Amplified restriction fragment length polymorphism-based mRNA fingerprinting using a single restriction enzyme that recognizes a 4-bp sequence

Using amplified restriction fragment length polymorphism (AFLP) technology, we have developed a new protocol for the fingerprinting of mRNA that allows systematic comparison of the differential expression of genes between mRNA samples. The major advantage of our protocol is the use of only a single restriction enzyme that recognizes a 4-bp sequence but allows screening of large numbers of different cDNAs. Using this new protocol, we compared mRNA samples obtained from the flower buds of two lines of the common morning glory (Ipomoea purpurea) with red and white flowers, respectively. Approximately 50 bands were observed in each lane of a denaturing polyacrylamide gel and the results were highly reproducible, as indicated by the results of analysis of two sets of independent mRNA samples. Two cDNA fragments, which were differentially amplified in the samples from the two lines, were shown to have been derived from a single gene that was actively expressed in the buds of red flowers but not in those of white flowers. A full-length cDNA of this gene was cloned from a bud cDNA library. Sequence analysis showed that this cDNA carries a sequence highly homologous to the chalcone synthase (CHS) genes, the key enzyme in the flavonoid biosynthetic pathway.     

The major late promoter and bipartite leader sequence of fowl adenovirus

Invasive pulmonary aspergillosis in immunocompromised patients (ICP) is the second most frequent opportunistic fungal infection. The causative organism includes 16 species of Aspergillus, of which A. fumigatus dominates the ubiquitous incidence of invasive or allergic broncho-pulmonary aspergillosis (ABPA). The definitive diagnosis of invasive aspergillosis is difficult. We have analyzed 24 strains of A. fumigatus recovered from ICP using the RAPD technique. The profiles generated with the 20 primers tested were mostly unique. These results may have a profound impact on the management of aspergillosis, especially in the ICP.     

The C-terminal domain of p53 recognizes DNA damaged by ionizing radiation

p53 accumulates after DNA damage and arrests cellular growth. These findings suggest a possible role for p53 in the cellular response to DNA damage. We have previously shown that the C terminus of p53 binds DNA nonspecifically and assembles stable tetramers. In this study, we have utilized purified segments of human and murine p53s to determine which p53 domains may participate in a DNA damage response pathway. We find that the C-terminal 75 amino acids of human or murine p53 are necessary and sufficient for the DNA annealing and strand-transfer activities of p53. In addition, both full-length wild-type p53 and the C-terminal 75 amino acids display an increased binding affinity for DNA damaged by restriction digestion, DNase I treatment, or ionizing radiation. In contrast, the central site-specific DNA-binding domain together with the tetramerization domain does not have these activities. We propose that interactions of the C terminus of p53 with damaged DNA may play a role in the activation of p53 in response to DNA damage.     

The CMRF-35 mAb recognizes a second leukocyte membrane molecule with a domain similar to the poly Ig receptor

In order to understand the problems of undesired infertility in the Gambia, where the desire for children and fertility is very high, a population based estimate of the frequency of sub-/infertility was undertaken. A survey was used in a representative random sample of the population. The study included an assessment of health care available for infertile couples in the different types and levels of the formal and traditional health system. Primary sterility was found to be fairly uncommon (3%), and secondary infertility to be more frequent (6%). Half of the infertile couples failed to seek formal health care, and they had to reach a certain level of care in order to be properly managed. As investigations are very basic and treatment possibilities scarce, many forms of alternative care are often sought. In addressing reproductive health in developing countries, a systematic primary health care approach to infertility in rural areas with limited resources should be developed.     

Mutagenesis of a buried polar interaction in an SH3 domain: sequence conservation provides the best prediction of stability effects

The SH3 domain from the Fyn tyrosine kinase possesses a buried hydrogen bond between the side chains of a glutamate (Glu24) and a serine (Ser41) residue. Multiple amino acid substitutions were made at these positions to determine the role of this interaction in the stability and conformational specificity of the domain and to assess the relationship between the thermodynamic stability of mutants and sequence conservation seen in the SH3 domain family. Analysis of single and double alanine mutations indicated that the Glu24-Ser41 interaction contributes 0.50 kcal/mol to the stability of the domain. However, disruption of the Glu24-Ser41 interaction did not impair peptide binding function, suggesting that the interaction is not critical for conformational specificity. The stability of the domain was not increased by the replacement of these residues with different combinations of hydrophobic residues or with potential salt bridge forming residues. Despite their similar structural roles in the Fyn SH3 domain, the Ser41 position was considerably more tolerant to substitution than was the Glu24 position. An alignment of >350 different SH3 domains has been completed in our laboratory. A statistically significant correlation was found between the conservation data for the Glu24 and Ser41 positions and the thermodynamic stabilities of the mutants constructed at these positions. Surprisingly, our analysis of sequence alignment data provided a more accurate prediction of the stability of mutants than did examination of the three-dimensional structure of the domain.     

