The critical role of urease in yogurt fermentation with various combinations of Streptococcus thermophilus and Lactobacillus delbrueckii ssp. bulgaricus.

The protocooperation between Streptococcus thermophilus and Lactobacillus delbrueckii ssp. bulgaricus relies on metabolite exchanges that accelerate acidification during yogurt fermentation. Conflicting results have been obtained in terms of the effect of the Strep. thermophilus urease and the NH3 and CO2 that it generates on the rate of acidification in yogurt fermentation. It is difficult to perform a systematic study of the effects of urease on protocooperation because it is necessary to distinguish among the direct, indirect, and strain-specific effects resulting from the combination of the strains of both species. To evaluate the direct effects of urease on protocooperation, we generated 3 urease-deficient mutants (ΔureC) of fast- and slow-acidifying Strep. thermophilus strains and observed the effects of NH3 or CO2 supplementation on acidification by the ΔureC strains. Further, we examined 5 combinations of 3 urease-deficient ΔureC strains with 2 CO2-responsive or CO2-unresponsive strains of L. bulgaricus. Urease deficiency induced a shortage of ammonia nitrogen and CO2 for the fast- and slow-acidifying Strep. thermophilus and for the CO2-responsive L. bulgaricus, respectively. Notably, the shortage of ammonia nitrogen had more severe effects than that of CO2 on yogurt fermentation, even if coculture with L. bulgaricus masked the effect of urease deficiency. Our work established (1) that urease deficiency inhibits the fermentative acceleration of protocooperation regardless of the Strep. thermophilus and L. bulgaricus strain combinations, and (2) that urease is an essential factor for effective yogurt acidification.

Development of Microbiome Biobanks - Challenges and Opportunities.

The microbiome research field is rapidly evolving, but the required biobanking infrastructure is currently fragmented and not prepared for the biobanking of microbiomes. The rapid advancement of technologies requires an urgent assessment of how biobanks can underpin research by preserving microbiome samples and their functional potential.

AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system.

We have implemented a genome annotation system for prokaryotes called AGMIAL. Our approach embodies a number of key principles. First, expert manual annotators are seen as a critical component of the overall system; user interfaces were cyclically refined to satisfy their needs. Second, the overall process should be orchestrated in terms of a global annotation strategy; this facilitates coordination between a team of annotators and automatic data analysis. Third, the annotation strategy should allow progressive and incremental annotation from a time when only a few draft contigs are available, to when a final finished assembly is produced. The overall architecture employed is modular and extensible, being based on the W3 standard Web services framework. Specialized modules interact with two independent core modules that are used to annotate, respectively, genomic and protein sequences. AGMIAL is currently being used by several INRA laboratories to analyze genomes of bacteria relevant to the food-processing industry, and is distributed under an open source license.

Plasmid addiction genes of bacteriophage P1: doc, which causes cell death on curing of prophage, and phd, which prevents host death when prophage is retained.

P1 lysogens of Escherichia coli carry the prophage as a stable low copy number plasmid. The frequency with which viable cells cured of prophage are produced is about 10(-5) per cell per generation. Here we show that a significant part of this remarkable stability can be attributed to a plasmid-encoded mechanism that causes death of cells that have lost P1. In other words, the lysogenic cells appear to be addicted to the presence of the prophage. The plasmid withdrawal response depends on a gene named doc (death on curing), encoding a 126 amino acid protein. Expression of doc is not SOS-inducing and killing by Doc is recA-independent. In cells that retain P1 the killing is prevented by the product of a gene named phd (prevent host death), encoding a 73 amino acid protein. The genes phd and doc have been cloned and expressed from a 0.7 kb segment of P1 DNA. The two genes constitute an operon and the synthesis of Doc appears to be translationally coupled to that of Phd. Homologs of the P1 addiction genes are found elsewhere, but phd and doc are unrelated to previously described genes of other plasmids that also cause an apparent increase in plasmid stability by post-segregational killing.

Developmental risk factors for youth violence.

PURPOSE: To replicate earlier research findings on risk factors for youth violence and to explore the effects on violent behavior of constructs shown to increase risk for other problem behaviors, within a developmental frame. METHODS: Data were from the Seattle Social Development Project (SSDP), a prospective study involving a panel of youths followed since 1985. Potential risk factors for violence at age 18 years were measured at ages 10, 14, and 16 years. Bivariate relationships involving risk factor constructs in the individual, family, school, peer and community domains and violence were examined at each age to assess changes in their strength of prediction over time. Attention was also given to the additive strength of increasing numbers of risk factors in the prediction of violence at age 18 years. A final set of analyses explored the extent to which youths were correctly classified as having committed a violent act (or not) at age 18 years on the basis of their overall level of risk at ages 10, 14, and 16 years. RESULTS: At each age, risk factors strongly related to later violence were distributed among the five domains. Ten of 15 risk factors constructs measured at age 10 years were significantly predictive of violence at age 18 years. Twenty of 25 constructs measured at age 14 years and 19 of 21 constructs measured at age 16 years were significantly predictive of later violence. Many constructs predicted violence from more than one developmental point. Hyperactivity (parent rating), low academic performance, peer delinquency, and availability of drugs in the neighborhood predicted violence from ages 10, 14, and 16 years. Analyses of the additive effects of risk factors revealed that youths exposed to multiple risks were notably more likely than others to engage in later violence. The odds for violence of youths exposed to more than five risk factors compared to the odds for violence of youths exposed to fewer than two risk factors at each age were seven times greater at age 10 years, 10 times greater at age 14 years, and nearly 11 times greater at age 16 years. However, despite information gained from all significant risk factors, the overall accuracy in predicting youths who would go on to commit violent acts was limited. CONCLUSIONS: Findings from the study have important implications for preventive intervention programs. Prevention efforts must be comprehensive and developmentally sensitive, responding to large groups or populations exposed to multiple risks.

