Validation of a scanning technique with minimal compression for measuring muscle volume with freehand 3D ultrasound

Freehand 3D ultrasound (3D-US) is a promising technique for measuring muscle volume but it requires gel pads or water tanks to limit probe compression on the skin which makes it hard to use in clinical applications. Our objectives were to measure the effect of different compressions on muscle volume in order to assess the clinical applicability of a minimal compression method for lower limb muscles. 4 muscles of the lower limb on 15 healthy volunteers were scanned with a new commercial freehand 3D-US setup accessible to clinical experimentators. Each muscle was scanned with 3 levels of compression: standard compression, minimal compression and gel pad (method validated against MRI). Volume was calculated using software segmentation tools. Acquisitions and segmentations were done by the same examiner. There was a significant impact of standard compression on volume measurements, but no difference between minimal compression and gel pad. Standard compression underestimated volume with a mean bias of 16 mL. For minimal compression, 75 % of measured differences were below the predefined clinically acceptable limits of 10 mL. Mean bias for this method was 1.1 mL. In conclusion, standard compression in freehand 3D-US induces a systematic bias in volume calculations. But, with a trained examiner and the necessary precautions to minimize compression, this bias could be abolished and become acceptable in clinical applications. When a high accuracy is required, gel pads could still be important to consider.

[Induced abortions for maternal indications: Retrospective study in Western Normandy between 2010 and 2019]

INTRODUCTION

Termination of pregnancy for maternal reasons (MTOP) are authorized in France without limit of term when "the continuation of the pregnancy puts in serious danger the health of the woman". The literature on the subject is rare and we wanted to make an inventory in our region.

METHODS

Retrospective observational study between 2010 and 2019 at the multidisciplinary center for prenatal diagnosis in Western Normandy.

RESULTS

Thirty-one cases of MTOP were included (2.5% of all TOP). At the CHU de Caen, they represented one in 1200 births. Twenty-three percent of MTOP had a psychosocial or psychiatric indication (average term=22 SA) and 29% an obstetric indication due to severe preeclampsia (23 SA). Finally, 48% were linked to a non-obstetric somatic disorder including 46% pre-existing pathologies (average term=11 SA), most often cardiological or nephrological and 54% diagnosed during pregnancy (17 SA) dominated by neoplasias. They were more often (68%) performed in the second trimester. Vaginal births were more frequent (74% against 26% of endouterine aspirations).

CONCLUSION

Strict medical contraindications to pregnancy are exceptional. Recourse to the medical termination of pregnancy within the framework of a preexisting pathology must remain rare, by systematizing of the preconception consultation.

Intervention of the obstetrician during childbirth in a supposedly low-risk population and influence of parity

OBJECTIVE

Compare obstetrician intervention and calling rates during labour and delivery between low-risk and high-risk women and study the influence of parity on these rates.

MATERIAL AND METHODS

Descriptive retrospective study conducted on 227 patients in a university maternity unit (level 3 university hospital maternity unit) between 1st and 30th January 2014. The low- and high-risk populations were characterised according to the French National Authority for Health (HAS) and NICE guidelines. The obstetrician intervention criteria were: Caesarean section, instrumental vaginal delivery, artificial delivery/uterus examination and postpartum haemorrhage. The obstetrical team also had to call the obstetrician in case of foetal heart rate abnormalities, scalp blood pH measurement, third and/or fourth degree perineal tears, labour dystocia, or any other severe event occurring during labour or delivery.

RESULTS

In univariate analysis, the obstetrician intervention rates were respectively 44.5% and 34.4% in the high- and low-risk groups (P=0.13). The obstetrician calling rates were similar between the two groups. Using logistic regression model including parity, the obstetrician intervention rate became significantly higher in the "high-risk" group (OR 2.044, 95% CI 1.129-3.703, P=0.018). In the low-risk population, the intervention rate was significantly increased for nulliparous women compared with multiparas (47.5% versus 9.7%, P<0.001, OR=8.2, CI 95% 2.2 to 46.9).

CONCLUSION

One third of the women defined as low-risk patients appear to need an obstetrician intervention during labour and delivery, with a major influence of parity.

The impact of compaction, moisture content, particle size and type of bulking agent on initial physical properties of sludge-bulking agent mixtures before composting

This study aimed to experimentally acquire evolution profiles between depth, bulk density, Free Air Space (FAS), air permeability and thermal conductivity in initial composting materials. The impact of two different moisture content, two particle size and two types of bulking agent on these four parameters was also evaluated. Bulk density and thermal conductivity both increased with depth while FAS and air permeability both decreased with it. Moreover, depth and moisture content had a significant impact on almost all the four physical parameters contrary to particle size and the type of bulking agent.

