Individual variation in recombination among human males

Studies of recombination between the markers D6S291 and D6S109 in individuals by sperm typing provide direct evidence for significant variation in recombination among humans. A statistically significant difference in the recombination fraction (range 5.1%-11.2%) was detected among five donors. This variation could reflect polymorphisms in genes affecting recombination or in chromosome structure. Ignoring this variability in studies designed to examine the relationship between physical and genetic distances could lead to incorrect inferences. Individual variation in recombination makes it difficult to predict the recombination fraction for an interval in any particular individual. This could be important in certain genetic counseling situations.

Expression of biologically active human granulocyte-macrophage colony-stimulating factor in the silkworm (Bombyx mori)

Using virus derived from Bombyx mori (silkworm) nuclear polyhedrosis virus (BmNPV), we constructed an infectious recombinant virus carrying the human granulocyte-macrophage colony-stimulating factor (hGM-CSF) cDNA placed downstream from the polyhedrin promoter. The BmN cells infected with the recombinant baculovirus BmNPV-GM-CSF expressed recombinant (r)hGM-CSF up to 3.9 x 10(5) colony-formation units/ml in the medium. The maximum activity of rhGM-CSF was 4.3 x 10(6) colony-formation units/ml in the haemolymph of silkworm (Bombyx mori) larvae infected with BmNPV-GM-CSF. Three distinct species of GM-CSF of molecular masses 15, 18 and 20 kDa were detected by immunoblotting. The specific activity of rhGM-CSF purified from the haemolymph was up to 2.92 x 10(7) colony-formation units/mg. The isoelectric point of the purified rhGM-CSF was 5.5-5.7.

GM-CSF induces the tyrosine phosphorylation of three isoforms of Shc and its association with Grb2 in TF-1 cell

This report demonstrates that GM-CSF induces the tyrosine phosphorylation of Shc protein which is implicated in Ras activation. Three isoforms of Shc are ubiquitously phosphorylated induced by GM-CSF in TF-1, a cell line of erythroid origin. It is also shown that Shc is associated with the adaptor protein Grb2. The formation of Shc-Grb2 complex may directly link tyrosine phosphorylation events to Ras activation in TF-1 cells.

Matrix-assisted laser desorption ion trap mass spectrometry: efficient trapping and ejection of ions

The present paper explores the coupling of a matrix-assisted laser desorption/ionization (MALDI) ion source with an ion trap mass analyzer, with particular emphasis on the development of methods for improving the efficiency of ion trapping and ejection. A technique is described for directly measuring, for the first time, the trapping efficiency of peptide ions produced in a remote external MALDI ion source. The technique was used to devise an improved scheme for trapping, which yielded efficiencies as high as 39%. An improved understanding of the resonant ejection process led us to a new resonant ejection parameter set that increased the ejection efficiency by 1 order of magnitude over more conventionally used parameter sets and allowed for marked improvements in the mass resolution of ions with m/z > 2500. The presently described improvements in the efficiencies of ion trapping and ejection together with improved methods for isolating and fragmenting ions (Qin, J.; Chait, B.T.Anal. Chem., following article in this tissue) lay the foundation for highly sensitive MALDI ion trap mass spectrometry of proteins (Qin, J.; et al. Anal. Chem. 1996, 68, 1784-1791).

Matrix-assisted laser desorption ion trap mass spectrometry: efficient isolation and effective fragmentation of peptide ions

Effective analysis of the sequence of peptides using matrix-assisted laser desorption/ionization (MALDI) tandem ion trap mass spectrometry requires efficient mass isolation and the ability to induce extensive sequence-specific fragmentation. The present paper describes a new excitation scheme, which we term red-shifted off-resonance large-amplitude excitation (RSORLAE), that can deposit higher amounts of internal energy in ions than is feasible with conventional resonant excitation. The new method provides an effective means for inducing fragmentation of MALDI-produced peptide ions with m/z values up to 3500. Prior to excitation, it is necessary to isolate ions of interest with high efficiency. We demonstrate that isolation efficiencies of > 95% can be achieved by careful design of the rf scan functions used during ion isolation. In particular, sudden transitions in the amplitude of the rf field (from low to high amplitudes) must be avoided. The combined improvements in the efficiency for ion isolation and the efficacy of ion activation make MALDI tandem ion trap mass spectrometry a practical tool for the characterization of proteins with high sensitivity.

