data confirmed that low voltage ES at 90 min of exsanguination had no effect on proteolysis and tenderness development in the longissimus dorsi, semimembranosus, adductor or gracilis in beef. PMID:23567127

Kim, Y H B; Lonergan, S M; Grubbs, J K; Cruzen, S M; Fritchen, A N; della Malva, A; Marino, R; Huff-Lonergan, E

2013-07-01

297

DNA vaccine-derived human IgG produced in transchromosomal bovines protect in lethal models of hantavirus pulmonary syndrome.  

PubMed

Polyclonal immunoglobulin-based medical products have been used successfully to treat diseases caused by viruses for more than a century. We demonstrate the use of DNA vaccine technology and transchromosomal bovines (TcBs) to produce fully human polyclonal immunoglobulins (IgG) with potent antiviral neutralizing activity. Specifically, two hantavirus DNA vaccines [Andes virus (ANDV) DNA vaccine and Sin Nombre virus (SNV) DNA vaccine] were used to produce a candidate immunoglobulin product for the prevention and treatment of hantavirus pulmonary syndrome (HPS). A needle-free jet injection device was used to vaccinate TcB, and high-titer neutralizing antibodies (titers >1000) against both viruses were produced within 1 month. Plasma collected at day 10 after the fourth vaccination was used to produce purified ?-HPS TcB human IgG. Treatment with 20,000 neutralizing antibody units (NAU)/kg starting 5 days after challenge with ANDV protected seven of eight animals, whereas zero of eight animals treated with the same dose of normal TcB human IgG survived. Likewise, treatment with 20,000 NAU/kg starting 5 days after challenge with SNV protected immunocompromised hamsters from lethal HPS, protecting five of eight animals. Our findings that the ?-HPS TcB human IgG is capable of protecting in animal models of lethal HPS when administered after exposure provides proof of concept that this approach can be used to develop candidate next-generation polyclonal immunoglobulin-based medical products without the need for human donors, despeciation protocols, or inactivated/attenuated vaccine antigen. PMID:25429055

Hooper, Jay W; Brocato, Rebecca L; Kwilas, Steven A; Hammerbeck, Christopher D; Josleyn, Matthew D; Royals, Michael; Ballantyne, John; Wu, Hua; Jiao, Jin-an; Matsushita, Hiroaki; Sullivan, Eddie J

2014-11-26

298

Hydration dynamics near a model protein surface  

SciTech Connect

The evolution of water dynamics from dilute to very high concentration solutions of a prototypical hydrophobic amino acid with its polar backbone, N-acetyl-leucine-methylamide (NALMA), is studied by quasi-elastic neutron scattering and molecular dynamics simulation for both the completely deuterated and completely hydrogenated leucine monomer. We observe several unexpected features in the dynamics of these biological solutions under ambient conditions. The NALMA dynamics shows evidence of de Gennes narrowing, an indication of coherent long timescale structural relaxation dynamics. The translational water dynamics are analyzed in a first approximation with a jump diffusion model. At the highest solute concentrations, the hydration water dynamics is significantly suppressed and characterized by a long residential time and a slow diffusion coefficient. The analysis of the more dilute concentration solutions takes into account the results of the 2.0M solution as a model of the first hydration shell. Subtracting the first hydration layer based on the 2.0M spectra, the translational diffusion dynamics is still suppressed, although the rotational relaxation time and residential time are converged to bulk-water values. Molecular dynamics analysis shows spatially heterogeneous dynamics at high concentration that becomes homogeneous at more dilute concentrations. We discuss the hydration dynamics results of this model protein system in the context of glassy systems, protein function, and protein-protein interfaces.

Russo, Daniela; Hura, Greg; Head-Gordon, Teresa

2003-09-01

299

Novel parasitic nematode-specific protein of bovine filarial parasite Setaria digitata displays conserved gene structure and ubiquitous expression.  

PubMed

Setaria digitata is an animal filarial parasite, which can cause fatal diseases to livestock such as cattle, sheep, goat, buffaloes, horses etc. inflicting considerable economic losses to livelihood of livestock farmers. In spite of this, the biology and parasitic nature of this organism is largely unknown. As a step towards understanding these, we screened the cDNA library of S. digitata and identified an open reading frame that code for parasitic nematode-specific protein, which showed a significant homology to functionally and structurally unannotated sequences of parasitic nematodes Wuchereria bancrofti, Brugia malayi, Onchocerca volvulus, Loa loa etc., suggesting its role in parasitism. RT-PCR analysis indicated that the S. digitata novel gene (SDNP) is expressed in adult female and male, and microfilariae. Southern hybridization studies revealed that this gene is a single-copy gene. Sequence analysis of the genomic region obtained from overlapping PCR amplification indicated that the size of the genomic region is 1819 bp in which four exons encoding 205 amino acids were interrupted by three introns of varying lengths of 419, 659 and 123 bp, and also the expansion of the size of the introns of S. digitata compared to its orthologues by integrating micro and mini-satellite containing sequence. Sequences around the splice junctions were conserved and agreed with the general GT-AG splicing rule. The gene was found to be AT rich with a GC content of 38.1%. Bioinformatic analysis indicated that the gene structure of SDNP and its orthologues is conserved and it expressed ubiqutously in all the stages of nematode's life cycle. Therefore, taking these outcomes together, it can be concluded that SDNP is a parasitic nematode-specific, single copy gene having conserved gene structure of four exons interrupted by three introns and that the gene is expressed ubiquitously throughout nematode's life cycle. PMID:25382479

Rodrigo, W W; Dassanayake, R S; Weerasena, S J; Silva Gunawardene, Y I

2014-09-01

300

Extracting Protein-Protein Interactions from MEDLINE using the Hidden Vector State model  

Microsoft Academic Search

A major challenge in text mining for biomedicine is automatically extracting protein-protein interactions from the vast amount of biomedical literature. We have constructed an information extraction system based on the Hidden Vector State (HVS) model for protein-protein interactions. The HVS model can be trained using only lightly annotated data whilst simultaneously retaining sufficient ability to capture the hierarchical structure. When

Deyu Zhou; Yulan He; Chee Keong Kwoh

2008-01-01

301

Model-building codes for membrane proteins.  

SciTech Connect

We have developed a novel approach to modeling the transmembrane spanning helical bundles of integral membrane proteins using only a sparse set of distance constraints, such as those derived from MS3-D, dipolar-EPR and FRET experiments. Algorithms have been written for searching the conformational space of membrane protein folds matching the set of distance constraints, which provides initial structures for local conformational searches. Local conformation search is achieved by optimizing these candidates against a custom penalty function that incorporates both measures derived from statistical analysis of solved membrane protein structures and distance constraints obtained from experiments. This results in refined helical bundles to which the interhelical loops and amino acid side-chains are added. Using a set of only 27 distance constraints extracted from the literature, our methods successfully recover the structure of dark-adapted rhodopsin to within 3.2 {angstrom} of the crystal structure.

Shirley, David Noyes; Hunt, Thomas W.; Brown, W. Michael; Schoeniger, Joseph S. (Sandia National Laboratories, Livermore, CA); Slepoy, Alexander; Sale, Kenneth L. (Sandia National Laboratories, Livermore, CA); Young, Malin M. (Sandia National Laboratories, Livermore, CA); Faulon, Jean-Loup Michel; Gray, Genetha Anne (Sandia National Laboratories, Livermore, CA)

2005-01-01

302

Effects of stage of lactation, milk protein genotype and body condition at calving on protein composition and renneting properties of bovine milk.  

PubMed

The lactational variation in milk protein composition and renneting properties and their relationship to the cow's body condition at calving were investigated in 39 Danish Holstein first lactation cows fed on a well balanced standard diet. All milk characteristics measured were significantly affected by stage of lactation (P < 0.01). Casein as a proportion of total milk nitrogen reached a maximum in mid lactation. The proportion of alpha s- and kappa-casein in total casein decreased and the proportion of beta-casein increased systematically during lactation while the proportion of gamma-casein was lowest in mid lactation. The alpha-lactalbumin content of milk and its proportion of total whey proteins decreased during lactation. Renneting time was highest and curd firmness lowest in mid lactation. These results appeared to reflect a low degree of proteolysis in late-lactation milks compared with several other investigations, probably because of the good nutritional state of the cows. The body condition at calving affected proteolysis and the renneting properties of milk. A good body condition increased the content of whey protein in total milk nitrogen and of gamma-casein in total caseins (P < 0.05); in addition, curd firmness was improved (P < 0.01) and aggregation time was reduced (P < 0.05). We suggest that these effects were related to the fat metabolism and energy status of the cows during lactation. The interrelationships between the milk characteristics were evaluated by factor analysis to support the interpretation. PMID:9161914

Ostersen, S; Foldager, J; Hermansen, J E

1997-05-01

303

Structure Modeling of All Identified G ProteinCoupled Receptors in the Human Genome  

PubMed Central

G proteincoupled receptors (GPCRs), encoded by about 5% of human genes, comprise the largest family of integral membrane proteins and act as cell surface receptors responsible for the transduction of endogenous signal into a cellular response. Although tertiary structural information is crucial for function annotation and drug design, there are few experimentally determined GPCR structures. To address this issue, we employ the recently developed threading assembly refinement (TASSER) method to generate structure predictions for all 907 putative GPCRs in the human genome. Unlike traditional homology modeling approaches, TASSER modeling does not require solved homologous template structures; moreover, it often refines the structures closer to native. These features are essential for the comprehensive modeling of all human GPCRs when close homologous templates are absent. Based on a benchmarked confidence score, approximately 820 predicted models should have the correct folds. The majority of GPCR models share the characteristic seven-transmembrane helix topology, but 45 ORFs are predicted to have different structures. This is due to GPCR fragments that are predominantly from extracellular or intracellular domains as well as database annotation errors. Our preliminary validation includes the automated modeling of bovine rhodopsin, the only solved GPCR in the Protein Data Bank. With homologous templates excluded, the final model built by TASSER has a global C? root-mean-squared deviation from native of 4.6 , with a root-mean-squared deviation in the transmembrane helix region of 2.1 . Models of several representative GPCRs are compared with mutagenesis and affinity labeling data, and consistent agreement is demonstrated. Structure clustering of the predicted models shows that GPCRs with similar structures tend to belong to a similar functional class even when their sequences are diverse. These results demonstrate the usefulness and robustness of the in silico models for GPCR functional analysis. All predicted GPCR models are freely available for noncommercial users on our Web site (http://www.bioinformatics.buffalo.edu/GPCR). PMID:16485037

Zhang, Yang; DeVries, Mark E; Skolnick, Jeffrey

2006-01-01

304

Study of the disulfide reduction of denatured proteins by liquid chromatography coupled with on-line cold-vapor-generation atomic-fluorescence spectrometry (LCCVGAFS)  

Microsoft Academic Search

Hydrophobic-interaction chromatography coupled on-line with chemical-vapor-generation atomic-fluorescence spectrometry (HICCVGAFS), optimized recently for the analysis of thiol-containing proteins under denaturing conditions, has been used to study the chemical reduction of denatured proteins. Four proteins chosen as models (human serum albumin (HSA), bovine serum albumin (BSA), ?-lactalbumin ( ?-Lac) from bovine milk, and lysozyme from chicken egg (Lys)) were denatured with urea

Emilia Bramanti; Cristina Lomonte; Massimo Onor; Roberto Zamboni; Giorgio Raspi; Alessandro DUlivo

2004-01-01

305

MODELING PROTEIN INTERACTIONS THROUGH STRUCTURE ALIGNMENT.  

E-print Network

??Rapid accumulation of the experimental data on protein-protein complexes drives the paradigm shift in protein docking from "traditional" template free approaches to template based techniques. (more)

Sinha, Rohita

2011-01-01

306

Sequences outside that of residues 93-102 of 3A protein can contribute to the ability of foot-and-mouth disease virus (FMDV) to replicate in bovine-derived cells.  

