On the Mechanism of Action of <Emphasis Type="Italic">lac</Emphasis> Repressor

Chen et al. have proved conclusively that lac repressor and RNA polymerase bind independently to wild type lac DNA in vitro. To explain the lacp ^s mutation, which causes competitive binding between repressor and polymerase, they suggest that a new promoter site has been created near the lac operator.     

Serology and Genetics of a New Blood Type Bm

TYPE Am, a variation of the A blood type, was discovered by Weiner et al.¹ and further studied by Salmon et al.² and HrubiSko et al.^3,4. Ikemoto et al.⁶ conducted family surveys on type Bm ⁵ in Japanese subjects. Although there have been genetic surveys and studies of the antigenicity of red cells, nobody has yet quantified the immune globulins in serum, the effect of the B and O decomposing enzymes on the Bm red cells, the genetic polymorphism of the plasma or the antigenicity of hairs and cells in the oral mucosa. Recently we surveyed a family, F, of type Bm which included monozygotic twins. We report now further surveys on some of the members of that family and discuss their antigenic relationships and Furuhata's⁷ triple allelomorph theory, that blood type antibodies are genetically determined.     

Feline Leukaemia Viral Antigens and Antisera to the Group Specific Antigens of the Murine Leukaemia Viruses

GEERING et al.¹ reported that feline leukaemia viruses shared one of the group specific antigens of the murine leukaemia viruses, gs-3, as detected by immunoprecipitation in agar gels with broadly reactive rat antisera to the group specific antigens of the murine leukaemia viruses (MuLV). Subsequently, they found that this shared group specific antigen was also present in the hamster and rat C-type viruses². Work by Schafer³ and our own immunodiffusion⁴ and complement fixation studies have confirmed the immunological reactivity between the feline leukaemia viral antigens and broad-reacting murine leukaemia group specific antisera. We have now applied this interspecies immunological reaction between the murine and feline C-type viruses to quantitative studies of the feline leukaemia viruses. Broad-reactive murine leukaemia-sarcoma group specific antisera prepared in rats by the induction of murine sarcoma virus (MSV) tumours^{5, 6} were found to be as useful and nearly as sensitive as a feline leukaemia-sarcoma specific, group specific antiserum for the in vitro detection and assay of the noncytopathogenic feline leukaemia virus (FeLV).     

Quinacrine Fluorescence Patterns and Terminal DNA Labelling of Human <Emphasis Type="Italic">C</Emphasis> Group Chromosomes

THE human C group chromosomes have been difficult to study because they have rather similar morphology. Application of the quinacrine fluorescent staining technique developed by Caspersson et al.¹ now allows the identification of individual chromosomes and of the chromosome segments involved in translocations because the fluorescent patterns are not altered by the translocation^2–4. We have reported the value of this technique in analysing abnormalities of the D⁴ and G³ groups. We report here a variety of structural changes of C group chromosomes which have been characterized in this way, as well as the terminal DNA replication pattern of the C group chromosomes.     

Poly U Tracts absent from Viral RNA

Polyadenylic acid (poly A) is covalently attached to the RNA molecules in which it occurs^1–4, but its exact location is not definitely established. It was at first thought to exist only at the 3′OH terminus of RNA molecules^5–6 but recently Ryskov et al. claimed to have found it at the 5′ terminus of light nuclear RNA7 and it is possible that it also exists internally.     

Transneuronal Degeneration as Basic Mechanism of Muscular Atrophy of Central Origin (Reply)

WE wish to report some findings which are relevant to the recent work of McComas et al.¹. Although our EMG examination was not so appropriate as that of McComas et al., Calcaianu and I² concluded that in some cases of central atrophy (especially those occurring with parietal tumours), spinal motoneurons released from the control of the parietal trophic centre may be disturbed.     

