ATF and Jun transcription factors, acting through an Ets/CRE promoter module, mediate lipopolysaccharide inducibility of the chemokine RANTES in monocytic Mono Mac 6 cells

The chemokine RANTES is produced by a variety of tissues, including cells of the monocyte/macrophage lineage. RANTES expression is rapidly and transiently up-regulated in primary monocytes and the monocytic cell line Mono Mac 6 in response to stimulation by the bacterial product lipopolysaccharide (LPS). Transient transfection of Mono Mac 6 cells with RANTES reporter-promoter deletion constructs, in conjunction with DNase I footprinting and heterologous reporter gene assays, allowed identification of an LPS-responsive region within the RANTES promoter. Electrophoretic mobility shift assays (EMSA), methylation interference and EMSA supershift experiments were used to characterize sequences and transcription factors responsible for this LPS inducibility. The region, termed RANTES site G [R(G)], contains consensus sites for Ets and CRE/AP-1-like elements. Site-directed mutagenesis of the Ets site resulted in a loss of only 15 % of promoter activity, while mutation of the CRE/AP-1 site led to a loss of 40 % of LPS-induced promoter activity. The Ets site constitutively binds the Ets family member PU.1. LPS stimulation leads to an induction of ATF-3 and JunD factor binding to the CRE/AP-1 site. Thus, LPS induction of RANTES transcription is mediated, in part, through the activation and selective binding of ATF and Jun nuclear factors to the R(G) promoter module.

Highly specific localization of promoter regions in large genomic sequences by PromoterInspector: a novel context analysis approach

We present a new algorithm called PromoterInspector to locate eukaryotic polymase II promoter regions in large genomic sequences with a high degree of specificity. PromoterInspector focuses on the genetic context of promoters, rather than their exact location. Application of PromoterInspector can serve as a crucial pre-processing step for other methods to locate exactly, or to analyze promoters. PromoterInspector does not depend on heuristics, because it is purely based on libraries of IUPAC words extracted from training sequences by an unsupervised learning approach. We compared PromoterInspector to in silico promoter prediction tools using the sequences from the review by J.W. Fickett. PromoterInspector compared favourably on Fickett's evaluation scheme. A true positive to false positive ratio of 2.3 was obtained, surpassing the best ratio of 0.6, reported for TSSG. The application of our method to several large genomic sequences of over 1.3 million base-pairs in total resulted in even more specific predictions. The coverage of annotated promoters was comparable to other in silico promoter prediction methods, while the true positive predictions increased by up to 100% of total matches. PromoterInspector scans 100 kb in less than one minute on a workstation, and thus is especially applicable for large genome analysis. The method is available at http://genomatix.gsf. de/cgi-bin/promoterinspector/promoterinspector.pl.

Analysis of 27 mammalian and 9 avian PrPs reveals high conservation of flexible regions of the prion protein

Prion diseases are fatal neurodegenerative disorders in man and animal associated with conformational conversion of a cellular prion protein (PrPc) into the pathologic isoform (PrPSc). The function of PrPcand the tertiary structure of PrPScare unclear. Various data indicate which parts of PrP might control the species barrier in prion diseases and the binding of putative factors to PrP. To elucidate these features, we analyzed the evolutionary conservation of the prion protein. Here, we add the primary PrP structures of 20 ungulates, three rodents, three carnivores, one maritime mammal, and nine birds. Within mammals and birds we found a high level of amino acid sequence identity, whereas between birds and mammals the overall homology was low. Various structural elements were conserved between mammals and birds. Using the CONRAD space-scale alignment, which predicts conserved and variable blocks, we observed similar patterns in avian and mammalian PrPs, although 130 million years of separate evolution lie in between. Our data support the suggestion that the repeat elements might have expanded differently within the various classes of vertebrates. Of note is the N-terminal part of PrP (amino acid residues 23-90), which harbors insertions and deletions, whereas in the C-terminal portion (91-231) mainly point mutations are found. Strikingly, we found a high level of conservation of sequences that are not part of the structured segment 121-231 of PrPcand of the structural elements therein, e.g. the N-terminal region from amino acid residue 23-90 and the regions located upstream of alpha-helices 1 and 3.