PubMed

Foot-and-mouth disease (FMD) is a highly contagious and economically devastating disease of cloven-hoofed animals. During 2010 and 2011, there was an epidemic of the Mya-98 lineage of the Southeast Asia (SEA) topotype in East Asia, including China. Changes in the FMDV 3A protein have been previously reported to be associated with the inability of FMDV to grow in bovine cells and cause disease in cattle. In this paper, we report the generation of a full-length infectious cDNA clone of FMDV O/SEA/Mya-98 strain O/GZSB/2011 for the first time along with two genetically modified viruses with deletion at positions 93-102 and 133-143 in 3A based on the established infectious clone. All the recombinant viruses grew well and displayed growth properties and plaque phenotypes similar to those of the parental virus in baby hamster kidney (BHK-21) cells, porcine kidney (PK-15) cells, and primary fetal porcine kidney (FPK) cells. While the recombinant viruses rvGZSB and rvSB?133-143 exhibited similar growth properties and plaque phenotypes with the parental virus in primary fetal bovine kidney (FBK) cells, the recombinant virus rvSB?93-102, containing deletion at positions 93-102 in 3A, grew at a slower rate and had a smaller plaque size phenotype in FBK cells than that of the parental virus. Therefore, the results suggest that the deletion at positions 93-102 of 3A protein does not affect FMDV replication efficiency in BHK-21, PK-15 and FPK cells, but affects virus replication efficiency in FBK cells, although, cannot alone account for the inability to replicate in bovine cells. PMID:25116389

Ma, Xueqing; Li, Pinghua; Bai, Xingwen; Sun, Pu; Bao, Huifang; Lu, Zengjun; Cao, Yimei; Li, Dong; Chen, Yingli; Qiao, Zilin; Liu, Zaixin

2014-10-13

307

A peptide derived from human bactericidal/permeability-increasing protein (BPI) exerts bactericidal activity against Gram-negative bacterial isolates obtained from clinical cases of bovine mastitis  

Technology Transfer Automated Retrieval System (TEKTRAN)

Gram-negative bacteria are responsible for approximately one-third of the clinical cases of bovine mastitis and can elicit a life-threatening, systemic inflammatory response. Lipopolysaccharide (LPS) is a membrane component of all Gram-negative bacteria and is largely responsible for evoking the de...

308

CSAW: a dynamical model of protein folding  

E-print Network

CSAW (conditioned self-avoiding walk) is a model of protein folding that combines SAW (self-avoiding walk) with Monte-Carlo. It simulates the Brownian motion of a chain molecule in the presence of interactions, both among chain residues, and with the environment. In a first model that includes the hydrophobic effect and hydrogen bonding, a chain of 30 residues folds into a native state with stable secondary and tertiary structures. The process starts with a rapid collapse into an intermediate "molten globule", which slowly decays into the native state afer a relatively long quiescent period. The behavior of the radius of gyration mimics experimental data.

Kerson Huang

2006-01-12

309

Protein viscoelastic dynamics: a model system  

E-print Network

A model system inspired by recent experiments on the dynamics of a folded protein under the influence of a sinusoidal force is investigated and found to replicate many of the response characteristics of such a system. The essence of the model is a strongly over-damped oscillator described by a harmonic restoring force for small displacements that reversibly yields to stress under sufficiently large displacement. This simple dynamical system also reveals unexpectedly rich behavior, exhibiting a series of dynamical transitions and analogies with equilibrium thermodynamic phase transitions. The effects of noise and of inertia are briefly considered and described.

Craig Fogle; Joseph Rudnick; David Jasnow

2015-02-02

310

Modeling and mitigating winter hay bale damage by elk in a low prevalence bovine tuberculosis endemic zone.  

PubMed

Wildlife causes extensive crop damage throughout much of North America and these shared feeds are a key risk factor in the transmission of diseases between wildlife and livestock, including bovine tuberculosis (TB). Predicting wildlife use of agricultural crops can provide insight directed toward targeted disease mitigation at areas of potential indirect interaction. In this study, we quantified use of hay bales by elk (Cervus canadensis) during the winter in southwestern Manitoba, Canada using a database of 952 damage claims paid compensation from 1994 to 2012. We evaluated environmental factors predicted to determine risk of hay bale damage on each quarter section by elk using a Resource Selection Probability Function (RSPF) model. The most important variables (as measured for each quarter section and based on cumulative Akaike weights that scale from 0 to 1) were distance to protected areas (1.00), forest including a buffer around the quarter section (1.00), forage crop including a buffer around the quarter section (1.00), distance from streams (0.99), forage crop (0.92), cereal and oilseed crop cover including a buffer (0.85), and forest cover (0.82). We then developed an RSPF-based predictive map of damage to hay bales by elk that identified key areas with high probability of damage (RSPF?0.6), accounting for 3.5% of the study area. We then multiplied the RSPF values by the inverse of the proximity to known cases of TB positive elk and determined that 0.51% of the study area had an overall high combined probability of hay bale damage and proximity to TB positive elk (i.e. adjusted probability of ?0.6). In the southern half of the study area where 164 hay yard barrier fences have been implemented since 2002, there has been a significant decrease in the number of annual claims. Barrier fencing around Riding Mountain National Park has been successful at reducing elk damage where it has been implemented. In our study area, prevalence of TB in both cattle (0.003%) and elk (0.89%) is very low, precluding conventional epidemiological analyses. In the absence of clear evidence of specific routes of TB transmission, we advocate that on-farm risk assessments and mitigation efforts should continue to address areas where elk cause damage to hay bales in winter using barrier fencing. Mitigation effort should especially focus on areas where TB positive elk have been identified, as these sites provide potential for indirect interaction between cattle and elk. PMID:24486094

Gooding, R M; Brook, R K

2014-05-01

311

Effects of exposure to calves persistently infected with bovine viral diarrhea virus type 1b and subsequent infection with Mannheima haemolytica on clinical signs and immune variables: model for bovine respiratory disease via viral and bacterial interaction.  

PubMed

The objective was to determine effects of an intratracheal Mannheimia haemolytica challenge after 72-h exposure to bovine viral diarrhea virus type 1b (BVDV1b) persistently infected (PI) calves on serum antibody production, white blood cell count (WBC), cytokine concentrations, and blood gases in feedlot steers. Twenty-four steers (initial BW = 314 +/- 31 kg) were randomly allocated to 1 of 4 treatments (6 steers/treatment) arranged as a 2 x 2 factorial. Treatments were 1) steers not exposed to steers PI with BVDV nor challenged with M. haemolytica (control; CON); 2) steers exposed to 2 steers PI with BVDV for 72 h (BVD); 3) steers intratracheally challenged with M. haemolytica (MH); and 4) steers exposed to 2 steers PI with BVDV for 72 h and challenged with M. haemolytica (BVD+MH). There were 12 h between exposure to PI steers and challenge with M. haemolytica. Rectal temperature was increased (P < 0.001) for MH and BVD+MH during the initial 24 h after the M. haemolytica challenge. For MH and BVD+MH, total WBC count was increased (P < 0.01) at 36 h post M. haemolytica challenge compared with CON, whereas in BVD steers, WBC count was decreased (P < 0.01). Total lymphocyte count was increased (P = 0.004) during the initial 72 h post BVDV exposure for the BVD and BVD+MH groups compared with MH and CON, and this difference remained at 96 h post M. haemolytica challenge. An increased (P < 0.001) total neutrophil count was observed during the initial 36 h for the MH group and at 72 h for the BVD+MH challenge group. Interleukin 1beta, IL-6, and tumor necrosis factor alpha (TNFalpha) concentrations were greater (P model was successful at inducing bovine respiratory disease (BRD) associated with BVDV and M. haemolytica. Understanding the physiological changes in morbid animals will lead to improved strategies for decreasing severity and economic losses associated with BRD. PMID:20154164

Burciaga-Robles, L O; Step, D L; Krehbiel, C R; Holland, B P; Richards, C J; Montelongo, M A; Confer, A W; Fulton, R W

2010-06-01

312

Neural retina limits the nonviral gene transfer to retinal pigment epithelium in an in vitro bovine eye model  

Microsoft Academic Search

We investigated the permeation of liposomal and polymeric gene delivery systems through neural retina into retinal pigment\\u000a epithelium (RPE) and determined the roles of various factors in permeation and subsequent uptake of the delivery systems by\\u000a RPE. Anterior parts and vitreous of fresh bovine eyes were removed. Retina was left intact or peeled away. Complexes of ethidium\\u000a monoazide (EMA)-labeled plasmid

Leena Pitknen; Jukka Pelkonen; Marika Ruponen; Seppo Rnkk; Arto Urtti

2004-01-01

313

Microwave radiation can alter protein conformation without bulk heating  

Microsoft Academic Search

Exposure to microwave radiation enhances the aggregation of bovine serum albumin in vitro in a time- and temperature-dependent manner. Microwave radiation also promotes amyloid fibril formation by bovine insulin at 60C. These alterations in protein conformation are not accompanied by measurable temperature changes, consistent with estimates from field modelling of the specific absorbed radiation (1520 mW kg?1). Limited denaturation of

David I. de Pomerai; Brette Smith; Adam Dawe; Kate North; Tim Smith; David B. Archer; Ian R. Duce; Donald Jones; E. Peter M. Candido

2003-01-01

314

Frustration in protein elastic network models  

NASA Astrophysics Data System (ADS)

Elastic network models (ENMs) are widely used for studying the equilibrium dynamics of proteins. The most common approach in ENM analysis is to adopt a uniform force constant or a non-specific distance dependent function to represent the force constant strength. Here we discuss the influence of sequence and structure in determining the effective force constants between residues in ENMs. Using a novel method based on entropy maximization, we optimize the force constants such that they exactly reporduce a subset of experimentally determined pair covariances for a set of proteins. We analyze the optimized force constants in terms of amino acid types, distances, contact order and secondary structure, and we demonstrate that including frustrated interactions in the ENM is essential for accurately reproducing the global modes in the middle of the frequency spectrum.

Lezon, Timothy; Bahar, Ivet

2010-03-01

315

Bovine viral diarrhoea virus infection alters global transcription profiles in bovine endothelial cells.  

PubMed

Bovine viral diarrhoea viruses (BVDV) are significant pathogens of cattle worldwide. These viruses exist in both non-cytopathic and cytopathic biotypes. Non-cytopathic BVDV can establish persistent lifelong infections in cattle and are a frequent contaminant of biological reagents such as cell cultures and foetal bovine serum. We identified commercially available bovine aortic endothelial cells (BAECs) contaminated with BVDV. In this study, to determine if BVDV alters endothelial gene transcription patterns, serial analysis of gene expression (SAGE) was used to compare gene expression profiles from uninfected and BVDV contaminated BAEC. SAGE is an open ended, quantitative method for characterizing global patterns of transcription. Comparison of expression profiles of BVDV-contaminated and noninfected cells revealed significant increases in the transcription of many genes including P-selectin, tryptophan tRNA synthetase and prostaglandin D2 synthase. These changes were validated by real-time PCR. Additionally, real-time PCR demonstrated that the response to LPS and dsRNA by contaminated cells, as well as cells acutely infected with noncytopathic BVDV, is altered. The altered response may be through the high level of expression of A20 and inhibition of activation of NF-kappaB. BAECs are commonly used as a model to study endothelial cell function in many different systems. As shown here, transcriptional and probable protein changes resulting from BVDV infection significantly alter cellular responses and may have a profound impact on experimental outcome. Transcriptomic analysis provided the initial clues leading to the characterization of this altered function. PMID:18817290

Neill, J D; Ridpath, J F; Lange, A; Zuerner, R L

2008-01-01

316

The effect of lutein, sesamol, ellagic acid and olive leaf extract on lipid oxidation and oxymyoglobin oxidation in bovine and porcine muscle model systems.  

PubMed

The effect of lutein (100, 200, 300?g/ml), sesamol (500, 1000, 2000?g/ml), ellagic acid (300, 600, 900?g/ml) and olive leaf extract (100, 200, 300?g/ml) on oxymyoglobin oxidation and lipid oxidation in bovine and porcine muscle model systems (25% M. longissimus thoracis et lumborum homogenates) was examined. Radical scavenging activity, using the DPPH assay, and iron-chelating activities of lutein, sesamol, ellagic acid and olive leaf extract were assessed at concentrations ranging from 200 to 1000ppm. The radical scavenging activity was of the order: ellagic acid>sesamol>olive leaf extract>lutein. None of the natural antioxidants examined exhibited iron chelating activity. Following induced lipid oxidation (FeCl(3)/sodium ascorbate addition), lipid oxidation and oxymyoglobin oxidation were measured after 24h at 4C. In bovine and porcine muscle model systems, lipid oxidation decreased (P<0.001) following addition of each of the natural antioxidants relative to the control and antioxidant potency followed the order: sesamol>ellagic acid>olive leaf extract>lutein. Ellagic acid and olive leaf extract decreased oxymyoglobin oxidation (P<0.001) while sesamol increased oxymyoglobin oxidation in both systems. The natural antioxidants examined may have applications in the development of nutritional enhanced meat products with enhanced shelf-life characteristics. PMID:20416759

Hayes, J E; Stepanyan, V; Allen, P; O'Grady, M N; O'Brien, N M; Kerry, J P

2009-10-01

317

Simple micromechanical model of protein crystals for their mechanical characterizations  

NASA Astrophysics Data System (ADS)

Proteins have been known to perform the excellent mechanical functions and exhibit the remarkable mechanical properties such as high fracture toughness in spider silk protein [1]. This indicates that the mechanical characterization of protein molecules and/or crystals is very essential to understand such remarkable mechanical function of protein molecules. In this study, for gaining insight into mechanical behavior of protein crystals, we developed the micromechanical model by using the empirical potential field prescribed to alpha carbon atoms of a protein crystal in a unit cell. We consider the simple protein crystals for their mechanical behavior under tensile loading to be compared with full atomic models

Yoon, G.; Eom, K.; Na, S.