Response to Darting Primates: Steps toward Procedural and Reporting Standards

The safety of primates which are captured and released in the wild is a topic of concern for many field primatologists. Our article and the recent commentary by Fernandez-Duque et al. contribute to the discussion. Although Fernandez-Duque et al. found a slightly higher rate of fatalities (2.5 %) than Cunningham et al. (2.0 %), their combined rate of fatal and serious injuries was lower (4.0 % vs 5.0 %). The differences in rate are not substantial, given limitations of the data. However, as Fernandez-Duque et al. highlight the need for standardizing methods of analysis, we believe the methods they suggest merit careful consideration. We agree that variation in size, habitat, and the experience of the darting team are important factors. Cunningham et al. reported the influence of these factors on injury and fatality rates. There are, however, some important differences in the methods of Cunningham et al. and Fernandez-Duque et al. We believe it is important to 1) acknowledge possible bias in the data, 2) report results of serious complications that arise during capture, 3) report results of capturing medically compromised primates, and 4) report rates of primates falling to the ground.     

Effect of 6-(<Emphasis Type="Italic">p</Emphasis>-Hydroxyphenyl)-azouracil on <Emphasis Type="Italic">B. subtilis</Emphasis> DNA Polymerases

DNA replication in Bacillus subtilis^1,2 and other Gram-positive organisms³ is specifically inhibited by 6-(p-hydroxyphenyl)-azouracil (HPUra). The site of action of this compound has not so far been identified, but important progress was made by Brown et al.⁴, who studied the effect of HPUra on DNA synthesis in B. subtilis cells made permeable to externally supplied deoxynucleoside triphosphates by treatment with toluene. In this in vitro system, HPUra had no inhibitory effect when added alone, but in the presence of NADPH or dithiothreitol (DTT) the drug was reduced to a colourless form which specifically inhibited DNA synthesis.     

Regulatory Properties of Intergeneric Hybrids of Aspartate Transcarbamylase

THE regulatory enzyme aspartate transcarbamylase (ATCase) from Escherichia coli contains two non-identical protein sub-units, one the catalytic subunit which provides the active sites of the enzyme and the other the regulatory subunit which provides the binding sites for nucleotide inhibitors and activators^1,2. The catalytic subunit is a trimer of “C” polypeptide chains, associated by three heterologous c: c domains of bonding (terminology given by Monod et al.³ and Cohlberg et al.⁴). The regulatory subunit is a dimer of “R” chains, associated by an isologous r: r domain. Two catalytic and three regulatory subunits interact specifically across six r: c domains of inter-subunit bonding to complete the quaternary structure of the ATCase molecule.     

Synthetic Scotophobin-mediated Passive Transfer of Dark Avoidance

A CHEMICAL rather than an electrical mode of long term storage of learned behavioural information was first suggested more than 20 yr ago¹. Experimental means for studying the nature of the storage molecule (by passive transfer from a trained donor to a naive recipient) were suggested by some provocative experiments^2,3. Jacobson et al.³ claimed that the causative factor was RNA. RNA, however, prepared similarly by others but analysed for impurities by a more sensitive method, was clearly contaminated with peptides⁴. Brain RNA labelled with ³²P and injected intraperitoneally (Jacobson et al.'s injection route) does not cross the blood-brain barrier⁵ although it is well known that peptides do get across. The inconsistency of activity of RNA fractions prepared by different investigators⁶ hinted that: (a) RNA might be acting as a carrier for the true active compound and (b) the binding between RNA and such an active compound might be labile.     