Effect of population aging on the international organ donation rates and the effectiveness of the donation process

This study analyzed the effect of population aging on organ donation for transplants in 43 countries and on the effectiveness of the donation process by comparing the results between Spain and the United States. The percentage of the population aged 65 or over accounted for 33% of the difference in the donation rates between the countries and for 91% of the variation in the rates after age adjustment. However, the level of aging of the Spanish (16.5%) and American (12.3%) populations failed to account for the percentages of deceased donors 65 or over (28% vs. 10%), due to the different age-specific donation rates, much higher in Spain above 50 years. These differences lead to a higher effectiveness of the process in the United States (3.1 transplanted organs per donor vs. 2.5 in Spain), though at lower rates of transplant per million population (73 vs. 87). We conclude that older populations have a greater donation potential as donation rates are strongly associated with population aging. It should therefore be mandatory to adjust donation rates for age before making comparisons. Additionally, effectiveness decreases with older donors, so age should be considered when establishing standards relating to organ donation and effectiveness of the process.

Structural characterization of two papaya chitinases, a family GH19 of glycosyl hydrolases

Two chitinases, able to use tetra-N-acetylglucosamine, chitin and chitosan as substrates, were characterized after purification from Carica papaya latex. The complete amino acid sequence of the major form and about 40% of the minor one were determined through proteolytic digestions and mass spectroscopy analysis. Sequencing demonstrated that both papaya chitinases are members of the family 19 of glycosyl hydrolases (GH19). Based on the known 3-D structures of other members of family GH19, it was expected that papaya chitinases would adopt all-alpha structures. However, circular dichroism and infrared spectroscopy indicated, for the papaya chitinases, a content of 15-20% of extended structures besides the expected 40% of alpha helices. Since the fully sequenced papaya chitinase contains a large number of proline residues the possibility that papaya chitinase contains polyproline II stretches was examined in the context of their resistance against proteolytic degradation.

Automation of sample mounting for macromolecular crystallography

A standard sample holder and vial for cryocooled macromolecular crystals has been defined for use with robotic sample changers. This SPINE standard sample holder is a modified version, with added features and specifications, of sample holders in common use. In particular, the SPINE standard meets the precision required for automatic sample exchange and includes a cap that is identified by a two-dimensional datamatrix code as well as an optional vial. At the ESRF, the sample holder standard is in use with the EMBL/ESRF/BM14 robotic sample changer (SC3) which is installed on eight beamlines. The SC3 can hold up to 50 crystals stored in five baskets. A datamatrix reader in the SC3 ensures safe management of the sample flow and facilitates fully automatic screening and characterization of samples. Tools for handling and transporting 50 samples in a dry shipping dewar have been developed. In addition to the SC3, the SPINE sample holder is currently compatible with a number of other robotic sample changers.

Fibromyxoma of the middle ear (a case report)

Fibromyxoma of the middle ear (a case report). We report an extremely rare case of fibromyxoma of the middle ear which was first suspected to be a cholesteatoma. Surgery was performed through a postauricular incision and pathologic study of the tumor gave us the final diagnosis. Fibromyxoma is an uncommon benign tumour of the head and neck region which usually arises in the jaw (1). Its local aggressivity and gelatinous consistency explain the difficulties to remove it radically and its frequent recurrences after treatment (2). Surgical resection with a wide excision seems to be the treatment of choice. Some authors advocate the use of Argon or CO2 laser to achieve the treatment. A review of the poor literature about this subject is discussed in this article.

Structure-activity relationships in platelet-activating factor (PAF). 11-From PAF-antagonism to phospholipase A(2) inhibition: syntheses and structure-activity relationships in 1-arylsulfamido-2-alkylpiperazines

1-Benzoyl-2-alkyl piperazines are strong inhibitors of Group I and II secreted PLA(2)s. An improvement of their activity was obtained by replacing the amide function by a sulfamide and by introduction of electrodonor substituents on the para position of the benzenesulfonyl moiety. Neither the position on one of the carbon of the piperazine ring nor the absolute configuration of this carbon have an effect on the affinity for one or the other group of PLA(2), but the lipophilicity remains for these series an essential parameter. In addition structure-activity relationships allow new hypothesis on interaction of these piperazine derivatives with the catalytic site of PLA(2)s.

Odorant and pheromone binding by aphrodisin, a hamster aphrodisiac protein

Aphrodisin is a soluble glycoprotein of hamster vaginal discharges, which stimulates male copulatory behavior. Natural aphrodisin was purified and its post-translational modifications characterized by MALDI-MS peptide mapping. To evaluate its ability to bind small volatile ligands, the aphrodisiac protein was expressed in the yeast Pichia pastoris as two major isoforms differing in their glycosylation degree, but close in conformation to the natural protein. Dimeric recombinant aphrodisins were equally able to efficiently bind odors (2-isobutyl-3-methoxypyrazine and methyl thiobutyrate) and a pheromone (dimethyl disulfide), suggesting that they could act as pheromone carriers instead of, or in addition to, direct vomeronasal neuron receptor activators.