2010-06-01

318

Preparation and characterization of iminodiacetic acid-functionalized magnetic nanoparticles and its selective removal of bovine hemoglobin  

NASA Astrophysics Data System (ADS)

In this study, a novel route for the preparation of magnetite (Fe3O4) nanoparticles (NPs) with immobilized metal affinity ligand iminodiacetic acid (IDA) charged with Cu2 + was developed. First, magnetite nanoparticles were synthesized by a hydrothermal method. Charged with Cu2 + , the magnetic nanoparticles (MNPs) were applied to separate a model protein mixture of bovine hemoglobin (BHb) and bovine serum albumin (BSA). They could be separated completely and showed low non-specific adsorption. The morphology, structure and composition of the magnetite MNPs were characterized by transmission electron microscopy, power x-ray diffraction, x-ray photoelectron spectrometry and Fourier transform infrared spectroscopy. The resulting magnetite MNPs charged with Cu2 + show not only a strong magnetic response to externally applied magnetic field, but are also highly specific to protein BHb. It is interesting that MNPs modified with metal ligands showed a property of magnetic colloid photonic crystals. Furthermore, they could efficiently remove the abundant protein bovine hemoglobin from bovine blood. They have potential application in removing abundant protein in proteomic analysis.

Zhang, Min; He, Xiwen; Chen, Langxing; Zhang, Yukui

2011-02-01

319

Unlocking the bovine genome  

Technology Transfer Automated Retrieval System (TEKTRAN)

The draft genome sequence of cattle (Bos taurus) has now been analyzed by the Bovine Genome Sequencing and Analysis Consortium and the Bovine HapMap Consortium, which together represent an extensive collaboration involving more than 300 scientists from 25 different countries. ...

320

IDENTIFICATION OF BOVINE MICRORNAS  

Technology Transfer Automated Retrieval System (TEKTRAN)

MicroRNAs are small ~22 nucleotides-long non-coding RNAs capable of controlling gene expression by inhibiting translation or targeting messenger RNA for degradation. Bovine genome sequence is not yet annotated for the microRNAs and there are currently no bovine miRNAs reported in the miRBase. Alignm...

321

Reconstitution of Membrane Proteins into Model Membranes: Seeking Better Ways to Retain Protein Activities  

PubMed Central

The function of any given biological membrane is determined largely by the specific set of integral membrane proteins embedded in it, and the peripheral membrane proteins attached to the membrane surface. The activity of these proteins, in turn, can be modulated by the phospholipid composition of the membrane. The reconstitution of membrane proteins into a model membrane allows investigation of individual features and activities of a given cell membrane component. However, the activity of membrane proteins is often difficult to sustain following reconstitution, since the composition of the model phospholipid bilayer differs from that of the native cell membrane. This review will discuss the reconstitution of membrane protein activities in four different types of model membranemonolayers, supported lipid bilayers, liposomes and nanodiscs, comparing their advantages in membrane protein reconstitution. Variation in the surrounding model environments for these four different types of membrane layer can affect the three-dimensional structure of reconstituted proteins and may possibly lead to loss of the proteins activity. We also discuss examples where the same membrane proteins have been successfully reconstituted into two or more model membrane systems with comparison of the observed activity in each system. Understanding of the behavioral changes for proteins in model membrane systems after membrane reconstitution is often a prerequisite to protein research. It is essential to find better solutions for retaining membrane protein activities for measurement and characterization in vitro. PMID:23344058

Shen, Hsin-Hui; Lithgow, Trevor; Martin, Lisandra L.

2013-01-01

322

In bovine binucleate trophoblast giant cells, pregnancy-associated glycoproteins and placental prolactin-related protein-I are conjugated to asparagine-linked N -acetylgalactosaminyl glycans  

Microsoft Academic Search

Bovine binucleate trophoblast giant cells (BNCs) produce large amounts of PAS-positive cytoplasmic granules. After fusion of BNCs with uterine epithelial cells, the contents of these granules are released into the maternal stroma which underlies the uterine epithelium. Histochemically, the granules can be labeled with N-acetylgalactosamine-specific lectins (Dolichos biflorus, Vicia villosa, and Wisteria floribunda agglutinins) and with Phaseolus vulgaris leucoagglutinin. In

Karl Klisch; Rudolf Leiser

2003-01-01

323

Adrenocorticotropin secretion by primary cultures of bovine adenohypophyseal cells in response to corticotropin releasing factor and vasopressin: evidence for modulation through both adenylate cyclase and protein kinase C  

E-print Network

of bovine adenohypophyseal cells were exposed to various doses of corticotropin releasing factor (CRF), arginine vasopressin (VP), forskolin (FSK), phorbol 12-myristate 13 ~tate (PNA), and J. ~ethyl-3=iaohutylxanthina (NTK) either alone... or MIX resulted in additive secretory responses that support the theory that CRF stimulation of ACTH secretion is through increases in intracellular cAMP concentrations. Co-treatment of the cells with various doses of VP and either MIX or FSK resulted...

Wagner, Kimberly Ann

1987-01-01

324

Proteolysis of Specific Muscle Structural Proteins by m-Calpain at Low pH and Temperature Is Similar to Degradation in Postmortem Bovine Muscle1,2  

Microsoft Academic Search

Postmortem (PM) and m-calpain- induced degradation of specific skeletal muscle pro- teins was monitored by SDS-PAGE and Western blotting. Samples were removed from bovine longissi- mus thoracis (LT) at approximately 45 min PM for the preparation of at-death (0-d) myofibrils (MF). The LT was excised at 1 d PM, vacuum-packaged, and stored at 2C. Samples were removed for Warner- Bratzler

Elisabeth Huff-Lonergan; Tomiko Mitsuhashi; Dirk D. Beekman; F. C. Parrish; Dennis G. Olson; Richard M. Robson

2010-01-01

325

Expression and localization of progesterone receptor membrane component 1 and 2 and serpine mRNA binding protein 1 in the bovine corpus luteum during the estrous cycle and the first trimester of pregnancy.  

PubMed

The aim of this study was to evaluate the mRNA and protein expression and the localization of progesterone receptor membrane component 1 (PGRMC1), PGRMC2, and the PGRMC1 partner serpine mRNA binding protein 1 (SERBP1) in the bovine CL on Days 2 to 5, 6 to 10, 11 to 16, and 17 to 20 of the estrous cycle as well as during Weeks 3 to 5, 6 to 8, and 9 to 12 of pregnancy (n = 5-6 per each period). The highest levels of PGRMC1 and PGRMC2 mRNA expression were found on Days 6 to 16 (P < 0.05) and 11 to 16, respectively, of the estrous cycle and during pregnancy (P < 0.001). The level of PGRMC1 protein was the highest (P < 0.05) on Days 11 to 16 of the estrous cycle compared with the other stages of the estrous cycle and pregnancy, whereas PGRMC2 protein expression (P < 0.001) was the highest on Days 17 to 20 and also during pregnancy. The mRNA expression of SERBP1 was increased (P < 0.05) on Days 11 to 16, whereas the level of its protein product was decreased (P < 0.05) on Days 6 to 10 of the estrous cycle and was at its lowest (P < 0.001) on Days 17 to 20. In pregnant cows, the patterns of SERBP1 mRNA and protein expression remained constant and were comparable with those observed during the estrous cycle. Progesterone receptor membrane component 1 and PGRMC2 localized to both large and small luteal cells, whereas SERBP1 was observed mainly in small luteal cells and much less frequently in large luteal cells. All proteins were also localized in the endothelial cells of blood vessels. The data obtained indicate the variable expression of PGRMC1, PGRMC2, and SERBP1 mRNA and protein in the bovine CL and suggest that progesterone may regulate CL function via its membrane receptors during both the estrous cycle and pregnancy. PMID:25168721

Kowalik, Magdalena K; Rekawiecki, Robert; Kotwica, Jan

2014-11-01

326

Thermodynamics of Protein Folding from Coarse-Grained Models' Perspectives  

E-print Network

8 Thermodynamics of Protein Folding from Coarse-Grained Models' Perspectives Michael Bachmann applications. In this lecture, we focus on the anal- ysis of mesoscopic models for protein folding, aggregation for a more universal description of the notoriously difficult problem of protein fold- ing. In this approach

Janke, Wolfhard

327

Modeling Protein Folding and Applying It to a Relevant Activity  

ERIC Educational Resources Information Center

The different levels of protein structure that can be easily understood by creating a model that simulates protein folding, which can then be evaluated by applying it to a relevant activity, is presented. The materials required and the procedure for constructing a protein folding model are mentioned.

Nelson, Allan; Goetze, Jim

2004-01-01

328

Modeling Protein Folding Pathways Christopher Bystroff, Yu Shao  

E-print Network

Modeling Protein Folding Pathways Christopher Bystroff, Yu Shao Dept of Biology Rensselaer Polytechnic Institute, Troy, NY. e-mail:{bystrc, shaoy}@rpi.edu Summary Proteins fold through a series of intermediate states called a pathway. Protein folding pathways have been modeled using either simulations

Bystroff, Chris

329

Domain specific association of small fluorescent probe trans-3-(4-monomethylaminophenyl)-acrylonitrile (MMAPA) with bovine serum albumin (BSA) and its dissociation from protein binding sites by Ag nanoparticles: spectroscopic and molecular docking study.  

PubMed

Photoinduced intramolecular charge transfer produced a polar excited state in trans-3-(4-monomethylaminophenyl)acrylonitrile (MMAPA), rendering the resulting emission sensitive to the medium polarity. Strong binding interaction of silver nanoparticles with the probe was observed, causing fluorescence quenching through the static quenching process. The probe MMAPA was found to bind to the less polar hydrophobic, restricted proteinous environment of bovine serum albumin (BSA) resulting in the blue shift of the emission maximum with an increase in emission intensity and fluorescence anisotropy. Studies using site markers of flufenamic acid and phenylbutazone coupled with molecular docking results predicted that the binding site of the probe is in between subdomains IIIA and IB of BSA and is different from the conventional Sudlow sites. The denaturation of the probe-bound BSA by urea or heat released the probe from this proteinous environment to water marked by exactly reverse spectral changes. On the interaction of silver nanoparticles with the probe bound protein, the probe was observed to move from its binding site in the protein to the Ag(0) nanoparticle surface involving conformational changes of the protein near the probe binding site. PMID:22126460

Ghosh, Shalini; Jana, Sankar; Guchhait, Nikhil

2012-01-26

330

The bovine renal parathyroid hormone (PTH) receptor has equal affinity for two different amino acid sequences: the receptor binding domains of PTH and PTH-related protein are located within the 14-34 region.  