Imide Products from Photo-oxidation of Bilirubin and Mesobilirubin

IN 1958 Cremer et al.¹ observed that the concentration of bilirubin (la) in the plasma could be reduced by exposing newborn infants to fluorescent light. Since that time phototherapy has come into wide use to lower elevated bilirubin levels associated with neonatal jaundice (hyperbilirubin-aemia)^{2, 3}. This condition in the newborn has been associated with retarded motor development, irreversible brain damage or even death. Phototherapy lowers bilirubin levels (by conversion of this lipid-soluble pigment to water-soluble products)⁴ and therefore presumably helps to prevent brain damage. But there are two possible dangers in this treatment: light may have other deleterious effects on the newborn and the photo-products of bilirubin may themselves be toxic. At present neither the structures of the bilirubin photo-products nor their toxicities have been established. Although the photo-destruction of bilirubin has been studied in vivo and in vitro by Ostrow^5–7, Schmid^{4, 7} and others^{8, 9}, these authors investigated principally the visible-ultraviolet spectral changes during the course of bilirubin photo-oxidation and recorded paper chromatographic separations of the photo-products for comparison with the bile or urine of the congenitally jaundiced Gunn rat. More recently McDonagh has shown that singlet oxygen is involved in the self-sensitized photo-oxidation of bilirubin¹⁰. In view of the paucity of structural.information on the bilirubin photo-products, we wish to report preliminary findings on the in vitro photo-oxidation products from bilirubin IXa (1a), mesobilirubin IXa (1b) and 5′-oxo-3′,4,4′-triethyl-3,5-dimethyl-l′,5′-dihydro-(2.2′)-dipyrrylmethene (2). We synthesized and carried out our initial studies on 2, which serves as a simplified model for rings I and II of 1a and 1b because it lacks the vinyl group of 1a and the propionic acid β-substituent of 1a and 1b. The visible-ultraviolet spectrum of 2 is quite similar to that of either 1a or 1b^11–13.     

Site of Nitrogenase Activity in the Blue-Green Alga <Emphasis Type="Italic">Anabaena</Emphasis> sp. L-31

MANY blue-green algae fix nitrogen, assimilate carbon dioxide and evolve oxygen and as algal nitrogenase is inhibited^1–3 by high oxygen pressure, enhanced nitrogen fixation accompanying photosynthesis is surprising. Heterocysts do not contain⁴ or have comparatively less amounts^4–7 of photosystem II (PS II) pigments, which are responsible for the evolution of oxygen. This tends to favour the suggestion of Fay et al.⁸ that these cells are the sites of nitrogenase activity. Until now, however, attempts at obtaining unequivocal evidence for heterocysts as principal loci for nitrogenase activity have yielded conflicting results. Stewart et al.⁷ first demonstrated nitrogenase activity in heterocysts incubated aerobically, a finding confirmed by Wolk and Wojciuch⁹ and Van Gorkom and Donze¹⁰. By contrast, Smith and Evans^3,11 and Kurz and La Rue¹² reported results favouring vegetative cells as the major site of nitrogenase activity. Other evidence^2,13 showed high nitrogenase activity in cell-free preparations of Anabaena cylindrica and the non-heterocystous alga Plectonema boryanum strain 594.     

Cross-platform comparability of microarray technology: Intra-platform consistency and appropriate data analysis procedures are essential

Background

The acceptance of microarray technology in regulatory decision-making is being challenged by the existence of various platforms and data analysis methods. A recent report (E. Marshall, Science, 306, 630–631, 2004), by extensively citing the study of Tan et al. (Nucleic Acids Res., 31, 5676–5684, 2003), portrays a disturbingly negative picture of the cross-platform comparability, and, hence, the reliability of microarray technology.

Results

We reanalyzed Tan's dataset and found that the intra-platform consistency was low, indicating a problem in experimental procedures from which the dataset was generated. Furthermore, by using three gene selection methods (i.e., p-value ranking, fold-change ranking, and Significance Analysis of Microarrays (SAM)) on the same dataset we found that p-value ranking (the method emphasized by Tan et al.) results in much lower cross-platform concordance compared to fold-change ranking or SAM. Therefore, the low cross-platform concordance reported in Tan's study appears to be mainly due to a combination of low intra-platform consistency and a poor choice of data analysis procedures, instead of inherent technical differences among different platforms, as suggested by Tan et al. and Marshall.