Structure-activity relationships in platelet-activating factor (PAF). 10. From PAF antagonism to inhibition of HIV-1 replication

Excessive levels of PAF and cells of macrophage lineage appear to play an important role in neuronal cell injury, inflammatory syndrome, and HIV replication in CNS resulting in AIDS dementia complex (ADC). The beneficial effects of PAF receptor antagonists are evident and give rise to expected therapeutic strategies for neurotrauma. Piperazine derivatives bearing a "cache-oreilles" (ear-muff) electronic distribution are able to inhibit in vitro PAF effects and, thus, could be used in pathologies where this mediator is involved. Therefore, their potential anti-HIV activity was investigated, and we find that (i) these PAF antagonists are effectively active in HIV-infected monocyte-derived macrophages (MDM) but there is no correlation between both anti-HIV and anti-PAF activities; (ii) the presence of a carbamate function (compounds 1a-d) is favorable to the antiviral activity; (iii) the lipophilicity of the substituent on the piperazinic cycle seems to be less important for the anti-PAF activity than for the antiviral one. Our leading compound, PMS 601 (compound 1a), presents a dual activity with IC(50) of 8 and 11 microM for anti-PAF and anti-HIV activity, respectively, without cytotoxic events at 1000 microM in MDM. Although its mode of action is not clearly defined, these data suggest that PMS 601, which displays no effect on acellular reverse transcriptase or protease tests, deserves further investigation in the treatment of HIV-1-associated dementia.

Design and synthesis of imidazoline derivatives active on glucose homeostasis in a rat model of type II diabetes. 2. Syntheses and biological activities of 1,4-dialkyl-, 1,4-dibenzyl, and 1-benzyl-4-alkyl-2-(4',5'-dihydro-1'H-imidazol-2'-yl)piperazines and isosteric analogues of imidazoline

Piperazine derivatives have been identified as new antidiabetic compounds. Structure-activity relationship studies in a series of 1-benzyl-4-alkyl-2-(4',5'-dihydro-1'H-imidazol-2'-yl)piperazines resulted in the identification of 1-methyl-4-(2', 4'-dichlorobenzyl)-2-(4',5'-dihydro-1'H-imidazol-2'-yl)piperazine, PMS 812 (S-21663), as a highly potent antidiabetic agent on a rat model of diabetes, mediated by an important increase of insulin secretion independently of alpha2 adrenoceptor blockage. These studies were extended to find additional compounds in these series with improved properties. In such a way, substitution of both piperazine N atoms was first optimized by using various alkyl, branched or not, and benzyl groups. Second, some modifications of the imidazoline ring and its replacement by isosteric heterocycles were carried out, proceeding from PMS 812, to evaluate their influence on the antidiabetic activity. The importance of the distance between the imidazoline ring and the piperazine skeleton was studied third. Finally, the influence of the N-benzyl moiety was also analyzed compared to a direct N-phenyl substitution. The pharmacological evaluation was performed in vivo using glucose tolerance tests on a rat model of type II diabetes. The most active compounds were 1,4-diisopropyl-2-(4', 5'-dihydro-1'H-imidazol-2'-yl)piperazine (41a), PMS 847 (S-22068), and 1,4-diisobutyl-2-(4',5'-dihydro-1'H-imidazol-2'-yl)piperazine (41b), PMS 889 (S-22575), which strongly improved glucose tolerance without any side event or hypoglycemic effect. More particularly, PMS 847 proved to be as potent after po (100 micromol/kg) as after ip administration and appears as a good candidate for clinical investigations.

[Diagnostic value of Gram staining of peri-catheter skin and the connection in the prediction of intravascular-catheter-related bacteremia]

BACKGROUND

To evaluate the diagnostic value of Gram stain of pericatheter skin swabs and the intravascular device hub in detecting catheter-related bacteremia (CRB) in critically-ill patients.

METHODS

Over a 12-month period, 170 intravascular catheters (> 7 days in place) suspected as being the primary source of CRB were prospectively examined in adult patients admitted to 10 intensive care units of different hospitals in Spain. Blood cultures, Gram staining and culture of swabs obtained from skin entry side and catheter hub were performed before catheter removal. A semiquantitative culture of the catheter tip was carried out. Catheter-associated bacteremia was considered to be present if the same organism was isolated from the catheter tip, skin and/or hub, and blood cultures.

RESULTS

The incidence rate of CRB was 15%. Staphylococcus epidermidis was the most frequently isolated microorganism. Considered together, the sensitivity, specificity, positive predictive value and negative predictive value for Gram staining of the skin and hub were 80, 81.9, 35.3 and 97.1%, respectively.

CONCLUSIONS

The Gram stain of skin and hub swabs has a great utility in predicting CRB, specially in the absence of microorganisms. Gram stains of the above mentioned sites could be recommended as an easy and fast method to rule out the presence of CRB.

Comparison of the new acceleration spectrum analysis with other time- and frequency-domain analyses of the signal-averaged electrocardiogram

AIM

To compare four analysis techniques of the signal-averaged-electrocardiogram, including time-domain, spectral temporal mapping, spectral turbulence analysis and the new acceleration spectrum analysis.