A practical ion trap mass spectrometer for the analysis of peptides by matrix-assisted laser desorption/ionization

The present paper describes the performance of a newly configured matrix-assisted laser desorption/ionization quadrupole ion trap mass spectrometer (MALDI-ITMS), designed for biological applications that require the determination of the primary structures of proteins, e.g., the rapid identification of proteins and the elucidation of posttranslational modifications. The strategy used for solving problems of this type involves enzymatic digestion of the protein, followed by MALDI ion trap mass spectrometric analysis of the components of the resulting complex mixture of peptide ions. The new instrument is demonstrated to be a highly practical tool for analyzing proteins. In particular, mixtures containing as many as 30 peptide components can be rapidly and sensitively analyzed without prior chromatographic separation of the components. Informative tandem mass spectra can be obtained from the peptide components with m/z values up to 3500. A single subpicomole sample loading of a complex peptide mixture is more than sufficient for a complete set of experiments that includes both low- and high-resolution molecular mass determinations as well as a complete MS/MS study of the various components present in the sample. Extensive use is made of improved methods for trapping, isolating, fragmenting, and detecting ions in the ITMS (details are to be provided in two future papers).

The solution structure of human thioredoxin complexed with its target from Ref-1 reveals peptide chain reversal

BACKGROUND

Human thioredoxin (hTRX) is a 12 kDa cellular redox protein that has been shown to play an important role in the activation of a number of transcriptional and translational regulators via a thiol-redox mechanism. This activity may be direct or indirect via another redox protein known as Ref-1. The structure of a complex of hTRX with a peptide comprising its target from the transcription factor NF kappa B has previously been solved. To further extend our knowledge of the recognition by and interaction of hTRX with its various targets, we have studied a complex between hTRX and a Ref-1 peptide. This complex represents a kinetically stable mixed disulfide intermediate along the reaction pathway.

RESULTS

Using multidimensional heteronuclear edited and filtered NMR spectroscopy, we have solved the solution structure of a complex between hTRX and a 13-residue peptide comprising residues 59-71 of Ref-1. The Ref-1 peptide is located in a crescent-shaped groove on the surface of hTRX, the groove being formed by residues in the active-site loop (residues 32-36), helix 3, beta strands 3 and 5, and the loop between beta strands 3 and 4. The complex is stabilized by numerous hydrogen-bonding and hydrophobic interactions that involve residues 61-69 of the peptide and confer substrate specificity.

CONCLUSIONS

The orientation of the Ref-1 peptide in the hTRX-Ref-1 complex is opposite to that found in the previously solved complex of hTRX with the target peptide from the transcription factor NF kappa B. Orientation is determined by three discriminating interactions involving the nature of the residues at the P-2' P-4 and P-5 binding positions. (P0 defines the active cysteine of the peptide, Cys65 for Ref-1 and Cys62 for NF kappa B. Positive and negative numbers indicate residues N-terminal and C-terminal to this residue, respectively, and vice versa for NF kappa B as it binds in the opposite orientation.) The environment surrounding the reactive Cys32 of hTRX, as well as the packing of the P+3 to P-4 residues are essentially the same in the two complexes, despite the opposing orientation of the peptide chains. This versatility in substrate recognition permits hTRX to act as a wide-ranging redox regulator for the cell.

Ionization equilibria for side-chain carboxyl groups in oxidized and reduced human thioredoxin and in the complex with its target peptide from the transcription factor NF kappa B