PubMed

Previous studies examining the interaction of PTH and PTH-related protein (PTHrP) with target tissue have for the most part emphasized the similarity between the two hormones in binding to and activating receptors. This observation that two peptides with limited homology have equal affinities for the same receptor is unusual. In this report we investigated two aspects of PTH/PTHrP-receptor interactions. First, the nonhomologous 14-34 regions of PTH and PTHrP were synthesized and evaluated. Second, hybrid peptides containing the 7-18 fragment of one hormone combined with the 19-34 region of the other hormone were studied to determine whether interactions between these two regions are required for receptor recognition. All four peptides were examined in bovine renal cortical membrane and rat osteosarcoma (ROS 17/2.8) cell PTH-binding and PTH-stimulated adenylate cyclase assays. The results indicate that the receptor-binding domains of PTH and PTHrP lie outside of the 1-13 region, the region containing sequence homology shared by the two hormones, and that two peptides of different amino acid sequence bind with equal affinity to the bovine renal PTH receptor. However, in the absence of the N-terminal region, the rat bone PTH receptor displays a preference for the C-terminal (19-34 sequence) region of PTHrP. PMID:2163327

Caulfield, M P; McKee, R L; Goldman, M E; Duong, L T; Fisher, J E; Gay, C T; DeHaven, P A; Levy, J J; Roubini, E; Nutt, R F

1990-07-01

331

A large-scale electrophoresis- and chromatography-based determination of gene expression profiles in bovine brain capillary endothelial cells after the re-induction of blood-brain barrier properties  

PubMed Central

Background Brain capillary endothelial cells (BCECs) form the physiological basis of the blood-brain barrier (BBB). The barrier function is (at least in part) due to well-known proteins such as transporters, tight junctions and metabolic barrier proteins (e.g. monoamine oxidase, gamma glutamyltranspeptidase and P-glycoprotein). Our previous 2-dimensional gel proteome analysis had identified a large number of proteins and revealed the major role of dynamic cytoskeletal remodelling in the differentiation of bovine BCECs. The aim of the present study was to elaborate a reference proteome of Triton X-100-soluble species from bovine BCECs cultured in the well-established in vitro BBB model developed in our laboratory. Results A total of 215 protein spots (corresponding to 130 distinct proteins) were identified by 2-dimensional gel electrophoresis, whereas over 350 proteins were identified by a shotgun approach. We classified around 430 distinct proteins expressed by bovine BCECs. Our large-scale gene expression analysis enabled the correction of mistakes referenced into protein databases (e.g. bovine vinculin) and constitutes valuable evidence for predictions based on genome annotation. Conclusions Elaboration of a reference proteome constitutes the first step in creating a gene expression database dedicated to capillary endothelial cells displaying BBB characteristics. It improves of our knowledge of the BBB and the key proteins in cell structures, cytoskeleton organization, metabolism, detoxification and drug resistance. Moreover, our results emphasize the need for both appropriate experimental design and correct interpretation of proteome datasets. PMID:21078152

2010-01-01

332

A Continuum Model for ProteinProtein Interactions: Application to the Docking Problem  

Microsoft Academic Search

The prediction of proteinprotein interactions in solution is a major goal of theoretical structural biology. Here, we implement a continuum description of the thermodynamic processes involved. The model differs considerably from previous models in its use of molecular surface' area to describe the hydrophobic component to the free energy of conformational change in solution. We have applied this model

Richard M. Jackson; Michael J. E. Sternberg

1995-01-01

333

Increasing Antiviral Activity of Surfactant Protein D Trimers By Introducing Residues From Bovine Serum Collectins: Dissociation of mannan-binding and antiviral activity  

PubMed Central

Collectins contribute to host defense through interactions with glycoconjugates on pathogen surfaces. We have prepared recombinant trimeric neck and carbohydrate recognition domains (NCRDs) of collectins and we now show that the NCRDs of bovine conglutinin and CL-46 (like that of CL-43) have greater intrinsic antiviral activity for influenza A virus (IAV) than the human SP-D NCRD (hSP-D-NCRD). The three serum collectins differ from SP-D by having insertions adjacent to amino acid 325 and substitution of hydrophobic residues for arginine 343. We previously showed that a 3 amino acid (RAK) insertion, as found in CL-43, increases antiviral activity and mannan binding activity of the hSP-D-NCRD, while the substitution of valine at 343, as in conglutinin, more strongly increased these activities. Mannan binding activity of collectins has been considered to predict for ability to bind to high mannose glycans on viruses or other pathogens. We now show, however, that combined mutants containing the RAK insertion and R343V or R343I substitutions have greatly increased mannan binding ability, but lower IAV binding or inhibiting activity than mutants containing R343V or R343I substitutions only. These findings indicate differences in the recognition of glycan structures of mannan and IAV by the NCRDs and emphasize the importance of the flanking sequences in determining the differing interactions of human SP-D and bovine serum collectins with mannose-rich glycoconjugates on IAV and other pathogens. Of interest, we show conservation of some monoclonal antibody binding epitopes between bovine collectin NCRDs and hSP-D, suggesting shared structural motifs. PMID:20591072

Hartshorn, Kevan L.; White, Mitchell R.; Smith, Kelly; Sorensen, Grith; Kuroki, Yoshio; Holmskov, Uffe; Head, James; Crouch, Erika C.

2012-01-01

334

Towards a Model for Protein Production Rates  

NASA Astrophysics Data System (ADS)

In the process of translation, ribosomes read the genetic code on an mRNA and assemble the corresponding polypeptide chain. The ribosomes perform discrete directed motion which is well modeled by a totally asymmetric simple exclusion process (TASEP) with open boundaries. Using Monte Carlo simulations and a simple mean-field theory, we discuss the effect of one or two "bottlenecks" (i.e., slow codons) on the production rate of the final protein. Confirming and extending previous work by Chou and Lakatos, we find that the location and spacing of the slow codons can affect the production rate quite dramatically. In particular, we observe a novel "edge" effect, i.e., an interaction of a single slow codon with the system boundary. We focus in detail on ribosome density profiles and provide a simple explanation for the length scale which controls the range of these interactions.

Dong, J. J.; Schmittmann, B.; Zia, R. K. P.

2007-07-01

335

A possible structural model of members of the CPF family of cuticular proteins implicating binding to components other than chitin.  

PubMed

The physical properties of cuticle are determined by the structure of its two major components, cuticular proteins (CPs) and chitin, and, also, by their interactions. A common consensus region (extended R&R Consensus) found in the majority of cuticular proteins, the CPRs, binds to chitin. Previous work established that beta-pleated sheet predominates in the Consensus region and we proposed that it is responsible for the formation of helicoidal cuticle. Remote sequence similarity between CPRs and a lipocalin, bovine plasma retinol binding protein (RBP), led us to suggest an antiparallel beta-sheet half-barrel structure as the basic folding motif of the R&R Consensus. There are several other families of cuticular proteins. One of the best defined is CPF. Its four members in Anopheles gambiae are expressed during the early stages of either pharate pupal or pharate adult development, suggesting that the proteins contribute to the outer regions of the cuticle, the epi- and/or exo-cuticle. These proteins did not bind to chitin in the same assay used successfully for CPRs. Although CPFs are distinct in sequence from CPRs, the same lipocalin could also be used to derive homology models for one A. gambiae and one Drosophila melanogaster CPF. For the CPFs, the basic folding motif predicted is an eight-stranded, antiparallel beta-sheet, full-barrel structure. Possible implications of this structure are discussed and docking experiments were carried out with one possible Drosophila ligand, 7(Z),11(Z)-heptacosadiene. PMID:20417215

Papandreou, Nikos C; Iconomidou, Vassiliki A; Willis, Judith H; Hamodrakas, Stavros J

2010-10-01

336

Protein sequestration of lipophilic furanocoumarins in grapefruit juice.  

PubMed

The sequestration of grapefruit furanocoumarins by foods was investigated by characterizing the binding between these compounds and foods with contrasting protein, fat, and carbohydrate compositions. Individual grapefruit furanocoumarins exhibited contrasting affinities to foods, where the lipophilic bergamottin and several structurally related dimers bound to foods more tightly than the more polar 6',7'-dihydroxybergamottin. From the investigation of different classes of macromolecules in foods, water-soluble proteins were found to be the major constituents responsible for furanocoumarin sequestration. Studies using bovine serum albumin as a model protein demonstrated the dissociation of grapefruit furanocoumarins from the insoluble juice cloud particles and the subsequent formation of water-soluble bovine serum albumin-furanocoumarin complexes. Fluorescence binding assays further demonstrated the binding of bergamottin and 6',7'-dihydroxybergamottin to bovine serum albumin. These results demonstrate that proteins can be sequestration agents of these important dietary furanocoumarins. PMID:23256844

Myung, Kyung; Manthey, John A; Narciso, Jan A

2013-01-23

337

Bioinorganic Chemical Modeling of Dioxygen-Activating Copper Proteins.  

ERIC Educational Resources Information Center

Discusses studies done in modeling the copper centers in the proteins hemocyanin (a dioxygen carrier), tyrosinase, and dopamine beta-hydroxylase. Copper proteins, model approach in copper bioinorganic chemistry, characterization of reversible oxygen carriers and dioxygen-metal complexes, a copper mono-oxygenase model reaction, and other topics are

Karlin, Kenneth D.; Gultneh, Yilma

1985-01-01

338

Tactile Teaching: Exploring Protein Structure/Function Using Physical Models  

ERIC Educational Resources Information Center

The technology now exists to construct physical models of proteins based on atomic coordinates of solved structures. We review here our recent experiences in using physical models to teach concepts of protein structure and function at both the high school and the undergraduate levels. At the high school level, physical models are used in a

Herman, Tim; Morris, Jennifer; Colton, Shannon; Batiza, Ann; Patrick, Michael; Franzen, Margaret; Goodsell, David S.

2006-01-01

339

Identification of bovine prolactin in seminal fluid, and expression and localization of the prolactin receptor and prolactin-inducible protein in the testis and epididymis of bulls exposed to ergot alkaloids.  

PubMed

The objectives of this study were to determine (1) the presence and expression levels of bovine prolactin receptor (PRLR) and prolactin-inducible protein (PIP) in bovine testis and epididymis, and (2) the presence and concentrations of prolactin (PRL) present in seminiferous fluid in bulls consuming diets with (E+) or without (E-) ergot alkaloids. Bulls (n=8) were sacrificed after 126days (group A) of E+ or E- treatment or 60days after all bulls (n=6) were switched to the E- ration (group B). End point and real-time quantitative reverse transcription-polymerase chain reaction and immunohistochemistry were conducted on testis and epididymis samples to establish the presence and relative expression of PRLR and PIP. Seminal fluid samples obtained from bulls consuming E- and E+ diets were subjected to RIA for PRL. Both PIP and PRLR were present in testis and epididymis as determined by reverse transcription-polymerase chain reaction and immunohistochemistry. Prolactin-inducible protein mRNA abundance was affected by time of slaughter in testis and epididymis head, respectively (P<0.05). Prolactin receptor mRNA expression was affected by time of slaughter in the epididymis (P<0.05) and differed in testis samples because of treatment (P<0.05). Radioimmunoassay establishes the presence of PRL in seminal fluid; however, differences in the concentration of PRL over two separate studies were inconsistent, possibly because of differences in diet. The presence and localization of the PRLR are consistent with expression data reported for other species, and the presence of PIP and PRL in seminal fluid is consistent with data generated in humans. PMID:25533929

Pratt, S L; Calcatera, S M; Stowe, H M; Dimmick, M A; Schrick, F N; Duckett, S K; Andrae, J G

2015-03-01

340

Infectious Bovine Rhinotracheitis  

E-print Network

Infectious bovine rhinotracheitis (IBR) is a complex of disease syndromes occuring throughout the United States and the other major cattle-producing areas of the world. It affects cattle and some wild ruminants. This publication describes...

Sprott, L. R.

1998-11-30

341

ASPDock: protein-protein docking algorithm using atomic solvation parameters model  

Microsoft Academic Search

BACKGROUND: Atomic Solvation Parameters (ASP) model has been proven to be a very successful method of calculating the binding free energy of protein complexes. This suggests that incorporating it into docking algorithms should improve the accuracy of prediction. In this paper we propose an FFT-based algorithm to calculate ASP scores of protein complexes and develop an ASP-based protein-protein docking method

Lin Li; Dachuan Guo; Yangyu Huang; Shiyong Liu; Yi Xiao

2011-01-01

342

Folic acid complexes with human and bovine serum albumins.  