METHODS AND RESULTS

We studied 634 subjects (77 with bundle branch block) divided into three groups. Group 1 comprised 117 post-myocardial infarction patients tested for inducibility of sustained ventricular tachycardia, and which was induced in 54 of them. Group 2 comprised 407 consecutive acute myocardial infarction survivors, followed for 1 year; 29 of them had suffered major arrhythmic events: 15 were cases of sustained ventricular tachycardia, three resuscitated ventricular fibrillation and 11 sudden cardiac death. Group 3 comprised 110 control subjects. The different analysis techniques were compared by their likelihood ratio for the prediction of ventricular tachycardia inducibility (Group 1) or major arrhythmic events (Group 2). The likelihood ratios of spectral-turbulence-analysis, acceleration spectrum analysis, spectral temporal mapping and time-domain were 8.0, 3.3, 1.7, 1.3 in Group 1, and 3.8, 2.1, 1.5, 2.6, in Group 2, while the corresponding false-positive rates in Group 3 (control) were 0.9%, 10.0%, 4.5%, and 3.6%, respectively.

CONCLUSION

Spectral turbulence analysis was the most accurate technique for the prediction of either ventricular tachycardia inducibility or major arrhythmic events after myocardial infarction. It also showed the highest specificity among control subjects.

Inhibition of tumor growth and polyamine uptake by tetracyclic amidines bearing a putrescine moiety

Tetracyclic amidines (tetrahydroquino[4.3-b][l]benzazepine: compound 11 and tetrahydrobenzo[k]naphthyridine: compound 12) bearing a putrescine moiety possess significant DNA-binding affinity. We report here that these compounds and their a and b isomers inhibit tumor cell growth and putrescine uptake in 3LL carcinoma cells in vitro. Moreover, compound 11 reduced by 50% the accumulation of putrescine in intestinal brush border membrane vesicles. In CHO-MG, a cell line deficient for the specific polyamine uptake system, the cytotoxicity of these compounds was significantly reduced compared to the CHO wild cell line. The IC50 for CHO-MG was significantly higher than for CHO, demonstrating that the polyamine transport system increased the efficacy of these compounds. The efficacy of compounds 11 and 12 might therefore be related to their ability to interact with DNA as well as their structural analogy with polyamines. Moreover, we clearly show that DFMO enhances the efficacy of these tetracyclic amidines in vivo. Potential mechanisms include: a) lower intracellular polyamine levels reduces polyamine DNA-stabilizing functions, increasing accessibility for DNA-binding drugs; b) DFMO enhances the polyamine uptake system in tumor cells, increasing the entry of tetracyclic amidines bearing a putrescine moiety as well as their accessibility to final DNA-binding sites. The fact that natural polyamine uptake is reduced by the same compounds constitutes an additive mechanism for antitumoral efficiency.

Functional interchangeability of TFIIIB components from yeast and human cells in vitro

In eukaryotes, TFIIIB is required for proper initiation by RNA polymerase III. In the yeast Saccharomyces cerevisiae a single form of TFIIIB (gammaTFIIIB) is sufficient for transcription of all pol III genes, whereas in extracts derived from human cells two different hTFIIIB complexes exist which we have previously designated as hTFIIIB-alpha and hTFIIIB-beta. Human TFIIIB-alpha is a TBP-free entity and must be complemented by TBP for transcription of pol III genes driven by gene external promoters, whereas hTFIIIB-beta is a TBP-TAF complex which governs transcription from internal pol III promoters. We show that hTFIIIB-beta cannot be replaced by yeast TFIIIB for transcription of tRNA genes, but that the B" component of gammaTFIIIB can substitute for hTFIIIB-alpha activity in transcription of the human U6 gene. Moreover, hTFIIIB-alpha can be chromatographically divided into activities which are functionally related to gammaTFIIIE and recombinant yB"90, suggesting that hTFIIIB-alpha is a human homolog of yeast TFIIIB". In addition, we show that yeast TBP can only be exchanged against human TBP for in vitro transcription of the human and yeast U6 gene but virtually not for that of the yeast tRNA4Sup gene. This deficiency can be counteracted by a mutant of human TBP (R231K) which is able to replace yeast TBP for transcription of yeast tRNA genes in vitro.

A cryptic DNA binding domain at the COOH terminus of TFIIIB70 affects formation, stability, and function of preinitiation complexes

TFIIIC-dependent assembly of yeast TFIIIB on class III genes unmasks a high avidity of TFIIIB for DNA. TFIIIB contains TATA-binding protein (TBP), TFIIIB90/B", and TFIIIB70/Brf1, which is homologous to TFIIB. Using limited proteolysis, we have found that the COOH terminus of TFIIIB70 (residues 510-596) forms a protease-resistant domain that binds DNA tightly as seen by Southwestern, DNase I footprinting, and gel shift assays. Consistent with a role for this DNA binding activity, preinitiation complexes were formed less efficiently with truncated TFIIIB70 lacking the COOH-terminal domain and displayed an increased sensitivity to heparin. B' (TFIIIB70 + TBP).TFIIIC.DNA complexes were also particularly unstable. In addition, TFIIIB.TFIIIC.DNA complexes containing truncated TFIIIB70 were impaired in promoting transcription initiation.