Conclusion

Our results illustrate the importance of establishing calibrated RNA samples and reference datasets to objectively assess the performance of different microarray platforms and the proficiency of individual laboratories as well as the merits of various data analysis procedures. Thus, we are progressively coordinating the MAQC project, a community-wide effort for microarray quality control.

     

Interaction profile-based protein classification of death domain

Background

The increasing number of protein sequences and 3D structure obtained from genomic initiatives is leading many of us to focus on proteomics, and to dedicate our experimental and computational efforts on the creation and analysis of information derived from 3D structure. In particular, the high-throughput generation of protein-protein interaction data from a few organisms makes such an approach very important towards understanding the molecular recognition that make-up the entire protein-protein interaction network. Since the generation of sequences, and experimental protein-protein interactions increases faster than the 3D structure determination of protein complexes, there is tremendous interest in developing in silico methods that generate such structure for prediction and classification purposes. In this study we focused on classifying protein family members based on their protein-protein interaction distinctiveness. Structure-based classification of protein-protein interfaces has been described initially by Ponstingl et al. [1] and more recently by Valdar et al. [2] and Mintseris et al. [3], from complex structures that have been solved experimentally. However, little has been done on protein classification based on the prediction of protein-protein complexes obtained from homology modeling and docking simulation.

Results

We have developed an in silico classification system entitled HODOCO (Homology modeling, Docking and Classification Oracle), in which protein Residue Potential Interaction Profiles (RPIPS) are used to summarize protein-protein interaction characteristics. This system applied to a dataset of 64 proteins of the death domain superfamily was used to classify each member into its proper subfamily. Two classification methods were attempted, heuristic and support vector machine learning. Both methods were tested with a 5-fold cross-validation. The heuristic approach yielded a 61% average accuracy, while the machine learning approach yielded an 89% average accuracy.

Conclusion

We have confirmed the reliability and potential value of classifying proteins via their predicted interactions. Our results are in the same range of accuracy as other studies that classify protein-protein interactions from 3D complex structure obtained experimentally. While our classification scheme does not take directly into account sequence information our results are in agreement with functional and sequence based classification of death domain family members.

     

Mutant tRNA<Superscript>His</Superscript> Ineffective in Repression and Lacking Two Pseudouridine Modifications

TRANSFER RNA has been implicated in the regulation of a number of amino-acid biosynthetic operons^1–4. Histidyl-tRNA^His has been shown to be involved in regulation of the histidine operon by analysis of six genes (hisO, hisR, hisS, hisT, hisU, hisW), mutation of which causes derepression of the enzymes of the histidine biosynthetic pathway in Salmonella typhimurium^5–7. A class of derepressed mutants (hisR) has only about 55% as much tRNA^His as the wild type⁴ and in the one example sequenced, contains tRNA^HIS with a structure identical to that of the wild type⁸. Studies of mutants of the gene for histidyl-tRNA synthetase (hisS) indicated that the derepressed phenotype was associated with defects in the charging of tRNA^HISin vitro². The amounts of charged and uncharged tRNA^His present in vivo during physiological derepression of the wild type and in the six classes of regulatory mutants, have been determined⁹. This work has shown that repression of the histidine operon is correlated directly with the concentration of charged histidyl-tRNA^Hisin vivo and not with the ratio of charged to uncharged or the absolute amount of uncharged tRNA^His. The derepression observed in mutants, of hisS (the gene for histidyl-tRNA synthetase), hisR (the presumed structural gene for the single species of tRNA^His) and hisU and hisW (genes presumably involved in tRNA modification) may be explained by the lower cellular concentration of charged tRNA^His which these mutants contain.     