Increased steady state mRNA levels of the STM and KNAT1 homeobox genes in cytokinin overproducing Arabidopsis thaliana indicate a role for cytokinins in the shoot apical meristem

This study investigates the consequences of endogenously enhanced biosynthesis of the plant hormone cytokinin in Arabidopsis thaliana (L.) Heynh. Transcriptional control of the bacterial ipt gene by the Drosophila melanogaster hsp70 promoter enabled temperature-dependent increased cytokinin production in transgenic plants. Heat-treated plants accumulated higher levels of unbound and bound zeatin-type cyto-kinins, the latter being preferentially N-conjugated glucosides. Cytokinin overproduction significantly increased the biomass of seedlings. Ipt transgenics had higher steady state mRNA levels of the shoot meristem specifying homeobox genes KNAT1 and STM, similar to the cytokinin-overproducing shoot meristem mutant amp1 (hpt, cop2, pt) This finding, together with previously described phenotypic similarities between transgenic cytokinin-overproducing plants and plants overexpressing the KNAT1 or KN1 genes, suggests that these factors act on the same pathway. We hypothesize that cytokinins act upstream of KNAT1 and STM. The influence of cytokinins on homeobox genes provides a link between the hormone and the developmental genes and indicates a role for cytokinins in the shoot apical meristem.

[Evaluating the pregnant cervix uteri by ultrasound with computer-assisted texture analysis]

BACKGROUND

Cervical ripening during pregnancy is associated with ultrastructural alterations, presumably correlated with structural changes of the ultrasonographic image. Analysing these changes might allow conclusions on cervical consistence without necessarily performing manual examination.

PATIENTS AND METHODS

Ultrasound findings of 112 patients with normal pregnancy (14th to 41st week of pregnancy) have been compared to those of 57 patients admitted because of cervical insufficiency (20th to 35th week). A representative region of interest was analysed using a computer based texture analysing system ("Ultra" written in "Interactive Data Language"). 125 parameters derive from various texture algorithms: 1st order gray scale statistics, row, slit and area statistics, gradient statistics, cooccurrence statistics. By means of factor and multiple regression analysis those parameters could be determined, which contribute significantly to the clinical assessment of cervical consistence. Weighting these parameters a so called texture score (TS) and--implementing the other parameters of the Bishop-Score (BS)--a texture based cervical score (TBCS) could be established.

RESULTS

Manual assessment of cervical consistence could be reproduced excellently by noninvasive texture analysis. TBCS was highly correlated to BS, correlation to remaining duration of pregnancy (RDOP) was highly significant for TBCS but insignificant for BS.

CONCLUSIONS

Manual assessment of cervical consistence may be replaced by noninvasive texture analysis. Using RDOP as target parameter TS and TBCS turn out to be superior to manual assessment and BS respectively.

DISCUSSION

Computer aided texture analysis of cervical ultrasound imaging provides a useful information, which can be obtained easily and might help to reduce palpatory controls and increase the accuracy of prediction of pregnancy prolongation.

Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarity

MOTIVATION

Gene regulation often depends on functional modules which feature a detectable internal organization. Overall sequence similarity of these modules is often insufficient for detection by general search methods like FASTA or even Gapped BLAST. However, it is of interest to evaluate whether modules, often known from experimental analysis of single sequences, are present in other regulatory sequences.

RESULTS

We developed a new method (FastM) which combines a search algorithm for individual transcription factor binding sites (MatInspector) with a distance correlation function. FastM allows fast definition of a model of correlated binding sites derived from as little as a single promoter or enhancer. ModelInspector results are suitable for evaluation of the significance of the model. We used FastM to define a model for the experimentally verified NFkappaB/IRF1 regulatory module from the major histocompatibility complex (MHC) class I HLA-B gene promoter. Analysis of a test set of sequences as well as database searches with this model showed excellent correlation of the model with the biological function of the module. These results could not be obtained by searches using FASTA or Gapped BLAST, which are based on sequence similarity. We were also able to demonstrate association of a hypothetical GRE-GRE module with viral sequences based on analysis of several GenBank sections with this module.