Design and modeling of new platelet-activating factor antagonists. 3. Relative importance of hydrophobicity and electronic distribution in piperazinic series

Extensive analysis of results obtained in earlier publications (Lamouri et al. (1993); Tavet et al. (1996) led us to reexamine our interpretations and conclusions about hydrophobic and electronic distribution effects. In terms of hydrophobicity balance, a bilinear regression has been derived between lipophilicity of the appendix in position-2, f(Z), versus anti-aggregant activity for 45 homogeneous compounds including data from both papers (Parts 1 and 2). These features reinforce the conclusion that the kinetic phase in the experimental medium is probably determinant. Consequently, the role of electronic distribution is preponderant at the level of the receptor. Two specific studies demonstrated that decrease of negative electrostatic potential effects of the largest "cache-oreilles' system lowered the anti-aggregant activity (comparison of compounds 1f, 2, 3 and 4), on one hand and, on the other hand, the combined effect of phenyl groups created negative wells, as observed there with a diphenyl-methyl moiety, instead of an usual trimethoxybenzoyl function (comparison of compounds 8 and 10). It was clearly demonstrated that this moiety does not work by means of a hydrophobic anchorage: comparison of compounds 9, 10 and 11.

Localization of yeast RNA polymerase I core subunits by immunoelectron microscopy

Immunoelectron microscopy was used to determine the spatial organization of the yeast RNA polymerase I core subunits on a three-dimensional model of the enzyme. Images of antibody-labeled enzymes were compared with the native enzyme to determine the localization of the antibody binding site on the surface of the model. Monoclonal antibodies were used as probes to identify the two largest subunits homologous to the bacterial beta and beta' subunits. The epitopes for the two monoclonal antibodies were mapped using subunit-specific phage display libraries, thus allowing a direct correlation of the structural data with functional information on conserved sequence elements. An epitope close to conserved region C of the beta-like subunit is located at the base of the finger-like domain, whereas a sequence between conserved regions C and D of the beta'-like subunit is located in the apical region of the enzyme. Polyclonal antibodies outlined the alpha-like subunit AC40 and subunit AC19 which were found co-localized also in the apical region of the enzyme. The spatial location of the subunits is correlated with their biological activity and the inhibitory effect of the antibodies.

Interactions between yeast TFIIIB components

Yeast transcription factor TFIIIB is a multicomponent factor comprised of the TATA-binding protein TBP and of associated factors TFIIIB70 and B". Epitope-tagged or histidine-tagged TFIIIB70 could be quantitatively removed from TFIIIB by affinity chromatography. TBP and B" (apparent mass 160-200 kDa) could be easily separated by gel filtration or ion-exchange chromatography. While only weak interactions were detected between TBP and B", direct binding of [35S]-labeled TBP to membrane-bound TFIIIB70 could be demonstrated in absence of DNA. On tRNA genes, there was no basal level of transcription in the complete absence of TBP. The two characterized TFIIIB components (recombinant rTFIIIB70 and rTBP) and a fraction cochromatographing with B" activity were found to be required for TFIIIC-independent transcription of the TATA-containing U6 RNA gene in vitro. Therefore, beside the TFIIIC-dependent assembly process, each TFIIIB component must have an essential role in DNA binding or RNA polymerase recruitment.

Interactions between yeast TFIIIB components

Yeast transcription factor TFIIIB is a multicomponent factor comprised of the TATA-binding protein TBP and of associated factors TFIIIB70 and B". Epitope-tagged or histidine-tagged TFIIIB70 could be quantitatively removed from TFIIIB by affinity chromatography. TBP and B" (apparent mass 160-200 kDa) could be easily separated by gel filtration or ion-exchange chromatography. While only weak interactions were detected between TBP and B", direct binding of [35S]-labeled TBP to membrane-bound TFIIIB70 could be demonstrated in absence of DNA. On tRNA genes, there was no basal level of transcription in the complete absence of TBP. The two characterized TFIIIB components (recombinant rTFIIIB70 and rTBP) and a fraction cochromatographing with B" activity were found to be required for TFIIIC-independent transcription of the TATA-containing U6 RNA gene in vitro. Therefore, beside the TFIIIC-dependent assembly process, each TFIIIB component must have an essential role in DNA binding or RNA polymerase recruitment.

Competition between chromatin and transcription complex assembly regulates gene expression during early development

Xenopus early development is characterized by a generalized absence of transcription, which resumes at the midblastula transition (MBT). We analyzed this regulation using a plasmid containing the c-myc promoter that is under the same developmental control when injected into fertilized eggs. We find that the repression of transcription can be relieved simply by preincubating the reporter plasmid with TATA binding protein (TBP). However, the repression of gene activity normally occurring before the MBT soon becomes dominant over this activation independent of cell cycle phases. This inactivation correlates with chromatin assembly, and titration of chromatin components not only relieves repression of TBP-dependent transcription but also permits the establishment of stable transcription during early development. Our data suggest that the large excess of histones represses gene activity during early development through a dynamic competition between chromatin assembly and transcription complex assembly.