PubMed

The interaction of folic acid with human serum (HSA) and bovine serum albumins (BSA) at physiological conditions, using constant protein concentration and various folic acid contents was investigated. FTIR, UV-visible and fluorescence spectroscopic methods as well as molecular modelling were used to analyse folic acid binding sites, the binding constant and the effect on HSA and BSA stability and conformations. Structural analysis showed that folic acid binds HSA and BSA via both hydrophilic and hydrophobic contacts with overall binding constants of Kfolic acid-HSA=8.1 (0.5)10(4)M(-1) and Kfolic acid-BSA=1.0 (0.3)10(5)M(-1). The number of bound acid molecules per protein was 1.7 (0.4) for HSA and 1.5 (0.3) for BSA complexes. Molecular modelling showed participation of several amino acids in folic acid-protein complexes stabilised by hydrogen bonding network. Folic acid complexation altered protein secondary structure by major reduction of ?-helix from 59% (free HSA) to 35% (acid-complex) and 62% (free BSA) to 25% (acid-complex) with an increase in random coil, turn and ?-sheet structures indicating protein unfolding. The results suggest that serum albumins might act as carrier proteins for folic acid in delivering it to target molecules. PMID:25212350

Bourassa, P; Hasni, I; Tajmir-Riahi, H A

2011-12-01

343

Equilibrium folding pathways for model proteins  

NASA Astrophysics Data System (ADS)

Protein conformations have been generated with both a Monte Carlo scheme and a simpler two-state noninteracting globule-coil model. Conformational energies are taken to consist of intraresidue and interresidue terms. Interresidue energies are taken to be proportional to the number of nativelike contacts. To describe probable folding pathways, either energy or the number of native residues are employed as simple one-dimensional folding-unfolding coordinates. By considering only conformations at each point on these coordinates, it is possible to obtain detailed conformational descriptions of relatively rare intermediates on the folding pathway. This technique of "trapping" intermediates and statistically characterizing them is useful for studying conformational transitions. Equilibrium folding-unfolding pathways have been constructed by connecting most probable conformations in order along the folding coordinate. Calculations with the noninteracting globule-coil model have been performed with details chosen to correspond to those in the Monte Carlo calculation for pancreatic trypsin inhibitor. Both pathways are similar. The ? helix appears prior to formation of the central beta sheet; beta sheet formation coincides with a large maximum in the free energy because of the attendant loss of conformational entropy. Subsequently the Monte Carlo method indicates two alternative pathways for growth toward either the amino or the carboxyl terminus, followed by completion of the native form. For the globule-coil model, the growth pattern differs somewhat, with the appearance of the single pathway for folding up to the carboxyl terminus prior to completion of folding. This difference may originate in the Monte Carlo sampling procedures or in the simplifications of the globule-coil model.

Miyazawa, Sanzo; Jernigan, Robert L.

1983-02-01

344

Viral channel forming proteins Modeling the target  

Microsoft Academic Search

The cellular and subcellular membranes encounter an important playground for the activity of membrane proteins encoded by viruses. Viral membrane proteins, similar to their host companions, can be integral or attached to the membrane. They are involved in directing the cellular and viral reproduction, the fusion and budding processes. This review focuses especially on those integral viral membrane proteins which

Wolfgang B. Fischer; Hao-Jen Hsu

2011-01-01

345

Mechanical Modeling and Computer Simulation of Protein Folding  

ERIC Educational Resources Information Center

In this activity, science education and modern technology are bridged to teach students at the high school and undergraduate levels about protein folding and to strengthen their model building skills. Students are guided from a textbook picture of a protein as a rigid crystal structure to a more realistic view: proteins are highly dynamic

Prigozhin, Maxim B.; Scott, Gregory E.; Denos, Sharlene

2014-01-01

346

MATHEMATICAL MODELS OF PROTEIN FOLDING Daniel B. Dix  

E-print Network

MATHEMATICAL MODELS OF PROTEIN FOLDING Daniel B. Dix Department of Mathematics University of South Carolina Abstract. We present an elementary introduction to the protein folding problem directed toward, and biological problem, protein folding can also be precisely formulated as a set of mathematics problems. We

Dix, Daniel B.

347

Transcriptomic profiling of intestinal epithelial cells in response to human, bovine and commercial bovine lactoferrins.  

PubMed

Lactoferrin (Lf) is an iron-binding glycoprotein present in high concentration in human milk. It is a pleiotropic protein and involved in diverse bioactivities, such as stimulation of cell proliferation and immunomodulatory activities. Lf is partly resistant to proteolysis in the gastrointestinal tract. Thus, Lf may play important roles in intestinal development. Due to differences in amino acid sequences and isolation methods, Lfs from human and bovine milk as well as commercially available bovine Lf (CbLf) may differ functionally or exert their functions via various mechanisms. To provide a potential basis for further applications of CbLf, we compared effects of Lfs on intestinal transcriptomic profiling using an intestinal epithelial cell model, human intestinal epithelial crypt-like cells (HIEC). All Lfs significantly stimulated proliferation of HIEC and no significant differences were found among these three proteins. Microarray assays were used to investigate transcriptomic profiling of intestinal epithelial cells in response to Lfs. Selected genes were verified by RT-PCR with a high validation rate. Genes significantly regulated by hLf, bLf, and CbLf were 150, 395 and 453, respectively. Fifty-four genes were significantly regulated by both hLf and CbLf, whereas 129 genes were significantly modulated by bLf and CbLf. Although only a limited number of genes were regulated by all Lfs, the three Lfs positively influenced cellular development and immune functions based on pathway analysis using IPA (Ingenuity). Lfs stimulate cellular and intestinal development and immune functions via various signaling pathways, such as Wnt/?-catenin signaling, interferon signaling and IL-8 signaling. PMID:24831230

Jiang, Rulan; Lnnerdal, Bo

2014-10-01

348

Structural changes of bovine milk fat globules during in vitro digestion.  

PubMed

An in vitro digestion model that simulated gastric and intestinal fasting conditions was used to monitor the physical, chemical, and structural changes of fat globules from raw bovine milk. During in vitro gastric digestion, the fat globules were stable under low-acidic conditions. Some peptides and ?-lactoglobulin were resistant to proteolysis by pepsin. Phospholipids, proteins, and peptides stabilized the globules in the stomach model. During in vitro intestinal digestion, most of the ?-lactoglobulin and residual peptides were hydrolyzed by trypsin and chymotrypsin, and the lipolytic products, released from the hydrolysis of the triglyceride core of the globules, led to destabilization and coalescence of the globules. By accumulating at the surface of the fat globules, the lipolytic products formed a lamellar phase and their solubilization by bile salts resulted in the formation of disk-shaped micelles. This study brings new interesting insights on the digestion of bovine milk. PMID:22720916

Gallier, S; Ye, A; Singh, H

2012-07-01

349

Interfacial Protein-Protein Associations  

PubMed Central

While traditional models of protein adsorption focus primarily on direct protein-surface interactions, recent findings suggest that protein-protein interactions may play a central role. Using high-throughput intermolecular resonance energy transfer (RET) tracking, we directly observed dynamic, protein-protein associations of bovine serum albumin on poly(ethylene glycol) modified surfaces. The associations were heterogeneous and reversible, and associating molecules resided on the surface for longer times. The appearance of three distinct RET states suggested a spatially heterogeneous surface with areas of high protein density (i.e. strongly-interacting clusters) coexisting with mobile monomers. Distinct association states exhibited characteristic behavior, i.e. partial-RET (monomer-monomer) associations were shorter-lived than complete-RET (protein-cluster) associations. While the fractional surface area covered by regions with high protein density (i.e. clusters) increased with increasing concentration, the distribution of contact times between monomers and clusters was independent of solution concentration, suggesting that associations were a local phenomenon, and independent of the global surface coverage. PMID:24274729

Langdon, Blake B.; Kastantin, Mark; Walder, Robert; Schwartz, Daniel K.

2014-01-01

350

Interfacial protein-protein associations.  

PubMed

While traditional models of protein adsorption focus primarily on direct protein-surface interactions, recent findings suggest that protein-protein interactions may play a central role. Using high-throughput intermolecular resonance energy transfer (RET) tracking, we directly observed dynamic, protein-protein associations of bovine serum albumin on polyethylene glycol modified surfaces. The associations were heterogeneous and reversible, and associating molecules resided on the surface for longer times. The appearance of three distinct RET states suggested a spatially heterogeneous surface - with areas of high protein density (i.e., strongly interacting clusters) coexisting with mobile monomers. Distinct association states exhibited characteristic behavior, i.e., partial-RET (monomer-monomer) associations were shorter-lived than complete-RET (protein-cluster) associations. While the fractional surface area covered by regions with high protein density (i.e., clusters) increased with increasing concentration, the distribution of contact times between monomers and clusters was independent of solution concentration, suggesting that associations were a local phenomenon, and independent of the global surface coverage. PMID:24274729

Langdon, Blake B; Kastantin, Mark; Walder, Robert; Schwartz, Daniel K

2014-01-13

351

Mechanisms of m-cresol induced protein aggregation studied using a model protein cytochrome c  

PubMed Central

Multi-dose protein formulations require an effective antimicrobial preservative (AP) to inhibit microbial growth during long-term storage of unused formulations. m-cresol is one such AP, but has been shown to cause protein aggregation. However, the fundamental physical mechanisms underlying such AP-induced protein aggregation are not understood. In this study, we used a model protein cytochrome c to identify the protein unfolding that triggers protein aggregation. m-cresol induced cytochrome c aggregation at preservative concentrations that are commonly used to inhibit microbial growth. Addition of m-cresol decreased the temperature at which the protein aggregated and increased the aggregation rate. However, m-cresol did not perturb the tertiary or secondary structure of cytochrome c. Instead, it populated an invisible partially unfolded intermediate where a local protein region around the methionine residue at position 80 was unfolded. Stabilizing the Met80 region drastically decreased the protein aggregation, which conclusively shows that this local protein region acts as an aggregation hot-spot. Based on these results, we propose that APs induce protein aggregation by partial rather than global unfolding. Because of the availability of site-specific probes to monitor different levels of protein unfolding, cytochrome c provided a unique advantage in characterizing the partial protein unfolding that triggers protein aggregation. PMID:21229618

Singh, Surinder M.; Hutchings, Regina L.; Mallela, Krishna M.G.

2014-01-01

352

Characterization of the major bovine brain Go alpha isoforms. Mapping the structural differences between the alpha subunit isoforms identifies a variable region of the protein involved in receptor interactions.  

PubMed

Go is the major G protein in bovine brain, with at least three isoforms, GoA, GoB, and GoC. Whereas alphaoA and alphaoB arise from a single Goalpha gene as alternatively spliced mRNAs, alphaoA and alphaoC are thought to differ by covalent modification. To test the hypothesis that alphaoA and alphaoC have different N-terminal lipid modifications, proteolytic fragments of alphao isoforms were immunoprecipitated with an N terminus-specific antibody and analyzed by matrix-assisted laser desorption ionization mass spectrometry. The major masses observed in immunoprecipitates were the same for all three alphao isoforms and corresponded to the predicted mass of a myristoylated N-terminal fragment. Structural differences between alphaoA and alphaoC were also compared before and after limited tryptic proteolysis using SDS-polyacrylamide gel electrophoresis containing 6 M urea. Based upon the alphao subunit fragments produced under activating and nonactivating conditions, differences between alphaoA and alphaoC were localized to a C-terminal fragment of the protein. This region, involved in receptor and effector interactions, implies divergent signaling roles for these two alphao proteins. Finally, the structural difference between alphaoA and alphaoC is associated with a difference of at most 2 daltons based upon measurements by electrospay ionization mass spectrometry. PMID:9837880

McIntire, W E; Dingus, J; Schey, K L; Hildebrandt, J D

1998-12-11

353

The evolution dynamics of model proteins Guido Tiana  

E-print Network

The evolution dynamics of model proteins Guido Tiana Department of Physics, University of Milano, Italy; and The Niels Bohr Institute, Bledgamvej 17, 2100 Copenhagen, Denmark Eugene I. Shakhnovich of simple models to investigate how protein sequences and structures change during evolution has been widely

Dokholyan, Nikolay V.

354

Automated protein model building combined with iterative structure refinement  

Microsoft Academic Search

In protein crystallography, much time and effort are often required to trace an initial model from an interpretable electron density map and to refine it until it best agrees with the crystallographic data. Here, we present a method to build and refine a protein model automatically and without user intervention, starting from diffraction data extending to resolution higher than 2.3

Richard Morris; Victor S. Lamzin; Anastassis Perrakis

1999-01-01

355

Construction and genetic selection of small transmembrane proteins that activate  

E-print Network

. The bovine papillomavirus E5 protein is a dimeric, 44-amino acid TM protein that transforms cells that control important biological processes (2). The 44-amino acid bovine papillomavirus type 1 (BPV) E5

356

Dose-dependent effects of Chlamydia psittaci infection on pulmonary gas exchange, innate immunity and acute-phase reaction in a bovine respiratory model.  