AVAILABILITY

The WWW version of FastM is accessible at: http://www.gsf.de/cgi-bin/fastm. pl and http://genomatix.gsf.de/cgi-bin/fastm2/fastm.pl

Oxidant-induced lung injury in anticancer therapy

Lung injury is one of the most frequent side effects in anticancer therapy. Especially simultaneous application of high doses of ionising radiation and radiosensitising cytotoxic drugs is considered to cause deleterious pneumonitis and pulmonary fibrosis. Growing evidence indicates that reactive oxygen species (ROS) play a key role in the development of these disorders. They are capable of causing cell component alterations and changing cellular protein expression. Observing these disease mechanisms reveals an impressive self-amplifying cascade of secondary ROS generation. Through intricate interactions between cells, cytokines and growth factors, fibroblasts are activated and thus pulmonary matrix content is massively increased. - As clinical appearance is uniform and unspecific, an early, reliable diagnosis of therapy-associated lung damage is not possible so far. However, improving this situation could enable us to take advantage of new multimodal therapeutic facilities. This review discusses mechanisms of ROS generation during radio-chemotherapy in the lung, antioxidant defense strategies and responses to oxidants, thereby assessing current diagnostic tools.

Erectile dysfunction caused by sacral gun-shot injury

A 22-year-old man suffering from isolated erectile dysfunction associated with damage to the right spinal nerve S2 caused by sacral gun-shot injury. He has no loss of bladder innervation. Treatment has been implantation of a penile prosthesis.

Radiosynthesis and autoradiographic evaluation of [11C]NAD-299, a radioligand for visualization of the 5-HT1A receptor

The selective 5-HT1A receptor antagonist NAD-299 ([R]-3-N,N-dicyclobutylamino-8-fluoro-3,4- dihydro-2H-1-benzopyran-5-carboxamide) was labeled with the positron-emitting radionuclide carbon-11. The radioligand was synthesized from NAD-195 ([R]-3-N,N-dicyclobutylamino-8-fluoro-5-trifluoromethylsulfonyl oxy-3,4- dihydro-2H-1-benzopyran) in two radiochemical steps. A palladium-catalyzed reaction of NAD-195 and [11C]cyanide was followed by hydrolysis of the carbon-11-labeled nitrile intermediate with basic hydrogen peroxide. The total radiochemical yield, based on [11C]CO2 and corrected for decay, was 20-40%. The specific radioactivity was 24 GBq/mumol (900 Ci/mmol) at end of synthesis, with a radiochemical purity better than 99% and a total synthesis time of 40-45 min. Autoradiographic examination of [11C]NAD-299 binding in human brain postmortem demonstrated high binding in hippocampus, raphe nuclei, and neocortex. The binding in the hippocampus was higher than in the neocortex. Within the hippocampus, the densest binding was observed in the CA1 region. [11C]NAD-299 binding was inhibited by addition of the 5-HT1A receptor ligands WAY-100635, pindolol, (+/-)-8-OH-DPAT, 5-HT, and buspirone, leaving a low background of nonspecific binding. The results indicate that [11C]NAD-299 binds specifically to 5-HT1A receptors in the human brain in vitro and is a potential radioligand for positron emission tomography (PET) examination of 5-HT1A receptors in vivo.

Coagulatory response after femoral instrumentation after severe trauma in sheep

OBJECTIVE

Pulmonary complications after intramedullary femoral nailing have been attributed to bone marrow fat embolization and a variety of cascade effects. We investigated whether the coagulatory response after intramedullary femoral nailing in merino sheep is altered after severe trauma.

METHODS

Adult merino sheep were submitted to hemorrhagic shock (2 hours, 50 mm Hg) and unilateral lung contusion. After recovery (day 3 of the study), reamed femoral intramedullary nailing (RFN), unreamed femoral intramedullary nailing (UFN), or plate osteosynthesis of the femur (P) was performed. Pulmonary artery pressure, central venous levels of factor V, protein C, antithrombin III, and fibrinogen, were determined. At 1 and 3 days before and after femur instrumentation, pulmonary capillary permeability was assessed on the basis of the comparative albumin content in bronchoalveolar lavage fluid.