The pH dependence of the 13C chemical shifts of the side-chain carboxyl carbons of all Asp and Glu residues in the reduced and oxidized states of human thioredoxin and in a mixed disulfide complex of human thioredoxin with a target peptide from the transcription factor NF kappa B has been investigated by multidimensional triple-resonance NMR spectroscopy. While the titration curves for most of the side-chain carboxyl resonances exhibit simple Henderson-Hasselbalch behavior with pKa values not far from those found for model compounds, several side chains give rise to two- or three-step titration curves, indicative of the influence of multiple ionizations. In particular, the triad formed by Asp58, Asp60, and Asp61 forms such a complex network of titrating groups. The ionization behavior of Asp26 shows an abnormally high pKa value for an aspartate residue in all states of human thioredoxin, with pKa values of 9.9 in the reduced state, 8.1 in the oxidized state, 8.9 in the mixed disulfide complex, and 8.6 in an active site mutant in which Cys35 was replaced by Ala. The unambiguous determination of the pKa values of Asp26 for a variety of states of human thioredoxin presented in this paper is highly significant in view of two recent reports on Escherichia coli thioredoxin which presented contradicting pKa values for Asp26 and Cys35 [Wilson et al. (1995) Biochemistry 34, 8931-8939; Jeng et al. (1995) Biochemistry 34, 10101-10105]. The stabilization of the protonated side chain of Asp26 in human thioredoxin is achieved via a hydrogen-bonding network involving the hydroxyl group of the neighboring Ser28 which is then connected to the active site region (comprising Cys32 and Cys35) via bound water molecules. The coupling of the buried Asp26 to the active site is responsible for the influence of the Asp26 ionization behavior on the titration shifts of active site residues.

Expression of human stem cell factor in the baculovirus expression system

A partial cDNA of human Stem Cell Factor (SCF) was isolated and transferred into the genome of Bombyx Mori Nuclear Polyhedrosis Virus adjacent to the polyhedrin promoter. The soluble form of the SCF protein was expressed in Bombyx Mori cells and silkworm larvae and was secreted into the medium in an active state. The recombinant SCF was similar to natural SCF with respect to its interaction with monoclonal antibody and its synergistic biological activity in conjunction with colony-stimulating factor.

Human macrophage colony stimulating factor (HM-CSF) expressed in baculovirus infected insect cells is biologically active in its monomeric form

hM-CSF was reported to have biological activity only in a dimeric form. Using oligonucleotide-directed mutagenesis of hM-CSF (1-149aa) cDNA, we have substituted Ser31 for Cys31 which forms intermolecular disulfide bond in native hM-CSF. The mutant hM-CSF cDNA was expressed in insect BmN cells using baculovirus as a vector under the control of polyhedrin promoter. Biological activity analysis and radioligand receptor assay both showed that there was little difference between the mutant hM-CSF and the native dimeric hM-CSF. These results strongly support that the biologically active human M-CSF in its monomeric form can be expressed in recombinant baculovirus infected insect cells.

[The DNA damage by photodynamic effects of hematoporphyrin derivatives (HPD)]

Photodynamic effects of HPD has been used for cancer therapy (PDT) successfuly. The biological mechanism of the PDT was studied by using DNA as a target in this work. After treatment of phage M13 DNA with HPD + light the molecule of the DNA kept intact in TE buffer. But the smear bands by puting DNA in 0.1 mol/L NaOH at 90 degrees C and separating with electrophoresis denoted the degradation of DNA at the alkali-labile sites of phosphodiester bond in which the groups of the bases were photooxydized. The primer extension experiment showed the aggregation of DNA template by photooxydation. The DNA sequencing results showed that some of the wrong sequences appeared both at the site of A,G,C,T bases. The mouse Ehrlich ascetes carcinoma cell DNA was treated as above then degraded by Bgl II and BamH I respectively. It was found that the restriction fragments became larger than the controls. It also meant the alteration of the bases of DNA by the photooxydation. So the four bases of A,G,C,T of DNA were altered by photodynamic effects of HPD.

Solution structure of human thioredoxin in a mixed disulfide intermediate complex with its target peptide from the transcription factor NF kappa B

BACKGROUND

Human thioredoxin is a 12 kDa cellular redox protein that plays a key role in maintaining the redox environment of the cell. It has recently been shown to be responsible for activating the DNA-binding properties of the cellular transcription factor, NF kappa B, by reducing a disulfide bond involving Cys62 of the p50 subunit. Using multidimensional heteronuclear-edited and hetero-nuclear-filtered NMR spectroscopy, we have solved the solution structure of a complex of human thioredoxin and a 13-residue peptide extending from residues 56-68 of p50, representing a kinetically stable mixed disulfide intermediate along the reaction pathway.