PubMed

The respiratory pathogen Chlamydia psittaci naturally occurs in bovine herds and was recently shown to impair calf health in a dose-dependent manner. The aim of this study was to determine whether the functional consequences and immunological reactions of infection were dose related by quantifying the consequences of acute respiratory chlamydial infection on respiratory signs, disturbances of pulmonary gas exchange, response of the innate immune system, and acute-phase reaction. Fourteen calves were challenged intrabronchially with different C. psittaci doses (from 10(6) to 10(9)inclusion-forming units (ifu) per animal). Ten controls received either UV-inactivated chlamydiae or cell culture medium. Compared to the controls, all animals challenged with live C. psittaci developed hypoxaemia linked to reduced haemoglobin oxygen saturation, increased alveolar-arterial oxygen partial pressure difference (A-aO2) and pulmonary shunt, with symptoms following a dose-dependent pattern. Increases in lipopolysaccharide-binding protein (LBP) and leukocytes were also dose-dependent and accompanied by a regenerative left shift in neutrophil granulocytes. With the exception of LBP, which reflected the load of chlamydial cell components in the host, pathophysiological reactions were only detected in calves challenged with viable chlamydiae. These results indicate that the pathophysiological consequences of respiratory C. psittaci infections are strongly dependent on the challenge dose of chlamydiae. For further studies, challenge doses between 10(6) and 10(8)ifu/calf are recommended. PMID:23265868

Ostermann, Carola; Schroedl, Wieland; Schubert, Evelyn; Sachse, Konrad; Reinhold, Petra

2013-06-01

357

Modeling the hydration layer around proteins: HyPred.  

PubMed

Protein hydration plays an integral role in determining protein function and stability. We develop a simple method with atomic level precision for predicting the solvent density near the surface of a protein. A set of proximal radial distribution functions are defined and calculated for a series of different atom types in proteins using all-atom, explicit solvent molecular dynamic simulations for three globular proteins. A major improvement in predicting the hydration layer is found when the protein is held immobile during the simulations. The distribution functions are used to develop a model for predicting the hydration layer with sub-1-Angstrom resolution without the need for additional simulations. The model and the distribution functions for a given protein are tested in their ability to reproduce the hydration layer from the simulations for that protein, as well as those for other proteins and for simulations in which the protein atoms are mobile. Predictions for the density of water in the hydration shells are then compared with high occupancy sites observed in crystal structures. The accuracy of both tests demonstrates that the solvation model provides a basis for quantitatively understanding protein solvation and thereby predicting the hydration layer without additional simulations. PMID:20816074

Virtanen, Jouko J; Makowski, Lee; Sosnick, Tobin R; Freed, Karl F

2010-09-01

358

Modeling the Hydration Layer around Proteins: HyPred  

PubMed Central

Protein hydration plays an integral role in determining protein function and stability. We develop a simple method with atomic level precision for predicting the solvent density near the surface of a protein. A set of proximal radial distribution functions are defined and calculated for a series of different atom types in proteins using all-atom, explicit solvent molecular dynamic simulations for three globular proteins. A major improvement in predicting the hydration layer is found when the protein is held immobile during the simulations. The distribution functions are used to develop a model for predicting the hydration layer with sub-1-ngstrom resolution without the need for additional simulations. The model and the distribution functions for a given protein are tested in their ability to reproduce the hydration layer from the simulations for that protein, as well as those for other proteins and for simulations in which the protein atoms are mobile. Predictions for the density of water in the hydration shells arethen compared with high occupancy sites observed in crystal structures. The accuracy of both tests demonstrates that the solvation model provides a basis for quantitatively understanding protein solvation and thereby predicting the hydration layer without additional simulations. PMID:20816074

Virtanen, Jouko J.; Makowski, Lee; Sosnick, Tobin R.; Freed, Karl F.

2010-01-01

359

ProteinDNA binding specificity predictions with structural models  

PubMed Central

ProteinDNA interactions play a central role in transcriptional regulation and other biological processes. Investigating the mechanism of binding affinity and specificity in proteinDNA complexes is thus an important goal. Here we develop a simple physical energy function, which uses electrostatics, solvation, hydrogen bonds and atom-packing terms to model direct readout and sequence-specific DNA conformational energy to model indirect readout of DNA sequence by the bound protein. The predictive capability of the model is tested against another model based only on the knowledge of the consensus sequence and the number of contacts between amino acids and DNA bases. Both models are used to carry out predictions of proteinDNA binding affinities which are then compared with experimental measurements. The nearly additive nature of proteinDNA interaction energies in our model allows us to construct position-specific weight matrices by computing base pair probabilities independently for each position in the binding site. Our approach is less data intensive than knowledge-based models of proteinDNA interactions, and is not limited to any specific family of transcription factors. However, native structures of proteinDNA complexes or their close homologs are required as input to the model. Use of homology modeling can significantly increase the extent of our approach, making it a useful tool for studying regulatory pathways in many organisms and cell types. PMID:16246914

Morozov, Alexandre V.; Havranek, James J.; Baker, David; Siggia, Eric D.

2005-01-01

360

Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions  

PubMed Central

The Anton supercomputing technology recently developed for efficient molecular dynamics simulations permits us to examine micro- to milli-second events at full atomic resolution for proteins in explicit water and lipid bilayer. It also permits us to investigate to what extent the collective motions predicted by network models (that have found broad use in molecular biophysics) agree with those exhibited by full-atomic long simulations. The present study focuses on Anton trajectories generated for two systems: the bovine pancreatic trypsin inhibitor, and an archaeal aspartate transporter, GltPh. The former, a thoroughly studied system, helps benchmark the method of comparative analysis, and the latter provides new insights into the mechanism of function of glutamate transporters. The principal modes of motion derived from both simulations closely overlap with those predicted for each system by the anisotropic network model (ANM). Notably, the ANM modes define the collective mechanisms, or the pathways on conformational energy landscape, that underlie the passage between the crystal structure and substates visited in simulations. In particular, the lowest frequency ANM modes facilitate the conversion between the most probable substates, lending support to the view that easy access to functional substates is a robust determinant of evolutionarily selected native contact topology. PMID:24089724

Gur, M.; Zomot, E.; Bahar, I.

2013-01-01

361

Isoelectric focusing of bovine major histocompatibility complex class I molecules.  

PubMed

The products of the major histocompatibility complex (MHC) loci regulate an individual's immune response to pathogens. Cattle provide an important model to study the relationship between disease susceptibility and MHC haplotype since large half-sibling families are common. The definitive demonstration, however, of a firm relationship between MHC phenotype and disease susceptibility in cattle will require a precise definition of the bovine MHC allelic products. Available reagents for serological characterization of the bovine MHC gene products have not been adequate for these purposes. We have shown that existing mouse monoclonal antibodies and rabbit anti-human antisera precipitate bovine class I molecules, that these structures separate well by one-dimensional isoelectric focusing (1-D IEF), and that immunoprecipitation followed by 1-D IEF allows the detection of bovine class I MHC allelic products. Through this technique, we have identified previously undetected class I products. This approach will facilitate a detailed characterization of the bovine MHC class I gene products. PMID:2614073

Watkins, D I; Shadduck, J A; Stone, M E; Lewin, H A; Letvin, N L

1989-06-01

362

Exact protein distributions for stochastic models of gene expression  

NASA Astrophysics Data System (ADS)

Stochasticity in gene expression gives rise to variations in protein levels across a population of genetically identical cells. Such fluctuations can drive phenotypic variation in clonal populations, hence there is considerable interest in quantifying noise in gene expression using stochastic models. However, obtaining exact analytical results for protein distributions has been an intractable task for all but the simplest models. We develop a novel mapping that significantly simplifies the analysis of stochastic models of gene expression. Using this mapping, we derive exact analytical results for steady-state and time-dependent protein distributions for the basic 2-stage model of gene expression. Considering extensions of the basic model, we obtain exact protein steady-state distributions for models that include the effects of post-transcriptional and post-translational regulation. The approach developed in this work is widely applicable and can contribute to a quantitative understanding of stochasticity in gene expression and its regulation.

Kulkarni, Rahul; Pendar, Hodjat; Platini, Thierry

2013-03-01

363

Arrangement of electron transport chain components in bovine mitochondrial  

E-print Network

Keywords: amphipols; electron cryo-microscopy; membrane protein complex; respiratory chain; single protein. The mechanisms of the electron and proton transfer reac- tions in the individual complexes have reported. Structures of the complex III dimer from chicken (Zhang et al, 1998), bovine heart (Iwata et al

364

Besnoitia besnoiti protein disulfide isomerase (BbPDI): molecular characterization, expression and in silico modelling.  

PubMed

Besnoitia besnoiti is an apicomplexan parasite responsible for bovine besnoitiosis, a disease with a high prevalence in tropical and subtropical regions and re-emerging in Europe. Despite the great economical losses associated with besnoitiosis, this disease has been underestimated and poorly studied, and neither an effective therapy nor an efficacious vaccine is available. Protein disulfide isomerase (PDI) is an essential enzyme for the acquisition of the correct three-dimensional structure of proteins. Current evidence suggests that in Neosporacaninum and Toxoplasmagondii, which are closely related to B. besnoiti, PDI play an important role in host cell invasion, is a relevant target for the host immune response, and represents a promising drug target and/or vaccine candidate. In this work, we present the nucleotide sequence of the B. besnoiti PDI gene. BbPDI belongs to the thioredoxin-like superfamily (cluster 00388) and is included in the PDI_a family (cluster defined cd02961) and the PDI_a_PDI_a'_c subfamily (cd02995). A 3D theoretical model was built by comparative homology using Swiss-Model server, using as a template the crystallographic deduced model of Tapasin-ERp57 (PDB code 3F8U chain C). Analysis of the phylogenetic tree for PDI within the phylum apicomplexa reinforces the close relationship among B. besnoiti, N. caninum and T. gondii. When subjected to a PDI-assay based on the polymerisation of reduced insulin, recombinant BbPDI expressed in E. coli exhibited enzymatic activity, which was inhibited by bacitracin. Antiserum directed against recombinant BbPDI reacted with PDI in Western blots and by immunofluorescence with B. besnoiti tachyzoites and bradyzoites. PMID:21756909

Marcelino, Eduardo; Martins, Tiago M; Morais, Joana B; Nolasco, Sofia; Cortes, Helder; Hemphill, Andrew; Leito, Alexandre; Novo, Carlos

2011-10-01

365

Ensemble modeling of [beta]-sheet proteins  

E-print Network

Our ability to characterize protein structure and dynamics is vastly outpaced by the speed of modern genetic sequencing, creating a growing divide between our knowledge of biological sequence and structure. Structural ...

O'Donnell, Charles William

2011-01-01

366

A physical map of the bovine genome  

Microsoft Academic Search

BACKGROUND: Cattle are important agriculturally and relevant as a model organism. Previously described genetic and radiation hybrid (RH) maps of the bovine genome have been used to identify genomic regions and genes affecting specific traits. Application of these maps to identify influential genetic polymorphisms will be enhanced by integration with each other and with bacterial artificial chromosome (BAC) libraries. The

Warren M Snelling; Readman Chiu; Jacqueline E Schein; Matthew Hobbs; Colette a Abbey; David L Adelson; Jan Aerts; Gary L Bennett; Ian E Bosdet; Mekki Boussaha; Rudiger Brauning; Alexandre R Caetano; Marcos M Costa; Allan M Crawford; Brian P Dalrymple; Andr'e Eggen; Annelie Everts-van der Wind; Sandrine Floriot; Mathieu Gautier; Clare a Gill; Ronnie D Green; Robert Holt; Oliver Jann; Steven Jm Jones; Steven M Kappes; John W Keele; Pieter J de Jong; Denis M Larkin; Harris a Lewin; John C McEwan; Stephanie McKay; Marco a Marra; Carrie a Mathewson; Lakshmi K Matukumalli; Stephen S Moore; Brenda Murdoch; Frank W Nicholas; Kazutoyo Osoegawa; Alice Roy; Hanni Salih; Laurent Schibler; Robert D Schnabel; Licia Silveri; Loren C Skow; Timothy Pl Smith; Tad S Sonstegard; Jeremy F Taylor; Ross Tellam; Curtis P Van Tassell; John L Williams; James E Womack; Natasja H Wye; George Yang; Shaying Zhao

2007-01-01

367

A physical map of the bovine genome  

Technology Transfer Automated Retrieval System (TEKTRAN)

Background Cattle are important agriculturally and relevant as a model organism. Previously described genetic and radiation hybrid (RH) maps of the bovine genome have been used to identify genomic regions and genes affecting specific traits. Application of these maps to identify influential geneti...

