Sequence protein alignment with composition new evolutions (SPACne): a program for the identification of polypeptides using amino acid composition. A user friendly modification of SPAC

SPAC (sequence protein alignment with composition) is a software that retrieve from protein or nucleic acid databases, the sequences corresponding to a protein or peptide whose only amino acid composition and molecular weight are known. By accurately matching a DNA or a protein sequence to candidate protein or peptide fragment, this software may be used as a fast and cheap method for protein characterization. This paper describes a modification of the SPAC software, SPAC new evolutions (SPACne), which enables a more efficient and user friendly method of protein identification using amino acids composition. SPACne is available online at the web site: http://bioweb.pasteur.fr/seqanal/interfaces/spacne.html.

Reactive airways dysfunction syndrome caused by bromochlorodifluoromethane from fire extinguishers

Although the neurological and cardiovascular effects of Freons have been extensively described, the respiratory effects have been less well documented. We report four cases of occupational asthma following accidental exposure to bromochlorodifluoromethane (Halon 1211) due to release of the contents of a fire extinguisher. All subjects developed an irritative reaction of the upper airways and lower respiratory symptoms immediately after exposure. Non-specific bronchial hyperreactivity was present for at least two months in all subjects and was still present more than two years after exposure in one case. The diagnosis of reactive airways dysfunction syndrome can be adopted in at least three of these four cases.

MalK, the ATP-binding cassette component of the Escherichia coli maltodextrin transporter, inhibits the transcriptional activator malt by antagonizing inducer binding

MalK, the ATP-binding cassette component of the Escherichia coli maltodextrin transporter, has long been known to control negatively the activity of MalT, a transcriptional activator dedicated to the maltose regulon. By using a biochemical approach and the soluble form of MalK as a model substrate, we demonstrate that MalK alone inhibits transcription activation by MalT in a purified transcription system. The inhibitory effect observed in vitro is relieved by maltotriose and by two malT mutations and one malK mutation known to interfere with MalT repression by MalK in vivo. MalK interacts directly with the activator in the absence of maltotriose but not in the presence of maltotriose. Conversely, MalK inhibits maltotriose binding by MalT. Altogether, these data strongly suggest that MalK and maltotriose compete for MalT binding. Part, if not all, of the MalK-binding site is located on DT1, the N-terminal domain of MalT. All of these features indicate that MalK inhibits MalT by the same mechanism as two other proteins, MalY and Aes, that also act as negative effectors of MalT by antagonizing maltotriose binding by MalT. These results offer new insights into the mechanism by which gene regulation can be accomplished by the ATPase component of a bacterial ATP-binding cassette-type importer.

Transient unidirectional acoustic streaming in annular resonators

Theoretical description of the transient process of the acoustic streaming excitation in a toroidal waveguide with driven walls is developed. Particular attention is paid to the analysis of the closed-loop (unidirectional) streaming excitation by purely propagating acoustic mode. This mode might be excited by proper phasing of the two localized acoustic sources. It is demonstrated that the evolution of the local streaming velocity can be non-monotonous in some points of the resonator cross-section. A numerical evaluation of the analytical solutions highlights the influence of the ratio of the acoustic boundary layer thickness to the waveguide width on the acoustic-streaming stabilization time. The results obtained for the acoustic streaming in the annular resonator can be useful for the analysis of the annular thermoacoustic engines and refrigerators. They might be also applied in microfluidics where there is a growing interest to different possible physical mechanisms of fluid pumping in microscale channels.

Supercontinuum and four-wave mixing with Q-switched pulses in endlessly single-mode photonic crystal fibres

Photonic crystal fibres exhibiting endlessly single-mode operation and dispersion zero in the range 1040 to 1100 nm are demonstrated. A sub-ns pump source at 1064 nm generates a parametric output at 732 nm with an efficiency of 35%, or parametric gain of 55 dB at 1315 nm. A broad, flat supercontinuum extending from 500 nm to beyond 1750 nm is also demonstrated using the same pump source.

[Outcome at 2 years of very premature infants cared at the hospital of Cayenne in 1998]

Perinatal mortality in French Guyana is twice as high as the national rates. Within a global project rallying all the people working around the birth, a catching up program benefited the neonatal unit of the Cayenne hospital in order to make up for the important lack of modern structures and means.

OBJECTIVES

To establish some quality care for the less than 33 weeks preterm infants born in 1998, and to estimate the medical and familial future for these infants after they have reached 2 years of age.

METHODS

All less than 33 weeks old infants born alive and admitted at the neonatology unit of the CHC were included in the study. The obstetrical and neonatal data were recorded from the medical files. A survey was conducted through a questionnaire including the familial and medical outcome and was led from december 1999 to july 2001. Results were analysed with Epi-info 6.0 software (CDC, Atlanta, USA).

RESULTS

Eighty-eight infants issue from 78 pregnancies were included. Among them, 29 were transferred in utero and 12 were transferred after birth. The mothers' situations were mainly characterized by precariousness, a poor follow-up of the pregnancy (27% non-declared), a higher morbidity of their newborns. Neonatal results did not differ from national results from Epipage cohort in terms of gestational age (29.9 weeks), weight at birth (1411 g), mortality (90.9 alive when released from the hospital), morbidity, growth at 2. However, 26% were hypotrophic (15% in Epipage cohort) in relation with the 29% pregnancies complicated with hypertension. Four infants were suffering from acquisition retardation due to motor handicaps; 2 infants had severe socio-educative difficulties. The postnatal follow-up was mainly performed by the Mother and Children Health Centers. A third of medical exams were not recorded in the health book, sensory screening exams were not performed. The opening of a medicosocial actions center in 2001, will allow a prospective follow-up of this population.