RESULTS

The NF kappa B peptide is located in a long boot-shaped cleft on the surface of human thioredoxin delineated by the active-site loop, helices alpha 2, alpha 3 and alpha 4, and strands beta 3 and beta 4. The peptide adopts a crescent-like conformation with a smooth 110 degrees bend centered around residue 60 which permits it to follow the path of the cleft.

CONCLUSIONS

In addition to the intermolecular disulfide bridge between Cys32 of human thioredoxin and Cys62 of the peptide, the complex is stabilized by numerous hydrogen-bonding, electrostatic and hydrophobic interactions which involve residues 57-65 of the NF kappa B peptide and confer substrate specificity. These structural features permit one to suggest the specificity requirements for human thioredoxin-catalyzed disulfide bond reduction of proteins.

Interaction of silkworm larvae expressed monomeric hM-CSF with its receptor on murine bone marrow derived macrophage

Human macrophage colony-stimulating factor (hM-CSF) expressed in the silkworm larvae was monomeric. The nature of the interaction of iodinated monomeric M-CSF with murine bone marrow derived macrophage (BMM) was studied. On incubation with 2 nM [125I]M-CSF at 4 degrees C, approximately 90% of the maximal binding occurred within 15 min with a plateau around 1hr which then gradually declined. Scatchard plot analysis showed that the Kd for the monomeric M-CSF is 5.3 x 10(-10) M and the number of binding sites per cell is 4 x 10(4). Competition experiment indicated that cellular binding of the iodinated monomeric rhM-CSF was almost as effective as the native M-CSF. The results show that the interchain disulfide bond of M-CSF is not essential for the natural folding of active M-CSF.

Yeast-prepro-alpha-factor-leader-region-directed synthesis and secretion of truncated human macrophage colony-stimulating factor in the silkworm Bombyx mori

Human macrophage colony-stimulating factor (hM-CSF) cDNA joined to the leader region of the precursor of the yeast mating pheromone alpha-factor (MF alpha L) was expressed at high levels in BmN cells and in silkworm (Bombyx mori) larvae, using recombinant Bombyx mori nuclear polyhedrosis virus, as a vector. The biological activity of rhM-CSF detected in the haemolymph was 1 x 10(6) colony-formation units/ml, approximately half of the expression level directed by the native signal peptide of hM-CSF in silkworm larvae. The secreted rhM-CSF was purified to homogeneity. N-terminal analysis showed that the signal peptide had been removed, indicating that insect cells possess the enzymic activity necessary to cleave the pro-alpha-factor leader region from the fusion protein at the carboxy side of Lys-Arg dibasic residues, which is the cleavage site recognized by KEX2 endopeptidase in yeast cells.

The high-resolution three-dimensional solution structures of the oxidized and reduced states of human thioredoxin

BACKGROUND

Thioredoxin is a ubiquitous protein and is involved in a variety of fundamental biological functions. Its active site is conserved and has two redox active cysteines in the sequence Trp-Cys-Gly-Pro-Cys. No structures of the oxidized and reduced states from the same species have been determined at high resolution under the same conditions and using the same methods. Hence, any detailed comparison of the two oxidation states has been previously precluded.

RESULTS

The reduced and oxidized states of the (C62A, C69A, C73A) mutant of human thioredoxin have been investigated by multidimensional heteronuclear NMR. Structures for both states were determined on the basis of approximately 28 experimental restraints per residue, and the resulting precision of the two structures is very high. Consequently, subtle differences between the oxidized and reduced states can be reliably assessed and evaluated. Small differences, particularly within and around the active site can be discerned.

CONCLUSIONS

Overall, the structures of the reduced and oxidized states of the (C62A, C69A, C73A) mutant of human thioredoxin are very similar (with a backbone atomic root mean square difference of about 0.9 A) and the packing of side chains within the protein core is nearly identical. The conformational change between oxidized and reduced human thioredoxin is very small and localized to areas in spatial proximity to the redox active cysteines. These subtle structural differences, in addition to the restriction of conformational freedom within the active site upon oxidation, may be important for the different activities of thioredoxin involving a variety of target proteins.