Point mutations 5' to the tRNA selenocysteine TATA box alter RNA polymerase III transcription by affecting the binding of TBP

The selenocysteine tRNA(Sec) gene possesses two external promoter elements, one of which is constituted by a strong TATA box. Point mutant analysis performed in this study led to the conclusion that the functional TATA promoter actually encompasses the sequence -34 GGGTATAAAAGG-23. Individual changes at T-31 do not affect transcription much. Position T-29 is less permissive to mutation since transversion to a G, for example, is less well tolerated than at T-31. Interestingly, a double point mutation, converting GG(-33/-32) to TT, causes abrogation of transcription in vivo and severe reduction of transcription in vitro with human TBP. Therefore, data obtained underscore the fact that, in the Xenopus tRNA(Sec), these two Gs are an integral part of the TATA promoter. Gel retardation experiments indicate that the GG to TT substitution, which led human TBP to lose its ability to support efficient transcription in vitro, correlates with the appearance of an altered pattern of retarded complexes. Altogether, the data presented in this report support a model in which TBP interacts directly with the TATA element of the tRNA(Sec) gene, in contrast to the type of interaction proposed for classical TATA-less tRNA genes.

TFIIIC relieves repression of U6 snRNA transcription by chromatin

The U6 small nuclear (sn)RNA gene (SNR6) from the yeast Saccharomyces cerevisiae is transcribed by RNA polymerase III in vivo. This gene is unusual in having a TATA box at position -30, and an essential B-block element located downstream of the T-rich termination signal. The B block is one of the two intragenic promoter elements of transfer RNA genes that are recognized by transcription factor (TF)IIIC (ref. 4). But accurate in vitro transcription of yeast U6 snRNA gene by PolIII in a purified system requires only TFIIIB components, including the TATA-box binding protein TBP. Here we report that, after nucleosome reconstitution or chromatin assembly, U6 snRNA synthesis becomes dependent on TFIIIC and on the integrity of the B-block element. This observation resolves an apparent paradox between in vitro and in vivo results concerning the necessity of the downstream B-block element and sheds light on a new role of TFIIIC in gene activation.

The TATA-binding protein participates in TFIIIB assembly on tRNA genes

The TATA-binding protein TBP has been recently recognized as a general class III transcription factor. Using the gel shift assay to monitor initiation complex assembly on a yeast tRNA gene, we show that TBP is required for the TFIIIC-dependent assembly of TFIIIB. TFIIIB depleted of TBP by a simple chromatographic step does not bind stably to the TFIIIC-tDNA complex. Addition of yeast or human recombinant TBP allows the formation of a TFIIIB-TBP-TFIIIC-tDNA complex. The presence of TBP in the complex was inferred from the effect of anti-TBP antibodies and from the different migration properties of TFIIIB-TBP-tDNA complexes formed with yeast or human TBP.

Influence of pretreatment clinical characteristics on the response rate to mitomycin/vindesine/cisplatin (MVP) in unresectable non-small cell lung cancer. ATTIT (Association pour le Traitement des Tumeurs Intra-Thoraciques)

The authors report their experience with the MVP (mitomycin/vindesine/cisplatin) regimen of the Memorial Sloan-Kettering Cancer Center (MSKCC) which showed the highest response rate in non-small cell lung cancer (NSCLC). The aim was to respect the original reported schedule to appreciate its activity, because the same drug combination with dose and schedule variations used by other investigators has failed to reproduce the original report results. 82 consecutive previously untreated patients with unresectable and/or metastatic NSCLC received mitomycin (8 mg/m2 days 1, 29, 71), vindesine (3 mg/m2, days 1, 8, 15, 22, 29, 43, 57, 71) and cisplatin (120 mg/m2, days 1, 29, 71), with evaluation on day 71. 24 objective responses were noted (29%) (2 complete response/22 partial response) (95% CI 19%-39%), without differences according to histology. Differences in median survival were noted according to the performance status and type of response. Overall survival rates in responding patients were similar to those noted with the original schedules. Analysis of selection criteria showed that there were more patients with bone (P less than 0.01) or liver metastases (P less than 0.05), less women (P less than 0.001) and less adenocarcinoma (P less than 0.001) than the MSKCC trial. A dose intensity analysis showed only a minimal difference in the average weekly doses of vindesine (10% lower than MSKCC trial: 1.8 mg/m2 vs. 2.25 mg/m2). Disease improvement, a subjective response criterion used in the MSKCC trial, was probably underestimated in the current study. We conclude that the potential benefit of chemotherapy with a three-drug combination in NSCLC is greatest in patients with stage IIIa and IIIb disease or stage IV disease with a good performance status and a low metastatic volume.