Photoinduced cleavage of single and double stranded DNA at single guanine proximal to target sequence by dibenzoyldiazomethane-ODN conjugate

DBDM-ODN conjugates selectively cleaved single and double stranded DNA at a specific guanine residue proximal to the target sequence upon exposure to 366 nm light.     

The relationship between sequence and interaction divergence in proteins

There is currently a gap in knowledge between complexes of known three-dimensional structure and those known from other experimental methods such as affinity purifications or the two-hybrid system. This gap can sometimes be bridged by methods that extrapolate interaction information from one complex structure to homologues of the interacting proteins. To do this, it is important to know if and when proteins of the same type (e.g. family, superfamily or fold) interact in the same way. Here, we study interactions of known structure to address this question. We found all instances within the structural classification of proteins database of the same domain pairs interacting in different complexes, and then compared them with a simple measure (interaction RMSD). When plotted against sequence similarity we find that close homologues (30-40% or higher sequence identity) almost invariably interact the same way. Conversely, similarity only in fold (i.e. without additional evidence for a common ancestor) is only rarely associated with a similarity in interaction. The results suggest that there is a twilight zone of sequence similarity where it is not possible to say whether or not domains will interact similarly. We also discuss the rare instances of fold similarities interacting the same way, and those where obviously homologous proteins interact differently.     

The interaction of myristylated peptides with the catalytic domain of protein kinase C revealed by their sequence palindromy and the identification of a myristyl binding site

The nature of products of contamination intake were investigated in cattle dosed with [14C]di-n-butylphthalate (DBP). Radio-labelled metabolites were extracted from bile, faeces, plasma and urine onto solid-phase media, fractionated by ion-exchange chromatography, separated by reverse phase HPLC and analysed by negative ion atmospheric pressure chemical ionization mass spectrometry(n) (LCQ, Finnigan). All matrices contained a common major metabolite [deprotonated molecular ion (M-H)- m/z 221] which coeluted with and had an identical daughter ion spectrum to reference monobutylphthalate (MBP). MBP was metabolised to a beta-glucuronidase sensitive compound (M-H)- m/z 397 whose spectrum contained daughter ions (m/z 175 and 221) consistent with the parent glucuronide. A further three beta-glucuronidase resistant radio-labelled metabolites were also produced (M-H- m/z 165, 193 and 237); comparison of daughter ion spectra with those of reference MBP and phthalic acid indicated identity with phthalic acid, monoethylphthalate (MEP) and monohydroxybutylphthalate (MHBP) respectively. The presence of a benzoate daughter ion (m/z 121) in all spectra was indicative of side chain biotransformation. Both MBP and MEP contained a phthalate daughter ion (m/z 165) indicating loss of a butyl and ethyl side chain respectively. A daughter ion of m/z 89 derived from the side chain provided evidence that the third metabolite was MHBP. Incubation of DBP with isolated bovine hepatocytes produced the same metabolites and provided relatively clean samples for LC/MSn analysis. Detection of these DBP metabolites in meat or dairy food products will provide evidence for environmental exposure and biotransformation in vivo, whereas the presence of the parent compound would suggest contamination during food processing and packaging.     

A PCR-based strategy for extensive mutagenesis of a target DNA sequence

A mixed population of mutagenic oligonucleotide primers was used to generate a set of point mutations in a short region of a retroviral gene by PCR amplification. The mixed population of mutagenic primers was generated by incorporating a mixture of A, G, C and T at specific sites during oligonucleotide synthesis. With the proportions of mutagenic nucleotides used for our experiments, 47 percent of the 213 clones analyzed had one or more point mutation in the target DNA sequence. In addition, unpredicted mutations were observed that contributed to the mutagenic complexity of the population. We have found this approach to be an efficient means for extensive mutagenesis of a defined target DNA sequence.     