368

Protein Shift and Antigenic Variation in the SLayer ofCampylobacter fetussubsp.venerealisduring Bovine Infection Accompanied by Genomic Rearrangement ofsapAHomologs  

Microsoft Academic Search

Campylobacter fetussubsp.venerealisisolated from a case of human vaginosis was inoculated into the uterus of a C. fetus-negative heifer. Isolates obtained weekly from the vaginal mucus exhibited variations in high- molecular-mass-protein profiles from that of the original inoculum, which had a dominant 110-kDa S-layer protein. Immunoblots of the weekly isolates with monoclonal antibody probes against the 110-kDa S-layer protein and other

MANUEL M. GARCIA; CHERYL L. LUTZE-WALLACE; AZUCENA S. DENES; MATTHEW D. EAGLESOME; ELISABET HOLST

369

Sequence-based Gaussian network model for protein dynamics  

PubMed Central

Motivation: Gaussian network model (GNM) is widely adopted to analyze and understand protein dynamics, function and conformational changes. The existing GNM-based approaches require atomic coordinates of the corresponding protein and cannot be used when only the sequence is known. Results: We report, first of its kind, GNM model that allows modeling using the sequence. Our linear regression-based, parameter-free, sequence-derived GNM (L-pfSeqGNM) uses contact maps predicted from the sequence and models local, in the sequence, contact neighborhoods with the linear regression. Empirical benchmarking shows relatively high correlations between the native and the predicted with L-pfSeqGNM B-factors and between the cross-correlations of residue fluctuations derived from the structure- and the sequence-based GNM models. Our results demonstrate that L-pfSeqGNM is an attractive platform to explore protein dynamics. In contrast to the highly used GNMs that require protein structures that number in thousands, our model can be used to study motions for the millions of the readily available sequences, which finds applications in modeling conformational changes, proteinprotein interactions and protein functions. Contact: zerozhua@126.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24336646

Zhang, Hua; Kurgan, Lukasz

2014-01-01

370

Raw bovine milk improves gut responses to feeding relative to infant formula in preterm piglets.  

PubMed

For preterm neonates, the quality of the first milk is crucial for intestinal maturation and resistance to necrotizing enterocolitis (NEC). Among other factors, milk quality is determined by the stage of lactation and processing. We hypothesized that unprocessed mature bovine milk (BM; raw bovine milk) would have less bioactivity than corresponding bovine colostrum (BC) in a preterm pig model, but have improved bioactivity relative to its homogenized, pasteurized, spray-dried equivalent, whole milk powder (WMP), or a bovine milk protein-based infant formula (IF). For 5 days, newborn preterm pigs received parenteral and enteral nutrition consisting of IF (n = 13), BM (n = 13), or BC (n = 14). In a second study, WMP (n = 15) was compared with IF (n = 10) and BM (n = 9). Compared with pigs fed IF, pigs that were fed BM had significantly improved intestinal structure (mucosal weight, villus height) and function (increased nutrient absorption and enzyme activities, decreased gut permeability, nutrient fermentation, and NEC severity). BC further improved these effects relative to BM (lactase activity, lactose absorption, plasma citrulline, and tissue interleukin-8). WMP induced similar effects as BM, except for lactase activity and lactose absorption. In conclusion, the maturational and protective effects on the immature intestine decreased in the order BC>BM>WMP, but all three intact bovine milk diets were markedly better than IF. The stage of lactation (colostrum vs. mature milk) and milk processing (e.g., homogenization, fractionation, pasteurization, spray-drying) are important factors in determining milk quality during the early postnatal period of preterm neonates. PMID:24157971

Li, Yanqi; Jensen, Mikkel L; Chatterton, Dereck E W; Jensen, Bent B; Thymann, Thomas; Kvistgaard, Anne S; Sangild, Per T

2014-01-01

371

Inferring functional modules of protein families with probabilistic topic models  

PubMed Central

Background Genome and metagenome studies have identified thousands of protein families whose functions are poorly understood and for which techniques for functional characterization provide only partial information. For such proteins, the genome context can give further information about their functional context. Results We describe a Bayesian method, based on a probabilistic topic model, which directly identifies functional modules of protein families. The method explores the co-occurrence patterns of protein families across a collection of sequence samples to infer a probabilistic model of arbitrarily-sized functional modules. Conclusions We show that our method identifies protein modules - some of which correspond to well-known biological processes - that are tightly interconnected with known functional interactions and are different from the interactions identified by pairwise co-occurrence. The modules are not specific to any given organism and may combine different realizations of a protein complex or pathway within different taxa. PMID:21554720

2011-01-01

372

Protein Structure Idealization: How accurately is it possible to model protein structures with dihedral angles?  

PubMed

: Previous studies show that the same type of bond lengths and angles fit Gaussian distributions well with small standard deviations on high resolution protein structure data. The mean values of these Gaussian distributions have been widely used as ideal bond lengths and angles in bioinformatics. However, we are not aware of any research done to evaluate how accurately we can model protein structures with dihedral angles and ideal bond lengths and angles.Here, we introduce the protein structure idealization problem. We focus on the protein backbone structure idealization. We describe a fast O(nm/?) dynamic programming algorithm to find an idealized protein backbone structure that is approximately optimal according to our scoring function. The scoring function evaluates not only the free energy, but also the similarity with the target structure. Thus, the idealized protein structures found by our algorithm are guaranteed to be protein-like and close to the target protein structure.We have implemented our protein structure idealization algorithm and idealized the high resolution protein structures with low sequence identities of the CULLPDB_PC30_RES1.6_R0.25 data set. We demonstrate that idealized backbone structures always exist with small changes and significantly better free energy. We also applied our algorithm to refine protein pseudo-structures determined in NMR experiments. PMID:23442792

Cui, Xuefeng; Li, Shuai Cheng; Bu, Dongbo; Alipanahi, Babak; Li, Ming

2013-01-01

373

Diffusion Kernel-Based Logistic Regression Models for Protein Function Prediction  

Microsoft Academic Search

Assigning functions to unknown proteins is one of the most important problems in proteomics. Several approaches have used protein-protein interaction data to predict protein functions. We previously developed a Markov random fields (MRF) based method to infer a protein's func- tions using protein-protein interaction data and the functional annotations of its protein inter- action partners. In the original model, only

Hyunju Lee; Zhidong Tu; Minghua Deng; Fengzhu Sun; Ting Chen

2006-01-01

374

Developing algorithms for predicting protein-protein interactions of homology modeled proteins.  

SciTech Connect

The goal of this project was to examine the protein-protein docking problem, especially as it relates to homology-based structures, identify the key bottlenecks in current software tools, and evaluate and prototype new algorithms that may be developed to improve these bottlenecks. This report describes the current challenges in the protein-protein docking problem: correctly predicting the binding site for the protein-protein interaction and correctly placing the sidechains. Two different and complementary approaches are taken that can help with the protein-protein docking problem. The first approach is to predict interaction sites prior to docking, and uses bioinformatics studies of protein-protein interactions to predict theses interaction site. The second approach is to improve validation of predicted complexes after docking, and uses an improved scoring function for evaluating proposed docked poses, incorporating a solvation term. This scoring function demonstrates significant improvement over current state-of-the art functions. Initial studies on both these approaches are promising, and argue for full development of these algorithms.

Martin, Shawn Bryan; Sale, Kenneth L.; Faulon, Jean-Loup Michel; Roe, Diana C.

2006-01-01

375

Vaccine-induced antibodies linked to bovine neonatal pancytopenia (BNP) recognize cattle major histocompatibility complex class I (MHC I).  

PubMed

A mysterious disease affecting calves, named bovine neonatal pancytopenia (BNP), emerged in 2007 in several European countries. Epidemiological studies revealed a connection between BNP and vaccination with an inactivated vaccine against bovine virus diarrhea (BVD). Alloantibodies reacting with blood leukocytes of calves were detected in serum and colostrum of dams, which have given birth to calves affected by BNP. To understand the linkage between vaccination and the development of alloantibodies, we determined the antigens reacting with these alloantibodies. Immunoprecipitation of surface proteins from bovine leukocytes and kidney cells using sera from dams with a confirmed case of BNP in their gestation history reacted with two dominant protein species of 44 and 12 kDa. These proteins were not detected by sera from dams, free of BVDV and not vaccinated against BVD, and from sera of animals vaccinated with a different inactivated BVD vaccine. The 44 kDa protein was identified by mass spectrometry analysis as MHC I, the other as ?-2-microglobulin. The presence of major histocompatibility complex class I (MHC I) in the vaccine was confirmed by Western blot using a MHC I specific monoclonal antibody. A model of BNP pathogenesis is proposed. PMID:21878124

Deutskens, Fabian; Lamp, Benjamin; Riedel, Christiane M; Wentz, Eveline; Lochnit, Gnter; Doll, Klaus; Thiel, Heinz-Jrgen; Rmenapf, Till

2011-01-01

376

Vaccine-induced antibodies linked to bovine neonatal pancytopenia (BNP) recognize cattle major histocompatibility complex class I (MHC I)  

PubMed Central

A mysterious disease affecting calves, named bovine neonatal pancytopenia (BNP), emerged in 2007 in several European countries. Epidemiological studies revealed a connection between BNP and vaccination with an inactivated vaccine against bovine virus diarrhea (BVD). Alloantibodies reacting with blood leukocytes of calves were detected in serum and colostrum of dams, which have given birth to calves affected by BNP. To understand the linkage between vaccination and the development of alloantibodies, we determined the antigens reacting with these alloantibodies. Immunoprecipitation of surface proteins from bovine leukocytes and kidney cells using sera from dams with a confirmed case of BNP in their gestation history reacted with two dominant protein species of 44 and 12 kDa. These proteins were not detected by sera from dams, free of BVDV and not vaccinated against BVD, and from sera of animals vaccinated with a different inactivated BVD vaccine. The 44 kDa protein was identified by mass spectrometry analysis as MHC I, the other as ?-2-microglobulin. The presence of major histocompatibility complex class I (MHC I) in the vaccine was confirmed by Western blot using a MHC I specific monoclonal antibody. A model of BNP pathogenesis is proposed. PMID:21878124

2011-01-01

377

Quantum Mechanical Model for Information Transfer from DNA to Protein  

E-print Network

A model for the information transfer from DNA to protein using quantum information and computation techniques is presented. DNA is modeled as the sender and proteins are modeled as the receiver of this information. On the DNA side, a 64-dimensional Hilbert space is used to describe the information stored in DNA triplets (codons). A Hamiltonian matrix is constructed for this space, using the 64 possible codons as base states. The eigenvalues of this matrix are not degenerate. The genetic code is degenerate and proteins comprise only 20 different amino acids. Since information is conserved, the information on the protein side is also described by a 64-dimensional Hilbert space, but the eigenvalues of the corresponding Hamiltonian matrix are degenerate. Each amino acid is described by a Hilbert subspace. This change in Hilbert space structure reflects the nature of the processes involved in information transfer from DNA to protein.

Ioannis G. Karafyllidis

2008-01-18

378

A minimalist model protein with multiple folding funnels.  

PubMed

Kinetic and structural studies of wild-type proteins such as prions and amyloidogenic proteins provide suggestive evidence that proteins may adopt multiple long-lived states in addition to the native state. All of these states differ structurally because they lie far apart in configuration space, but their stability is not necessarily caused by cooperative (nucleation) effects. In this study, a minimalist model protein is designed to exhibit multiple long-lived states to explore the dynamics of the corresponding wild-type proteins. The minimalist protein is modeled as a 27-monomer sequence confined to a cubic lattice with three different monomer types. An order parameter-the winding index-is introduced to characterize the extent of folding. The winding index has several advantages over other commonly used order parameters like the number of native contacts. It can distinguish between enantiomers, its calculation requires less computational time than the number of native contacts, and reduced-dimensional landscapes can be developed when the native state structure is not known a priori. The results for the designed model protein prove by existence that the rugged energy landscape picture of protein folding can be generalized to include protein "misfolding" into long-lived states. PMID:11470921

Locker, C R; Hernandez, R

2001-07-31

379

Interaction of bovine serum albumin with gemini surfactants.  