Angular Alteration of the DNA Helix by <Emphasis Type="Italic">E. coli</Emphasis> RNA Polymerase

IT has been a source of speculation whether the reading of the genetic code of DNA by RNA polymerase involves the disruption of the DNA helix. While circuitous evidence favouring either affirmative or negative answer has been accumulating, direct experiments have been few^1–11. Kosaganov et al. investigated the possibility of a local unwinding of DNA during RNA synthesis by measuring the kinetics of formaldehyde-induced denaturation of DNA during RNA synthesis¹². They concluded that the binding of RNA polymerase did not cause local unwinding but RNA synthesis produced “defects” in the double helix. Unfortunately, the interpretation of formaldehyde-induced denaturation is not clear, nor is the nature of a “defect”.     

Blockade by Polyphloretin Phosphate of the Prostaglandin F<Subscript>2α</Subscript>, Action on Isolated Human Bronchi

POLYPHLORETIN phosphate (PPP), a polymer with an inhibitory effect on some enzyme systems, such as alkaline phosphatase and hyaluronidase, has been synthesized by Diczfalusy et al.¹ by phosphorylating phloretin with phosphorus oxychloride. PPP has a molecular weight of about 15,000 and is readily soluble in water at pH 7. It has been tried in the treatment of oedema^2,3 and in vitro it inhibits the aggregation of red blood corpuscles⁴ and selectively antagonizes the effect of prostaglandin E₂ (PGE₂) on the intraocular pressure of the rabbit eye⁵. In the light of this finding we have examined whether PPP (supplied by Dr B. Högberg) could also modify the action of prostaglandins, when tested on some other preparation— in this case isolated human bronchi. During this study an investigation of the inhibition by PPP of the PGE₂ and PGF_2α action on isolated bird colon, rabbit jejunum and uterus has been reported⁶. It has been shown that PGE₁ and usually also PGE₂ have a bronchodilating effect in guinea-pig^7,8 and man⁹, while PGF_2α constricts bronchial smooth muscle in vivo and invitro^8,10,11. PGF_2α and PGE₂ have been isolated from human lungs^12,13 and both seem to be released in the anaphylactic reaction of isolated guinea-pig lung.     

Isolation and Characterization of Antigenic Components of a New Heptavalent <Emphasis Type="Italic">Pseudomonas</Emphasis> Vaccine

ONE of the most serious opportunistic bacterial pathogens is Pseudomonas aeruginosa¹ and the inability of the common antimicrobial agents to combat such infections suggested the investigation of specific immunological prophylactic and therapeutic approaches. Therefore Fisher et al. began to develop a new serotype schema as a prerequisite for an immunizing preparation which would protect humans against the most prevalent strains of Pseudomonas. This communication describes the isolation, purification and preliminary characterization of seven new lipopolysaccharide antigens which were obtained from strains representative of each of the seven protective serotypes identified by Fisher et al.².     

Reversible Blocking Effect of Anti-mouse Immunoglobulin Serum on the Induction of Immunity and Tolerance <Emphasis Type="Italic">in vitro</Emphasis>

THE induction of blast transformation by incubating lymphocytes with anti-immunoglobulin¹ and anti-allotype² sera has suggested that these cells have immunoglobulin on their surface. This hypothesis was directly verified by the demonstration of immunoglobulin on living mouse lymphoid cells by Raff et al.³. There is much evidence to indicate that immunocompetent cells have surface receptors for antigen. This idea is based on the finding that lymphocytes can bind radioactively labelled antigen to their surface^4,5 and that specific immune unresponsiveness occurs if lymphoid cells are exposed to either highly radioactive antigen⁶ or haptens capable of forming covalent bonds with proteins^7,8. The immunoglobulin nature of these antigen receptors is suggested by recent work showing that the binding of radioactively labelled antigen can be blocked by anti-immunoglobulin sera^5,9. Reports that the adoptive immune response of mouse spleen cells can be inhibited by anti-mouse immunoglobulin sera (AMS)^9,10 suggest that the interaction of antigen with the immunoglobulin receptor sites is a crucial step in the induction of the antibody response. We report here that the inhibitory action of AMS on the immune response is potentially reversible and that the induction of immune tolerance to polymerized flagellin (POL) in vitro may be blocked in the presence of AMS.