Identification of the genes coding for the second-largest subunits of RNA polymerases I and III of Drosophila melanogaster

We have isolated cDNA and genomic clones of Drosophila melanogaster by cross-hybridization with a 658 bp fragment of the yeast gene coding for the second-largest subunit of RNA polymerase III (RET1). Determination of the sequence by comparison of genomic and cDNA regions reveals an ORF of 3405 nucleotides which is interrupted in the genomic sequence by an intron of 48 bp. The deduced polypeptide consists of 1135 amino acids with a calculated molecular weight of 128 kDa. The protein sequence shows the same conserved regions of homology as those observed for all the second-largest subunits of RNA polymerases cloned so far. The gene (DmRP128) obviously codes for a second-largest subunit of an RNA polymerase which is different from DmRP140 and DmRP135. We have purified three distinct RNA polymerase activities from D. melanogaster. By using specific RNA polymerase inhibitors in enzyme assays and by comparing their subunit composition we were able to distinguish between RNA polymerase I, II, and III. RNA polymerase preparations of D. melanogaster were blotted and the second-largest subunits were identified with antibodies raised against polypeptides expressed from DmRP128 and DmRP135. Anti-DmRP135 antibodies react strongly with the second-largest subunit of RNA polymerase I but do not react with the respective subunits of RNA polymerase II and III. The second-largest subunit of RNA polymerase III is only recognized by anti-DmRP128. Previously, we have claimed that DmRP135 codes for the second-largest subunit of RNA polymerase III.(ABSTRACT TRUNCATED AT 250 WORDS)

Participation of the TATA factor in transcription of the yeast U6 gene by RNA polymerase C

Fractionation of transcription extracts has led to the identification of multiple transcription factors specific for each form of nuclear RNA polymerase. Accurate transcription in vitro of the yeast U6 RNA gene by RNA polymerase C requires at least two factors. One of them was physically and functionally indistinguishable from transcription factor IID (TFIID or BTF1), a pivotal component of polymerase B transcription complexes, which binds to the TATA element. Purified yeast TFIID (yIID) or bacterial extracts that contained recombinant yIID were equally competent to direct specific transcription of the U6 gene by RNA polymerase C. The results suggest the formation of a hybrid transcription machinery, which may imply an evolutionary relation between class B and class C transcription factors.

Contacts between the factor TUF and RPG sequences

The yeast TUF factor binds specifically to RPG-like sequences involved in multiple functions at enhancers, silencers, and telomeres. We have characterized the interaction of TUF with its optimal binding sequence, rpg-1 (1-ACACCCATACATTT-14), using a gel DNA-binding assay in combination with methylation protection and mutagenesis experiments. As many as 10 base pairs appear to be engaged in factor binding. Analysis of a collection of 30 different RPG mutants demonstrated the importance of 8 base pairs at position 2, 3, 4, 5, 6, 7, 10, and 12 and the critical role of the central GC pair at position 5. Methylation protection data on four different natural sites confirmed a close contact at positions 4, 5, 6, and 10 and suggested additional contacts at base pairs 8, 12, and 13. The derived consensus sequence was RCAAYCCRYNCAYY. A quantitative band shift analysis was used to determine the equilibrium dissociation constant for the complex of TUF and its optimal binding site rpg-1. The specific dissociation constant (K8) was found to be 1.3 x 10(-11) M. The comparison of the K8 value with the dissociation constant obtained for nonspecific DNA sites (Kn8 = 8.7 x 10(-6) M) shows the high binding selectivity of TUF for its specific RPG target.

Electron microscopic study of yeast RNA polymerase A: analysis of single molecular images

The structural features of the yeast DNA-dependent RNA polymerase A (I) were examined by Scanning Transmission Electron Microscopy. The enzyme was absorbed in its monomeric form and negatively stained prior to digital image acquisition at low dose. The signal to noise ratio of single particle images was improved through averaging of a large number of previously aligned and partitioned images. Six classes of images were obtained reproducibly which corresponded to different projections of the enzyme. The enzyme structure was characterized by its presence of two curved arms which defined a longitudinal cleft. By analogy with the Escherichia coli enzyme, these arms could correspond to the two large subunits A135 and A190.

A yeast activity can substitute for the HeLa cell TATA box factor

Most class B (II) promoter regions from higher eukaryotes contain the TATA box and upstream and enhancer elements. Both the upstream and enhancer elements and their cognate factors have regulatory functions, whereas the TATA sequence interacts with the TATA box factor BTF1 to position RNA polymerase B and its ancillary initiation factors (STF, BTF2 and BTF3) to direct the initiation of transcription approximately 30 base pairs downstream. In many respects, class B promoter regions from the unicellular eukaryote Saccharomyces cerevisiae are similarly organized, containing upstream activating sequences that bear many similarities to enhancers. Although they are essential for initiation, the yeast TATA sequences are located at variable distances and further from the start sites (40-120 base pairs), whose locations are primarily determined by an initiator element. The basic molecular mechanisms that control initiation of transcription are known to be conserved from yeast to man: the yeast transcriptional transactivator GAL4 can activate a minimal TATA box-containing promoter in human HeLa cells, and a human inducible enhancer factor, the oestrogen receptor, can activate a similar minimal promoter in yeast. This striking evolutionary conservation prompted us to look for the presence in yeast of an activity that could possibly substitute for the human TATA box factor. We report here the existence of such an activity in yeast extracts.