RESULTS

Group RFN, n=8; group UFN, n=7; group P, n=6. A significant (p < 0.05) postoperative increase in the relative albumin content in terms of the BAL/plasma albumin ratio was measured in group RFN (day 3 preoperatively: 0.38+/-0.05 day 3 postoperatively: 0.53+/-0.06, p < 0.05 (RFN vs. P), which contrasted with group UFN (day 3 preoperatively: 0.44+/-0.09, day 3 postoperatively: 0.46+/-0.09, no significant difference). This evidence of increased pulmonary permeability occurred in association with evidence of increased activation of coagulation factors (data presented as percentage of day 3 preoperative baseline values). The data for fibrinogen (15 min postoperatively) is as follows: group RFN, 74+/-9% (p < 0.05 vs. P); group UFN, 83+/-8% (not significant); group P, 98+/-6%. The data for antithrombin III (15 min. postoperatively) is as follows: group RFN, 72+/-6% (p < 0.05 vs. P); group UFN, 79+/-8% (not significant); group P, 92+/-8% (not significant).

CONCLUSION

After severe trauma, an increase of pulmonary permeability after reamed femoral nailing was associated with increased consumption of coagulation factors. After unreamed nailing, a similar trend was apparent, but this was not found to be statistically significant. These data provide support for the theory that after severe trauma, unreamed femoral nailing reduces but does not abolish pulmonary sequelae when compared with reamed femoral nailing.

Proviral structure, chromosomal location, and expression of HERV-K-T47D, a novel human endogenous retrovirus derived from T47D particles

We previously described that type B retrovirus-like particles released from the human mammary carcinoma cell line T47D are pseudotypes and package retroviral RNA of different origins (W. Seifarth, H. Skladny, F. Krieg-Schneider, A. Reichert, R. Hehlmann, and C. Leib-Mösch, J. Virol. 69:6408-6416, 1995). One preferentially packaged retroviral sequence, ERV-MLN, has now been used to isolate the corresponding full-length provirus from a human genomic library. The 9,315-bp proviral genome comprises a complete retroviral structure except for a 3' long terminal repeat (LTR) truncation. A lysine tRNA primer-binding site and phylogenetic analyses assign this human endogenous retroviral element, now called HERV-K-T47D, to the HML-4 subgroup of the HERV-K superfamily. The gag, prt, pol, and env genes exhibit 40 to 60% amino acid identity to HERV-K10. HERV-K-T47D is located on human chromosome 10, with five closely related elements on chromosomes 8, 9, 15, 16, and 19 and several hundred HERV-K-T47D-related solitary LTRs dispersed over the human genome. HERV-K-T47D-related sequences are detected in the genomes of higher primates and Old World monkeys but not in those of New World monkeys. High HERV-K-T47D transcription levels were observed in human placenta tissue, whereas transcription in T47D cells was strictly steroid dependent.

Kappa-casein polymorphisms in Indian dairy cattle and buffalo: a new genetic variant in buffalo

We screened 57 Sahiwal cattle (Bos indicus) and 53 Murrah, 19 Nili-Ravi and 11 Egyptian buffaloes (Bubalus bubalis) to detect the polymorphisms at kappa-casein (CSN3) gene using the polymerase chain reaction (PCR). CSN3 A and B alleles were identified by PCR-RFLP using the restriction enzymes that detect the underlying nucleotide changes at codon 136 (Taql) and at codon 148 (HindIII or HinfI) in cattle. The frequency of CSN3 B allele in the Sahiwal cattle was estimated as 0.16 with no homozygous BB animal. Using the same set of primers as used in the Sahiwal cattle, a part of exon IV of buffalo CSN3 gene was amplified, but restriction enzyme analysis using HindIII/HinfI and TaqI did not reveal any polymorphism. However, DNA sequencing of the amplified fragment (GenBank Acc. No. U96662) revealed one polymorphism at codon 135 (ThrACC -->I1eATC) in buffalo; the frequencies of 135 Thr/Ile alleles were estimated as 0.88 and 0.12, respectively.

DIALIGN: finding local similarities by multiple sequence alignment

MOTIVATION

DIALIGN is a new method for pairwise as well as multiple alignment of nucleic acid and protein sequences. While standard alignment programs rely on comparing single residues and imposing gap penalties, DIALIGN constructs alignments by comparing whole segments of the sequences. No gap penalty is employed. This point of view is especially adequate if sequences are not globally related, but share only local similarities, as is the case in genomic DNA sequences and in many protein families.

RESULTS

Using four different data sets, we show that DIALIGN is able correctly to align conserved motifs in protein sequences. Alignments produced by DIALIGN are compared systematically to the results of five other alignment programs.