Synaptotagmin-syntaxin interaction: the C2 domain as a Ca2+-dependent electrostatic switch

Synaptotagmin I is a synaptic vesicle protein that is thought to act as a Ca2+ sensor in neurotransmitter release. The first C2 domain of synaptotagmin I (C2A domain) contains a bipartite Ca2+-binding motif and interacts in a Ca2+-dependent manner with syntaxin, a central component of the membrane fusion complex. Analysis by nuclear magnetic resonance spectroscopy and site-directed mutagenesis shows that this interaction is mediated by the cooperative action of basic residues surrounding the Ca2+-binding sites of the C2A domain and is driven by a change in the electrostatic potential of the C2A domain induced by Ca2+ binding. A model is proposed whereby synaptotagmin acts as an electrostatic switch in Ca2+-triggered synaptic vesicle exocytosis, promoting a structural rearrangement in the fusion machinery that is effected by its interaction with syntaxin.     

Assessing text representations with recognition: The interaction of domain knowledge and text coherence.

Readers construct at least 2 interrelated mental representations when they comprehend a text: a textbase and a situation model. Two experiments were conducted with recognition memory to examine how domain knowledge and text coherence influence readers' textbase and situation-model representations. In Experiment 1, participants made remember-know judgments to text ideas. Knowledge and coherence interacted to influence remember judgments differently than know judgments. In Experiment 2, the authors used the process-dissociation procedure to obtain recollection and familiarity estimates. Knowledge and coherence interacted to influence recollection estimates but not familiarity estimates. The authors claim that recollection and familiarity can be used as markers of the different processes involved in constructing a textbase and a situation model. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

The Ost1p subunit of yeast oligosaccharyl transferase recognizes the peptide glycosylation site sequence, -Asn-X-Ser/Thr-

Other laboratories have established that oligosaccharyl transferase (OST) from Saccharomyces cerevisiae can be purified as a protein complex containing eight different subunits. To identify the OST subunit that recognizes the peptide sites that can be glycosylated, we developed photoaffinity probes containing a photoreactive benzophenone derivative, p-benzoylphenylalanine (Bpa), as part of an 125I-labeled peptide that could be expected to be glycosylated. We found that Asn-Bpa-Thr peptides served as substrates for OST and that photoactivation of these probes in the presence of microsomes abolished the OST activity. Photoactivation of 125I-labeled Asn-Bpa-Thr in the presence of microsomes resulted in specific covalent labeling of a protein doublet of molecular mass 62 and 64 kDa. By carrying out the photoactivation of the probe using microsomes containing epitope-tagged Ost1p, we demonstrated that the 125I-labeled protein was Ost1p. Radiolabeling of this protein was dependent on irradiation at 350 nm. No labeling was detected using a probe containing Ala instead of Thr as the third amino acid residue. We conclude that Ost1p is the subunit of the OST complex that recognizes the peptide sites in the nascent chains that are destined to be glycosylated.     

Specificity and symmetry in the interaction of calmodulin domains with the skeletal muscle myosin light chain kinase target sequence

The specificity of interaction of the isolated N- and C-terminal domains of calmodulin with peptide WFFp (Ac-KRRWKKNFIAVSAANRFK-amide) and variants of the target sequence of skeletal muscle myosin light chain kinase was investigated using CD and fluorescence. Titrations show that two molecules of either domain bind to 18-residue target peptides. For WFFp, the C-domain binds with 4-fold higher affinity to the native compared with the non-native site; the N-domain shows similar affinity for either site. The selectivity of the C-domain suggests that it promotes occupancy of the correct binding site for intact calmodulin on the target sequence. Far UV CD spectra show the extra helicity induced in forming the 2:1 C-domain-peptide or the 1:1:1 C-domain-N-domain-peptide complex is similar to that induced by calmodulin itself; binding of the C-domain to the Trp-4 site is essential for developing the full helicity. Calmodulin-MLCK-peptide complexes show an approximate two-fold rotational relationship between the two highly homologous domains, and the 2:1 C (or N)-domain-peptide complexes evidently have a similar rotational symmetry. This implies that a given domain can bind sequences with opposite peptide polarities, significantly increasing the possible range of conformations of calmodulin in its complexes, and extending the versatility and diversity of calmodulin-target interactions.     