TUF, the yeast DNA-binding factor specific for UASrpg upstream activating sequences: identification of the protein and its DNA-binding domain

The factor TUF interacts specifically with RPG or HOMOL1 sequences, which are present upstream of many genes coding for the yeast translational apparatus. Here we present evidence that the RPG and HOMOL1 motifs are variants of a consensus UASrpg (upstream activating sequence) recognized by the same factor. Factor TUF was identified by using two highly selective methods. The DNA-protein complex was isolated by pore-limit electrophoresis in polyacrylamide gradient gels and found to contain a single polypeptide of 150 kDa. In a two-step protein-blotting/nuclease-protection ("footprinting") procedure, the same 150-kDa polypeptide blotted on nitrocellulose exhibited the same specific DNA-binding properties as TUF factor. A 50-kDa DNA-binding domain of TUF was isolated by selective proteolysis. This suggests a bipolarization of the TUF protein, with distinct functional domains.

Catalytic activity of a copper(II)-oxidized glutathione complex on aqueous superoxide ion dismutation

The study of the catalytic activity of a Cu(II)-oxidized glutathione system upon the disproportionation of superoxide radicals shows that the mononuclear complex MA catalyzes dismutation in the pH range 7-9. The corresponding first-order rate constant of value kcat congruent to 6 X 10(6) M-1 sec-1 is pH independent, whereas the second-order rate constant ks for the reference solutions is pH dependent. The kcat constant is about 10-, 100-, and 300-fold higher than the ks constant at pH 7, 8, and 9, respectively. The measured effect is explained in terms of free axial sites in the square-planar arrangement around the copper ion.

Isolation of structural genes for yeast RNA polymerases by immunological screening

A lambda gt11 yeast genomic library was screened with antibodies directed against yeast RNA polymerases A, B, and C. Thirty-five individual recombinant phages that expressed proteins in Escherichia coli that were antigenically related to RNA polymerases A, B, or C were isolated by using 22 distinct antisera. Thus, all 22 genes for the RNA polymerase subunits were potentially cloned. In three cases (lambda A-43, lambda A-40, and lambda A-34.5), an antigenic protein was expressed in E. coli with the same molecular weight as the corresponding subunit. When lambda A-40 DNA was used to hybrid-select yeast mRNA, the protein translated in vitro was the expected size for the A-40 subunit, further supporting our isolation of the A-40 gene. However, mRNA hybrid selected by lambda A-27 DNA did not code for a protein of the correct size. The lengths of the mRNA that hybridized to phage lambda A-190 or lambda C-160 DNA on RNA blots were in agreement with the predicted sizes of the coding regions of the corresponding genes. As predicted by our previous immunological results, yeast DNA inserts of the lambda A-190 and lambda C-160 clones cross-hybridized to the B-220 subunit gene. The cloned genes for the RNA polymerase subunits will prove to be valuable tools for the study of the function, regulation, and genetics of the yeast RNA polymerases.

A general upstream binding factor for genes of the yeast translational apparatus

Fractionation of yeast extracts on heparin-agarose revealed the presence of a DNA footprinting activity that interacted specifically with the 5'-upstream region of TEF1 and TEF2 genes coding for the protein synthesis elongation factor EF-1 alpha, and of the ribosomal protein gene RP51A. The protected regions encompassed the conserved sequences 'HOMOL1' (AACATC TA CG T A G CA) or RPG-box (ACCCATACATT TA) previously detected 200-400 bp upstream of most of the yeast ribosomal protein genes examined. Two types of protein-DNA complexes were separated by a gel electrophoresis retardation assay. Complex 1, formed on TEF1, TEF2 and RP51A 5'-flanking region, was correlated with the protection of a 25-bp sequence. Complex 2, formed on TEF2 or RP51A probes at higher protein concentrations, corresponded to an extended footprint of 35-40 bp. The migration characteristics of the protein-DNA complexes and competition experiments indicated that the same component(s) interacted with the three different promoters. It is suggested that this DNA factor(s) is required for activation and coordinated regulation of the whole family of genes coding for the translational apparatus.

Yeast RNA polymerase C and its subunits. Specific antibodies as structural and functional probes

Yeast RNA polymerase C purified by a simple large scale method was resolved into multiple components by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Specific antibodies directed against each polypeptide chain were prepared in rabbits and used as structural and functional probes. With minor exceptions, each antibody recognized specifically the corresponding polypeptide by blot-immunodetection. Cross-reactions with purified RNA polymerases A and B confirmed our previous description of the subunits shared by the three nuclear RNA polymerases. Immunoadsorption of RNA polymerase C at different stages of purification using antibodies to subunits C160 and C128 yielded the same collection of polypeptides as found in the purified enzyme: C160, C128, C82, C53, C40, C37, C34, C31, C27, C25, C23, C19, C14.5, C12.5, and C10. Subunit-specific antibodies were used to probe the activity of RNA polymerase C in a specific, reconstituted transcription system as well as on a nonspecific template. Transcription of the tRNAGlu3 gene in vitro was inhibited when RNA polymerase C was preincubated with antibodies directed to C128, C82, C53, C34, C23, or C19. Antibodies to C82, C53, and C34 were much less inhibitory in the nonspecific assay. Inhibition by anti-C128 or anti-C23 was relieved by preincubation of enzyme C with plasmid DNA prior to antibody addition. These results are discussed in terms of the participation of these polypeptides to the active enzyme molecule, and of their possible role in DNA binding or transcription factor recognition.