AVAILABILITY

DIALIGN is available to the scientific community free of charge for non-commercial use. Executables for various UNIX platforms including LINUX can be downloaded at http://www.gsf.de/biodv/dialign.html

CONTACT

werner, morgenstern@gsf.de

In vivo labelling of the mouse brain 5-hydroxytryptamine1A receptor with the novel selective antagonist 3H-NAD-299

The in vivo labelling of 5-hydroxytryptamine (5-HT)1A receptors in the mouse brain was studied with the novel selective 5-HT1A receptor antagonist, NAD-299 ((R)-3-N,N-dicyclobutylamino-8-fluoro-3,4-dihydro-2H-1-benzopyran- 5-carboxamide hydrogen (2R,3R)-tartrate monohydrate). 3H-NAD-299 was injected in a tail vein and the radioactivity in various brain regions was determined. More than 90% of the radioactivity in hippocampus, 15 min after the injection, was intact NAD-299. At this time the amount of 3H-NAD-299 was highest in hippocampus followed by frontal cortex, mesencephalon, hypothalamus, striatum and cerebellum. The specific accumulation of radioactivity (after subtracting cerebellum values) in frontal cortex and hippocampus was maximal 10 to 30 min after the injection and had almost disappeared after 2 h. Saturation kinetics derived Bmax (pmol/g wet weight tissue) values of 19.6+/-2.0 in frontal cortex and 38.0+/-3.5 in hippocampus. The apparent Kd values expressed in nmol/kg 3H-NAD-299 injected, were 12.3+/-2.2 in frontal cortex and 20.3+/-3.1 in hippocampus. The 5-HT1A receptor antagonist, WAY-100,635 competitively inhibited the specific accumulation of 3H-NAD-299 and was about equipotent with unlabelled NAD-299 with ED50 values of 20-30 nmol/kg s.c. These compounds were about 10 times more potent than the 5-HT1A receptor antagonists, p-MPPI and NDL-249 and 100 times more potent than (S)-UH-301. 5-HT1A receptor agonists, e.g. 8-OH-DPAT and flesinoxan and partial agonists, e.g. pindolol, buspirone and ipsapirone had low potency in this in vivo assay. Spiperone and methiothepin inhibited the 3H-NAD-299 accumulation at 10 micromol/kg s.c. The alpha1-adrenoceptor antagonist, prazosin at 2 micromol/kg s.c. increased significantly the specific accumulation of 3H-NAD-299. Pretreatment of the mice with the non-selective, irreversible receptor antagonist, EEDQ produced a dose related long-lasting decrease in the accumulation of 3H-NAD-299. It is concluded that NAD-299 is a very suitable ligand for studies of 5-HT1A receptors in the brain in vivo.

Liquid Chromatographic Method for Determining Thiodicarb in Technical Products and Formulations: CIPAC Collaborative Study

A liquid chromatographic method for determining thiodicarb in technical products and formulations was evaluated by 25 participants from 19 laboratories. Data from 19 laboratories were used in statistical analysis to characterize method performance.Two technical materials, a suspension concentrate, a wettable powder, and a water dispersable granule were analyzed. Thiodicarb was determined by reversed-phase liquid chromatography using a mobile phase of methanol and water. Chromatography was performed on a C8 column with detection at 254 nm. Quantitation was achieved by using an internal standard and peak area ratios.

Specific modelling of regulatory units in DNA sequences

Transcriptional control regions are usually composed of a complex arrangement of individual transcriptional elements like protein binding sites. This modular structure allows generation of enormous functional diversity of regulatory regions with a limited set of individual elements. We implemented simple formal representations of these general features of regulatory regions into an algorithm capable of developing complex models reflecting both the element composition and the functional organization of individual elements. Our method (ModelGenerator) requires a training set of at least 10 sequences containing the regulatory regions to be modelled and a very simple initial model which may consist of just two characteristic transcription factor binding sites. We show the capability of our algorithm to expand the initial model solely by comparative sequence analysis leading to complex, biologically meaningful models. A second program (ModelInspector) is capable to scan new sequence data for matches to models defined by ModelGenerator. We show two models for retroviral transcriptional control regions to be highly specific. A search against GenBank using one of the models is shown to be free of false negatives and to produce less than 2 false positives/million nucleotides. Thus, our algorithms appear to be useful tools for the analysis of extremely long genomic sequences which are now becoming available as results of various genome sequencing projects.