Expression of biologically active monomeric form of human M-CSF in baculovirus infected silkworm, Bombyx mori

The human macrophage colony stimulating factor (hM-CSF) in its monomeric form has been over-produced in BmN cells and in silkworm larvae infected with the recombinant baculovirus Bm284M-CSF. The recombinant monomeric M-CSF (rhM-CSF) exhibited the activity of 8-14 x 10(4) units/ml of cell culture medium. When the insect larvae were infected with the recombinant virus, the maximum rhM-CSF was expressed 4-5 days post infection with an activity of 3 x 10(6) units/ml hemolymph. The monomeric rhM-CSF was purified to homogeneity through three steps of purification. A pilot purification yielded 1 mg of homogeneous monomeric rhM-CSF from 10 larvae. The purified rhM-CSF monomers gradually dimerized in vitro. In contrast, the crude or the semi-purified monomers did not dimerize in vitro, indicating that the presence of an unknown moiety in the rhM-CSF preparations obtained from hemolymph interfered with dimerization.

Correlation between the steric bulk of the distal E7 and E11 residues and the tilt of the FeCN unit in cyanometmyoglobin as determined by NMR from the orientation of the magnetic axes in single and double point mutants

The amino acids in the heme pocket of sperm whale myoglobin single E11 and double E7 and E11 point mutants in the metcyano form have been assigned by NMR methods to assess the role of steric bulk in modulating ligand tilt. The five mutants investigated are the single mutants His64(E7)-->Gly (H[E7]G), Val68(E11)-->Ile (V[E11]I), and Val68(E11)-->Ala (V[E11]A) and the double mutants His64-(E7)-->Gly:Val68(E11)-->Ile (H,V[E7,E11]G,I) and His64(E7)-->Gly:Val68(E11)-->Ala (H,V[E7,E11]G,A). The dipolar (NOESY) contacts on the proximal side of the heme confirm a conserved molecular structure for all of the mutants. The proximal residue coordinates, together with the dipolar shifts for proximal side residues, quantitatively yield the orientations of the magnetic susceptibility tensors, whose major axis corresponds to the orientation of the ligand. It is observed that upon reduction of the steric bulk in the V[E11]A mutant, the tilt of the ligand is significantly reduced (approximately 8 degrees) from that in the wild type (WT) (approximately 16 degrees), with little change in the direction of tilt. In the case of increased steric bulk at position 68 in the V[E11]I mutant, it is observed that the extent and direction of the tilt are essentially the same as in WT, and it is shown that this is due to the fact that Ile68 is oriented in the pocket with its C delta H3 directed away from the iron.(ABSTRACT TRUNCATED AT 250 WORDS)

Persuasive communities: a longitudinal analysis of references in the Philosophical Transactions of the Royal Society, 1665-1990

References from a single scientific journal were analyzed to show how the persuasive communities created by scientific references change over time. Articles that appeared in the Philosophical Transactions of the Royal Society of London were sampled over the journal's 325-year history of publication, to identify and characterize the references made in them. The data highlight changes in the practice of scholarly reference, and provide quantitative measures of the evolution of scientific publication. Types of publications, and the origin, language and age of the materials cited, were analyzed for the period studied. These measures show how persuasive communities have changed, and provide insights into the character of the scientific communities in question.

[24-hour electroencephalography monitoring in children: analysis of 403 cases]

24-hour EEG monitoring was performed in 403 children with repeated seizure of various types. The positive rate was 82.7% for defined epilepsy. Epileptic discharges mainly occurred in NREM stage and focal discharges accounted for 69%. More than 70% of the children suspected of epilepsy were excluded from epileptic seizures. 24-hour EEG monitoring is of significant value in determining seizure characteristics, epilepsy types, the relations between epilepsy and sleep and between clinical seizures and EEGs.

