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.     

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.     

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.     

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.     

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.     

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.     

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.     

Inheritance of Glucose-6-phosphate Dehydrogenase Variation in Kangaroos

THE production of glucose-6-phosphate dehydrogenase (EC 11149, G6PD) in human¹, horse and donkey² and brown and blue hare³ cells is governed by genes carried by the X chromosome. Two electrophoretic forms of G6PD have been found in wallaroos and euros (Macropus robustus Gould) and one in red kangaroos (Macropus rufus (Desm.)); members of the marsupial family Macropodidae (kangaroos). This analysis used electrophoresis of red blood cell haemolysates on cellulose acetate⁴. No polymorphic populations were found⁵ but electrophoretic phenotypes of euros (Macropus robustus erubescens Sclater) were characterized by a single slow moving band (G6PD-S) while those of wallaroos (Macropus r. robustus Gould) had a single fast moving band (G6PD-F). Red kangaroo populations were uniformly G6PD-S.     

Distribution of representatives of the genus <Emphasis Type="Italic">Neoabbottiella</Emphasis> (Rhodophyta: Halymeniales) in the Russian Far Eastern Seas and taxonomic status of <Emphasis Type="Italic">N. valentinae</Emphasis> N. Klochkova et Pisareva, 2013

The new information on distribution of the red algae Neoabbottiella in the Russian Far East changes the concept of the areal of these algae and their preferred temperatures. A comparison of N. valentinae N. Klochkova et Pisareva with Schizymenia dubyi f. palmata Yamada collected by Y. Yamada from Urup Island and stored with its type and paratypes in the collection of Hokkaido University Museum (Sapporo, Japan) showed their conspecificity. Based on the data, N. valentinae was recognized as a synonym of Schizymenia dubyi f. palmata. Since this form does not possess the main generic feature of the genus Schizymenia and at the same time has well-expressed generic features of Neoabbottiella, the form S. dubyi f. palmata is transferred to this genus with the name N. palmata (Yamada) N. Klochkova et Pisareva.     

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.

     

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.     

Addenda to the Revisions of the Genera <Emphasis Type="Italic">Gergithus</Emphasis> Stål and <Emphasis Type="Italic">Hemisphaerius</Emphasis> Schaum (Hemiptera,Auchenorrhyncha, Fulgoroidea: Issidae)

The genus Gnezdilovius Meng, Webb et Wang, 2017 is revised. Maculergithus Constant et Pham, 2016, which was described as a subgenus of Gergithus Stål, 1870, is upgraded to a genus. Ishiharanus Hori, 1969 is reinstalled from synonymy with Gergithus and considered a valid name. Two new genera are erected, Ceratogergithus Gnezdilov, gen. n. (type species: Gergithus spinosus Che, Zhang et Wang, 2007) and Ophthalmosphaerius Gnezdilov, gen. n. (type species: Hernisphaerius trilobulus Che, Zhang et Wang, 2006). Hernisphaerius bistriatus Schumacher, 1915, Gergithus carbonarius Melichar, 1906, G. rosticus Chan et Yang, 1994, G. nummarius Chan et Yang, 1994, and G. rotundus Chan et Yang, 1994 are transferred to the genus Epyhemisphaerius Chan et Yang, 1994, Gergithus quinquemaculatus Che, Zhang, Wang, 2007—to the genus Maculergithus, Gergithus chelatus Che, Zhang, Wang, 2007 and G. pseudotessellatus Che, Zhang, Wang, 2007—to the genus Ceratogergithus, Hernisphaerius binocularis Chen, Zhang, Chang, 2014—to the genus Ophthalmosphaerius, and Gergithus robustus hoozanensis Schumacher, 1915—to the genus Gnezdilovius. The male genitalia of Gergithus herbaceus (Kirby, 1891) and Hernisphaerius interclusus Noualhier, 1896 are illustrated for the first time.     

Hormone-activated Expression of the C-type RNA Tumour Virus Genome

THE concept of vertical transmission of specific viral information, particularly that possibly associated with the induction of malignancy in mice has been postulated. Moreover, it has been hypothesized that this genetic information may be expressed either in the form of whole virus in certain selected laboratory animal strains or as the operon involved in regulating cellular replication (oncogene)¹. To detect this proposed genetically transmitted message, one uses a group specific antisera against the C-type RNA tumour viruses having as one of its components, gs-3, first described by Gerring et al.². A similar group specific antigen has subsequently been reported by Schafer³, Gilden⁴ and Sarma et al.⁵ and designated “interspec”, meaning that the antigen is common to the internal components of the C-type RNA virion of several mammalian species.     

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.

     

Chromcrphore-Environment Interaction of Visual Pigments in Model System

SEVERAL laboratories^1–6 have recently been concerned with the mechanism of the bathochromic shift of about 120 nm which results when 11-cis retinal (λ _max 380 nm) combines with the protein opsin to form rhodopsin (λ_max 498 nm). A red shift of up to 186 nm is involved in the formation of iodopsin from 11-cis retinal and cone opsin^7,8. The active site of bovine rhodopsin consists of the 11-cis retinylidene chromophore attached to a primary amine group of the protein forming a Schiff-base linkage of the type shown in Fig. 1, Ia. On the basis of the chemical reactions of rhodopsin and its derivatives it has been suggested that an interaction between a protonated form of the chromophore (structure of the type Ib) and a lipophilic environment contributes¹¹ to the red shift.     

The genomic underpinnings of apoptosis in the silkworm, <Emphasis Type="Italic">Bombyx mori</Emphasis>

Background

Apoptosis is regulated in an orderly fashion by a series of genes, and has a crucial role in important physiological processes such as growth development, immunological response and so on. Recently, substantial studies have been undertaken on apoptosis in model animals including humans, fruit flies, and the nematode. However, the lack of genomic data for silkworms limits their usefulness in apoptosis studies, despite the advantages of silkworm as a representative of Lepidoptera and an effective model system. Herein we have identified apoptosis-related genes in the silkworm Bombyx mori and compared them to those from insects, mammals, and nematodes.

Results

From the newly assembled genome databases, a genome-wide analysis of apoptosis-related genes in Bombyx mori was performed using both nucleotide and protein Blast searches. Fifty-two apoptosis-related candidate genes were identified, including five caspase family members, two tumor necrosis factor (TNF) superfamily members, one Bcl-2 family member, four baculovirus IAP (inhibitor of apoptosis) repeat (BIR) domain family members and 1 RHG (Reaper, Hid, Grim, and Sickle; Drosophila cell death activators) family member. Moreover, we identified a new caspase family member, BmCaspase-New, two splice variants of BmDronc, and Bm3585, a mammalian TNF superfamily member homolog. Twenty-three of these apoptosis-related genes were cloned and sequenced using cDNA templates isolated from BmE-SWU1 cells. Sequence analyses revealed that these genes could have key roles in apoptosis.

Conclusions

Bombyx mori possesses potential apoptosis-related genes. We hypothesized that the classic intrinsic and extrinsic apoptotic pathways potentially are active in Bombyx mori. These results lay the foundation for further apoptosis-related study in Bombyx mori.

     

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.     

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.