PubMed

The interactions between bovine serum albumin and cationic gemini surfactants were investigated as a function of concentration, under different pH conditions. The investigation deals with dielectric relaxation, dynamic light scattering, zeta-potential, circular dichroism, and UV spectroscopy. The interactive behavior of the anionic form is quite different from the cationic species. It indicates that protein-surfactant interactions are mostly electrostatic in nature and depend on the state of charge of bovine serum albumin. The results indicate the presence of both hydrophobic and electrostatic contributions in the interactions of gemini with bovine serum albumin. Comparison of dynamic light scattering, dielectric relaxation, electrophoretic mobility, and optical circular dichroism allows drawing some preliminary hypotheses on the different contributions to surfactant binding and supports former studies on the formation of complexes between the bovine serum albumin and the above species. PMID:20362296

Tardioli, Silvia; Bonincontro, Adalberto; La Mesa, Camillo; Muzzalupo, Rita

2010-07-01

380

Fungal protein from corn waste effluents : a model study  

Microsoft Academic Search

The purpose of this investigation was to study the microbiological aspects of the production of microbial protein ('single cell protein'; SCP) from corn waste effluents with simultaneous reduction of the COD of these effluents.For practical reasons the corn waste water itself was not used in the experiments but a model was chosen, consisting of tap water to which corn steep

J. A. Schellart

1975-01-01

381

Bayesian hierarchical reconstruction of protein profiles including a digestion model  

E-print Network

Bayesian hierarchical reconstruction of protein profiles including a digestion model Pierre to recover the protein biomarkers content in a robust way. We will focus on the digestion step since and each branch to a molecular processing such as digestion, ionisation and LC-MS separation

Paris-Sud XI, Université de

382

Reply to comment on Critical micellar concentration and protein-surfactant interaction (Comment to Destructive and protective action of sodium dodecyl sulphate micelles on the native conformation of Bovine Serum Albumin: A study by extrinsic fluorescence probe 1-hydroxy-2-naphthaldehye)  

NASA Astrophysics Data System (ADS)

Reply to the comment on 'Critical micellar concentration and protein-surfactant interaction (Comment to Destructive and protective action of sodium dodecyl sulphate micelles on the native conformation of Bovine Serum Albumin: A study by extrinsic fluorescence probe 1-hydroxy-2-naphthaldehye)' [Chem. Phys. Lett. 463 (2008) 183]. We have measured the CMC of SDS micelle in aqueous solution and in tris-HCl buffer and the results are consistent with literature values.

Singh, Rupashree Balia; Mahanta, Subrata; Guchhait, Nikhil

2009-11-01

383

Analysis of mass transport models for protein adsorption to cation exchanger by visualization with confocal laser scanning microscopy  

Microsoft Academic Search

The mass transfer of bovine serum albumin (BSA) to a cation exchanger, SP Sepharose FF, has been studied by finite batch adsorption experiments. The uptake curve was simulated with three mass transport models (i.e., effective pore diffusion model, surface diffusion model and MaxwellStefan model) incorporating the particle size distribution of the adsorbent particles. All the three models can simulate the

Xiao-Peng Zhou; Wei Li; Qing-Hong Shi; Yan Sun

2006-01-01

384

Genotyping bovine coronaviruses.  

Technology Transfer Automated Retrieval System (TEKTRAN)

Bovine coronaviruses (BoCV) are enveloped, single-stranded, positive-sense RNA viruses of the Coronaviridae family. Infection is associated with enteritis and pneumonia in calves and Winter Dysentery in adult cattle. Strains, isolated more than 50 years ago, are used in vaccines and as laboratory ...

385

Bovine milk exosome proteome  

Technology Transfer Automated Retrieval System (TEKTRAN)

Exosomes are 40-100 nm membrane vesicles of endocytic origin and are found in blood, urine, amniotic fluid, bronchoalveolar lavage (BAL) fluid, as well as human and bovine milk. Exosomes are extracellular organelles important in intracellular communication/signaling, immune function, and biomarkers ...

386

Comparative 2D-DIGE Proteomic Analysis of Bovine Mammary Epithelial Cells during Lactation Reveals Protein Signatures for Lactation Persistency and Milk Yield  

PubMed Central

Mammary gland is made up of a branching network of ducts that end with alveoli which surrounds the lumen. These alveolar mammary epithelial cells (MEC) reflect the milk producing ability of farm animals. In this study, we have used 2D-DIGE and mass spectrometry to identify the protein changes in MEC during immediate early, peak and late stages of lactation and also compared differentially expressed proteins in MEC isolated from milk of high and low milk producing cows. We have identified 41 differentially expressed proteins during lactation stages and 22 proteins in high and low milk yielding cows. Bioinformatics analysis showed that a majority of the differentially expressed proteins are associated in metabolic process, catalytic and binding activity. The differentially expressed proteins were mapped to the available biological pathways and networks involved in lactation. The proteins up-regulated during late stage of lactation are associated with NF-?B stress induced signaling pathways and whereas Akt, PI3K and p38/MAPK signaling pathways are associated with high milk production mediated through insulin hormone signaling. PMID:25111801

Janjanam, Jagadeesh; Singh, Surender; Jena, Manoj K.; Varshney, Nishant; Kola, Srujana; Kumar, Sudarshan; Kaushik, Jai K.; Grover, Sunita; Dang, Ajay K.; Mukesh, Manishi; Prakash, B. S.; Mohanty, Ashok K.

2014-01-01

387

fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data  

PubMed Central

Motivation: fast_protein_cluster is a fast, parallel and memory efficient package used to cluster 60 000 sets of protein models (with up to 550 000 models per set) generated by the Nutritious Rice for the World project. Results: fast_protein_cluster is an optimized and extensible toolkit that supports Root Mean Square Deviation after optimal superposition (RMSD) and Template Modeling score (TM-score) as metrics. RMSD calculations using a laptop CPU are 60 faster than qcprot and 3 faster than current graphics processing unit (GPU) implementations. New GPU code further increases the speed of RMSD and TM-score calculations. fast_protein_cluster provides novel k-means and hierarchical clustering methods that are up to 250 and 2000 faster, respectively, than Clusco, and identify significantly more accurate models than Spicker and Clusco. Availability and implementation: fast_protein_cluster is written in C++ using OpenMP for multi-threading support. Custom streaming Single Instruction Multiple Data (SIMD) extensions and advanced vector extension intrinsics code accelerate CPU calculations, and OpenCL kernels support AMD and Nvidia GPUs. fast_protein_cluster is available under the M.I.T. license. (http://software.compbio.washington.edu/fast_protein_cluster) Contact: lhhung@compbio.washington.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24532722

Hung, Ling-Hong; Samudrala, Ram

2014-01-01

388

Coarse-Grained Model for Colloidal Protein Interactions, B22, and Protein Cluster Formation  

PubMed Central

Reversible protein cluster formation is an important initial step in the processes of native and non-native protein aggregation, but involves relatively long time and length scales for detailed atomistic simulations and extensive mapping of free energy landscapes. A coarse-grained (CG) model is presented to semi-quantitatively characterize the thermodynamics and key configurations involved in the landscape for protein oligomerization, as well as experimental measures of interactions such as the osmotic second virial coefficient (B22). Based on earlier work, this CG model treats proteins as rigid bodies composed of one bead per amino acid, with each amino acid having specific parameters for its size, hydrophobicity, and charge. The net interactions are a combination of steric repulsions, short-range attractions, and screened long-range charge-charge interactions. Model parametrization was done by fitting simulation results against experimental values of the B22 as a function of solution ionic strength for ?-chymotrypsinogen A and ?D-crystallin (gD-Crys). The CG model is applied to characterize the pairwise interactions and dimerization of gD-Crys and the dependance on temperature, protein concentration, and ionic strength. The results illustrate that at experimentally relevant conditions where stable dimers do not form, the entropic contributions are predominant in the free-energy of protein cluster formation and colloidal protein interactions, arguing against interpretations that treat B22 primarily from energetic considerations alone. Additionally, the results suggest that electrostatic interactions help to modulate the population of the different stable configurations for protein nearest-neighbor pairs, while short-range attractions determine the relative orientations of proteins within these configurations. Finally, simulation results are combined with Principal Component Analysis to identify those amino-acids / surface patches that form inter-protein contacts at conditions that favor dimerization of gD-Crys. The resulting regions agree with previously found aggregation-prone sites, as well as suggesting new ones that may be important. PMID:24289039

Blanco, Marco A.; Sahin, Eric; Robinson, Anne S.; Roberts, Christopher J.

2014-01-01

389

A predictive theoretical model for electron tunneling pathways in proteins  

NASA Technical Reports Server (NTRS)

A practical method is presented for calculating the dependence of electron transfer rates on details of the protein medium intervening between donor and acceptor. The method takes proper account of the relative energetics and mutual interactions of the donor, acceptor, and peptide groups. It also provides a quantitative search scheme for determining the important tunneling pathways (specific sequences of localized bonding and antibonding orbitals of the protein which dominate the donor-acceptor electronic coupling) in native and tailored proteins, a tool for designing new proteins with prescribed electron transfer rates, and a consistent description of observed electron transfer rates in existing redox labeled metalloproteins and small molecule model compounds.

Onuchic, Jose Nelson; Beratan, David N.

1990-01-01

390

Frequency Factors in a Landscape Model of Filamentous Protein Aggregation  

NASA Astrophysics Data System (ADS)

Using quantitative measurements of protein aggregation rates, we develop a kinetic picture of protein conversion from a soluble to a fibrillar state which shows that a single free energy barrier to aggregation controls the addition of protein molecules into amyloid fibrils, while the characteristic sublinear concentration dependence emerges as a natural consequence of finite diffusion times. These findings suggest that this reaction does not follow a simple chemical mechanism, but rather operates in a way analogous to the landscape models of protein folding defined by stochastic dynamics on a characteristic energy surface.

Buell, Alexander K.; Jamie R. Blundell; Dobson, Christopher M.; Welland, Mark E.; Terentjev, Eugene M.; Knowles, Tuomas P. J.

2010-06-01

391

Rigidity Analysis for Modeling Protein Motion  

E-print Network

. . . . . . . . 20 1. Motion Planning and C-space . . . . . . . . . . . . . . 20 2. The PRM Algorithm . . . . . . . . . . . . . . . . . . . 21 3. Modifications to PRMs for Proteins . . . . . . . . . . 24 D. Rigidity Analysis... validity. These motion planning solutions are based on the Probabilistic RoadmapMethod (PRM) [20]. PRMs work by first building a graph, or roadmap, of the motion space. The roadmap nodes correspond to specific, valid, placements of the movable object...

Thomas, Shawna L.

2010-07-14

392

Modeling structurally variable regions in homologous proteins with rosetta  

Microsoft Academic Search

A major limitation of current com- parative modeling methods is the accuracy with which regions that are structurally divergent from homologues of known structure can be modeled. Because structural differences between homolo- gous proteins are responsible for variations in pro- tein function and specificity, the ability to model these differences has important functional conse- quences. Although existing methods can provide

Carol A. Rohl; Charlie E. M. Strauss; Dylan Chivian; David Baker

2004-01-01

393

Comparative Modeling and Protein-Like Features of HP Models on a Two-Dimensional Lattice  

PubMed Central

Lattice models of proteins have been extensively used to study protein thermodynamics, folding dynamics and evolution. Our study considers two different hydrophobic-polar models on the two-dimensional square lattice: the purely hydrophobic-polar (HP) model and a model where a compactness-favoring term is added. We exhaustively enumerate all the possible structures in our models and perform the study of their corresponding folds, HP arrangements in space and shapes. The two models considered differ greatly in their numbers of structures, folds, arrangements and shapes. Despite their differences both lattice models have distinctive protein-like features: (1) Shapes are compact in both models, especially when a compactness-favoring energy term is added. (2) The residue composition is independent of the chain length and is very close to 50% hydrophobic in both models, as we observe in real proteins. (3) Comparative modeling works well in both models, particularly in the more compact one. The fact that our models show protein-like features suggests that lattice models incorporate the fundamental physical principles of proteins. Our work supports the use of lattice models to study questions about proteins that require exactness and extensive calculations, such as protein design and evolution, which are often too complex and computationally demanding to be addressed with more detailed models. PMID:22411636

Moreno-Hernndez, Sergio; Levitt, Michael

2012-01-01

394

Towards accurate structural characterization of metal centres in protein crystals: the structures of Ni and Cu T6 bovine insulin derivatives  

PubMed Central

Using synchrotron radiation (SR), the crystal structures of T6 bovine insulin complexed with Ni2+ and Cu2+ were solved to 1.50 and 1.45? resolution, respectively. The level of detail around the metal centres in these structures was highly limited, and the coordination of water in Cu site II of the copper insulin derivative was deteriorated as a consequence of radiation damage. To provide more detail, X-ray absorption spectroscopy (XAS) was used to improve the information level about metal coordination in each derivative. The nickel derivative contains hexacoordinated Ni2+ with trigonal symmetry, whereas the copper derivative contains tetragonally distorted hexacoordinated Cu2+ as a result of the JahnTeller effect, with a significantly longer coordination distance for one of the three water molecules in the coordination sphere. That the copper centre is of type II was further confirmed by electron paramagnetic resonance (EPR). The coordination distances were refined from EXAFS with standard deviations within 0.01?. The insulin derivative containing Cu2+ is sensitive towards photoreduction when exposed to SR. During the reduction of Cu2+ to Cu+, the coordination geometry of copper changes towards lower coordination numbers. Primary damage, i.e. photoreduction, was followed directly by XANES as a function of radiation dose, while secondary damage in the form of struct