CONCLUSION

Early neonatal mortality decreased from 10.3 for 1000 births to 4.4 in 1998. This reflects the improvement of the new-born caring possibilities. However, an improvement of mortality rates will not be possible without a better pregnancy follow-up.

The Aes protein directly controls the activity of MalT, the central transcriptional activator of the Escherichia coli maltose regulon

MalT, the transcriptional activator of the maltose regulon from Escherichia coli, is the prototype of a new family of transcription factors. Its activity is controlled by multiple regulatory signals. ATP and maltotriose (the inducer) are two effectors of the activator that positively control its multimerization, a critical step in promoter binding. In addition, MalK, the ABC component of the maltodextrin transport system, and the two enzymes MalY and Aes down-regulate MalT activity in vivo. By using a biochemical approach, we demonstrate here that (i) Aes controls MalT activity through direct protein-protein interaction, (ii) Aes competes with maltotriose for MalT binding, (iii) ATP and ADP differentially affect the competition between Aes and the inducer, and (iv) part, if not all, of the Aes binding site is located in DT1, the N-terminal domain of the activator, which also contains the ATP binding site. All of these characteristics point toward an identical mode of action for MalY and Aes. However, we have identified an amino acid substitution in MalT that suppresses MalT inhibition by Aes without interfering with its inhibition by MalY, suggesting that the binding sites of the two inhibitory proteins do not coincide. The differential effects of ATP and ADP on the competition between the inducer and Aes (or MalY) suggest that the ATPase activity displayed by MalT plays a role in the negative control of its activity.

Suppression of Q-switch instabilities by feedback control in passively mode-locked lasers

We propose a feedback technique for obtaining stable mode-locked operation in lasers that would normally exhibit Q switching. Using the Haus model with population dynamics, we examine numerically the case in which the intensity is monitored by a slow detector and fed back to the pump power after electronic derivation. This approach allows elimination of Q switching in all situations considered, in particular, in lasers with a long upper-state lifetime.

Genome-wide protein interaction screens reveal functional networks involving Sm-like proteins

A set of seven structurally related Sm proteins forms the core of the snRNP particles containing the spliceosomal U1, U2, U4 and U5 snRNAs. A search of the genomic sequence of Saccharomyces cerevisiae has identified a number of open reading frames that potentially encode structurally similar proteins termed Lsm (Like Sm) proteins. With the aim of analysing all possible interactions between the Lsm proteins and any protein encoded in the yeast genome, we performed exhaustive and iterative genomic two-hybrid screens, starting with the Lsm proteins as baits. Indeed, extensive interactions amongst eight Lsm proteins were found that suggest the existence of a Lsm complex or complexes. These Lsm interactions apparently involve the conserved Sm domain that also mediates interactions between the Sm proteins. The screens also reveal functionally significant interactions with splicing factors, in particular with Prp4 and Prp24, compatible with genetic studies and with the reported association of Lsm proteins with spliceosomal U6 and U4/U6 particles. In addition, interactions with proteins involved in mRNA turnover, such as Mrt1, Dcp1, Dcp2 and Xrn1, point to roles for Lsm complexes in distinct RNA metabolic processes, that are confirmed in independent functional studies. These results provide compelling evidence that two-hybrid screens yield functionally meaningful information about protein-protein interactions and can suggest functions for uncharacterized proteins, especially when they are performed on a genome-wide scale.

Genome-wide protein interaction screens reveal functional networks involving Sm-like proteins

A set of seven structurally related Sm proteins forms the core of the snRNP particles containing the spliceosomal U1, U2, U4 and U5 snRNAs. A search of the genomic sequence of Saccharomyces cerevisiae has identified a number of open reading frames that potentially encode structurally similar proteins termed Lsm (Like Sm) proteins. With the aim of analysing all possible interactions between the Lsm proteins and any protein encoded in the yeast genome, we performed exhaustive and iterative genomic two-hybrid screens, starting with the Lsm proteins as baits. Indeed, extensive interactions amongst eight Lsm proteins were found that suggest the existence of a Lsm complex or complexes. These Lsm interactions apparently involve the conserved Sm domain that also mediates interactions between the Sm proteins. The screens also reveal functionally significant interactions with splicing factors, in particular with Prp4 and Prp24, compatible with genetic studies and with the reported association of Lsm proteins with spliceosomal U6 and U4/U6 particles. In addition, interactions with proteins involved in mRNA turnover, such as Mrt1, Dcp1, Dcp2 and Xrn1, point to roles for Lsm complexes in distinct RNA metabolic processes, that are confirmed in independent functional studies. These results provide compelling evidence that two-hybrid screens yield functionally meaningful information about protein-protein interactions and can suggest functions for uncharacterized proteins, especially when they are performed on a genome-wide scale.

Slow heat rate increases yeast thermotolerance by maintaining plasma membrane integrity

Thermal resistance of Saccharomyces cerevisiae was found to be drastically dependent on the kinetics of heat perturbation. Yeasts were found to be more resistant to a plateau of 1 h at 50 degrees C after a slope of temperature increase (slow and linear temperature increments) than after a shock (sudden temperature change). Thermotolerance was mainly acquired between 40-50 degrees C during a heat slope, i.e., above the maximal temperature of growth. The death of the yeasts subjected to a heat shock might be related to the loss of membrane integrity: intracellular contents extrusion, i.e., membrane permeabilization, was found to precede cell death. However, the permeabilization did not precede cell death during a heat slope and, therefore, membrane permeabilization was a consequence rather than a cause of cell death. During a slow temperature increase, yeasts which remain viable may have time to adapt their plasma membrane and thus maintain membrane integrity.