The basic domain in HIV-1 Tat protein as a target for polysulfonated heparin-mimicking extracellular Tat antagonists

Heparin binds extracellular HIV-1 Tat protein and modulates its HIV long terminal repeat (LTR)-transactivating activity (M. Rusnati, D. Coltrini, P. Oreste, G. Zoppetti, A. Albini, D. Noonan, F. d'Adda di Fagagna, M. Giacca, and M. Presta (1997) J. Biol. Chem. 272, 11313-11320). On this basis, the glutathione S-transferase (GST)-TatR49/52/53/55/56/57A mutant, in which six arginine residues within the basic domain of Tat were mutagenized to alanine residues, was compared with GST-Tat for its capacity to bind immobilized heparin. Dissociation of the GST-TatR49/52/53/55/56/57A.heparin complex occurred at ionic strength significantly lower than that required to dissociate the GST-Tat.heparin complex. Accordingly, heparin binds immobilized GST-Tat and GST-TatR49/52/53/55/56/57A with a dissociation constant equal to 0.3 and 1.0 microM, respectively. Also, the synthetic basic domain Tat-(41-60) competes with GST-Tat for heparin binding. Suramin inhibits [3H]heparin/Tat interaction, 125I-GST-Tat internalization, and the LTR-transactivating activity of extracellular Tat in HL3T1 cells and prevents 125I-GST-Tat binding and cell proliferation in Tat-overexpressing T53 cells. The suramin derivative 14C-PNU 145156E binds immobilized GST-Tat with a dissociation constant 5 times higher than heparin and is unable to bind GST-TatR49/52/53/55/56/57A. Although heparin was an antagonist more potent than suramin, modifications of the backbone structure in selected suramin derivatives originated Tat antagonists whose potency was close to that shown by heparin. In conclusion, suramin derivatives bind the basic domain of Tat, prevent Tat/heparin and Tat/cell surface interactions, and inhibit the biological activity of extracellular Tat. Our data demonstrate that tailored polysulfonated compounds represent potent extracellular Tat inhibitors of possible therapeutic value.     

An orphan nuclear receptor lacking a zinc-finger DNA-binding domain: interaction with several nuclear receptors

BACKGROUND: Affections of the lacrimal drainage system are often seen by ophthalmologists. Inspection, palpation, diagnostic rinsing and sounding can distinguish anatomical stops before or after tear sac. For final diagnostics however more apparative examinations are necessary. The ultrasonic examination with contrast media is a simple method for diagnostics of affections of the lacrimal drainage system besides the dacryocystography, the scintigraphy and other ones. PATIENTS AND METHODS: On 12 patients with a dysfunctional lacrimal drainage system and 12 normal controls the ultrasonic examination with instillation of contrast media: silicon oil, glycerine, dispersions of almond oil and viscoelastic substances was performed. All examinations were performed with the 13 B-scan. RESULTS: The lacrimal drainage way was detectable from the canaliculus to the middle nasolacrimal duc CONCLUSION: An additional advantage of the ultrasonic examination with contrast-media is the neglect of radiation, the simple and often repeatable examination method, especially the enhancement of the contrast of different valves and stenoses and mucinous deposits in stationary anatomical variations and dynamic defects.     

Streptolysin O: a proposed model of allosteric interaction between a pore-forming protein and its target lipid bilayer

Streptolysin O, a polypeptide of 571 amino acids, belongs to the family of thiol-activated toxins that permeabilize animal cell membranes. The protein binds as a monomer to membrane cholesterol. Binding involves a conserved region close to the C-terminus and triggers subsequent polymerization into large arc- and ring-shaped structures surrounding pores of up to 30 nm. Besides the C-terminus, a distantly located region spanning residues 213-305 is involved in oligomerization and in membrane insertion. Here, we searched for conformational effects of monomer binding to the latter functionally important region. To this end, single cysteine substitution mutants were produced and derivatized with the polarity-sensitive fluorophore acrylodan. Fluorimetric measurements revealed that binding of the monomer to membranes is accompanied by distinct environmental changes at amino acid residues 218, 248, 266, and 277. Conspicuously, the environment of residues 218 and 266 became more hydrophilic, suggesting movement of these residues out of hydrophobic protein pockets. Upon oligomerization, further alterations in all side-chain environments were observed. The membrane-bound monomer thus differs in conformation from both the monomer in solution and the subunit of the oligomer. The putative binding site of the molecule is linked to remote domains involved in oligomerization and membrane insertion in an apparently allosteric fashion. It is proposed that allostery is responsible for restricting oligomerization to the membrane-bound state of the toxin.