1H NMR study of the solution molecular and electronic structure of engineered distal myoglobin His64(E7) Val/Val68(E11) His double mutant. Coordination of His64(E11) at the sixth position in both low-spin and high-spin states

A genetically engineered human myoglobin (Mb) in which the distal His, His64(E7), and the distal Val, Val68(E11), are replaced by Val and His, respectively, has been expressed in Escherichia coli, for the purpose of assessing the potential role of a E11 residue in providing a hydrogen bond donor to the coordinated ligand. Molecular modeling indicates that such an interaction is possible. The 1H NMR spectrum of the ferric form of the double mutant Mb exhibits large hyperfine shifts and strong paramagnetic relaxation for which the temperature dependence of the hyperfine shifts reveals a thermal equilibrium between a low-spin and high-spin state (70, 30% at 25 degrees C, respectively). Standard sequence specific two-dimensional (2D) NMR assignments of the E and F helical backbones allow the identification of the peptide protons for the proximal His93(F8) and substituted distal His68(E11). Steady-state nuclear Overhauser effect from these peptide protons locate strongly hyperfine shifted His93(F8) and His68(E11) side chain protons which dictate that both the imidazole rings are coordinated to the iron. 2D bond correlation and one-dimensional and 2D dipolar correlation experiments locate and assign the resonances for the heme. The pattern of the heme contact shifts in both the low-spin and high-spin state, together with the nature of the temperature dependence of the His93(F8) and His68(E11) resonances, establish that the two His are ligated in the high-spin as well as low-spin forms. The pattern of heme methyl hyperfine shifts in the low-spin state, and the smaller hyperfine shifts for His68(E11) as compared to His93(F8) in the high-spin state, indicate that the axial bond to the distal His68(E11) is weakened or strained as compared with that for the proximal His93(F8) in both spin states. This weak ligation originates from a tilted iron-His68 bond, the only conformation in which His68 can place its imidazole group sufficiently close to bind to the heme iron in the conventional Mb folding. Not only do these results support the belief that distal His is indispensable for the control of the ligand binding in Mb and hemoglobin, but also reveal the significance of the evolution that the stereochemical disposition of both His64 and Val68 are unique and non-exchangeable for interacting with the bound ligand.

1H NMR study of the dynamics of the pH modulation of axial coordination in Aplysia limacina (Val(E7)) and sperm whale double mutant His(E7)-->Val,Thr(E10)-->Arg metmyoglobin

The molecular and electronic structure, thermodynamics, dynamics, and mechanism of interconversion of the pH-modulated reversible equilibria of Aplysia limacina metmyoglobin, (metMb), have been investigated by 1H NMR spectroscopy. The four identified species which interconvert slowly on the NMR time scale (lifetime > 1 ms) are metMbOH (B) at alkaline pH, five coordinate metMb (N) at acidic to neutral pH, an acidic form, A, near pH approximately 4 and an extremely low pH form, D, attributed to an equilibrium unfolded species. The presence of strong distal hydrogen bonding by Arg (E10) to bound hydroxide is detected via a significant solvent isotope effect on the metMbOH (B) hyperfine shifts. Integration of the peak intensities yields pK values of 7.7 and approximately 4 for the B<-->N and N<-->A equilibria, respectively. Saturation transfer via chemical exchange is observed for B<-->N and N<-->A, where the rates for forming metMbOH (B) and the acidic form A from N are base- and acid-catalyzed, respectively, while the reverse rates are first-order. The much slower interconversion rate for N<-->B in A. limacina metMb than His(E7) containing mammalian metMb is attributed to the fact that a ligand bond is broken rather than just proton transferred and that the equilibrium involves a major rearrangement of the orientation of Arg(E10). This conclusion is supported by 1H NMR data for the sperm whale double mutant His(E7)-->Val/Thr(E10)-->Arg metMb, which exhibits a pK approximately 8.7 for the equilibrium between five-coordinate metMb (N) and metMbOH (B) with an even slower interconversion rate than in A. limacina metMb. This double mutant metMbOH (B) exhibits hydrogen bonding by Arg (E10) with coordinated hydroxide similar to that in A. limacina metMbOH. The slow but acid-catalyzed rates of conversion of A. limacina metMb (N) to the acid species A with significantly weakened bonding of the heme iron to the axial His(F8) residue is consistent with protonation of an inaccessible residue and/or a structural change accompanying the protonation equilibrium. It is concluded that metMb will coordinate water strongly only when there is a distal hydrogen bond acceptor residue, while the hydroxide ion is coordinated strongly only if there is a distal hydrogen bond donor residue.