Exploring the effects of age of alcohol use initiation and psychosocial risk factors on subsequent alcohol misuse.

OBJECTIVE: This study examines whether the age of initiation of alcohol use mediates the effects of other variables that predict alcohol misuse among adolescents and also whether the age of initiation of alcohol use accounts for known gender differences in the severity of alcohol misuse. METHOD: Data were taken from an ethnically diverse sample of 808 (412 male) students who were recruited in grade 5 at age 10-11 and followed prospectively on an annual basis for the next 7 years to age 17-18. State-of-the-art missing data methodology was used to address nonresponse due to noninitiation of alcohol use. Structural equation modeling was used to examine hypotheses for the prediction of alcohol misuse. RESULTS: A younger age of alcohol initiation was strongly related to a higher level of alcohol misuse at age 17-18 and fully mediated the effects of parent drinking, proactive parenting, school bonding, peer alcohol initiation and ethnicity, all measured at age 10-11, and perceived harmfulness of alcohol use, measured at age 10-11 and age 11-12. However, age of alcohol initiation did not fully account for gender differences in the level of alcohol misuse at age 17-18. To further examine the role of gender, interactions between gender and school bonding, and gender and friend's alcohol initiation, were evaluated. However, neither of the interaction terms had direct effects on either age of initiation or level of alcohol-related problems. CONCLUSIONS: Most measured risk factors for alcohol misuse were mediated through age of alcohol initiation. Only gender differences in alcohol misuse at age 17-18 were not mediated by age of alcohol initiation. Variables associated with these differences require further study. The results of this study indicate the importance of prevention strategies to delay the age of initiation of alcohol use.

Alcohol, drugs, and violence in children's lives.

This chapter reviews the current state of knowledge concerning the interrelationship between the cycle of alcohol and other drugs (AOD) use and the cycle of violence. This issue is framed in terms of two questions. The first is the extent to which AOD use by the perpetrator is related to the perpetration of violence toward children, defined here as including both physical and sexual abuse. The second question is whether the experience of abuse during childhood is related to the subsequent development of the abuse of alcohol and other drugs. The review indicates that parental AOD abuse is related to physical and sexual abuse. However, because most perpetrators are not parents, the relationship is not yet clear. The data do support the link between experiencing childhood violence and the development of later AOD abuse. Theoretical explanations for each link are reviewed and mediating variables are identified. The review concludes with a presentation of methodological issues and the directions for future research.

Assessment of sensitivity to interpersonal stress in stutterers.

The Willoughby Personality Schedule-R was administered to adult male Yugoslav stutterers who were not yet in treatment. Internal consistency of the WPS-R was assessed by computing item-scale score correlations. Twenty-two of 25 items were significantly correlated with WPS-R total score. Confirmatory factor analysis revealed three separate and reliable dimensions: Social Isolation (ssca .85), Social Confidence (ssca .74), and Social Sensitivity (ssca = .62), that were identical to those previously found for American stutterers. Although WPS-R scores were unrelated to several measures of stuttering severity, analysis of extreme scores suggested support for the hypothesis that general anxiety moderates stuttering severity. Overall the results are consistent with the contention that hypersensitivity to interpersonal stress is manifested in stutterers as general anxiety, which is better conceptualized as occurring along a continuum than as reflecting generic "overwhelming anxiety" in stutterers.

Time spent with child and parental agreement about preschool children's behavior.

Although there is a common core of agreement in parental perceptions of their preschool-age sons' problem behavior, perceptions of 107 parents became more concordant as fathers increased the amount of time they spent with their sons. At least within the context of a sample who were at risk for developing abuse of alcohol or other substances and antisocial behavior, fathers who spent less time with their sons perceived them to be less troubled than mothers perceived them to be.

Induction of heavy-metal-transporting CPX-type ATPases during acid adaptation in Lactobacillus bulgaricus.

Lactobacillus bulgaricus is a lactic acid bacteria (LAB) that, through the production of lactic acid, gradually acidifies its environment during growth. In the course of this process, L. bulgaricus acquires an improved tolerance to acidity. A survey of the recently established genome sequence shows that this bacterium possesses few of the pH control functions that have been described in other LAB and raises the question of what other mechanisms could be involved in its adaptation to the decreasing environmental pH. In some bacteria other than LAB, ion transport systems have been implicated in acid adaptation. We therefore studied the expression of this type of transport system during acid adaptation in L. bulgaricus by reverse transcription and real-time quantitative PCR and mapped transcription start sites. Intriguingly, the most significantly induced were three ATPases carrying the CPX signature of heavy-metal transporters. Protein homology and the presence of a conserved sequence motif in the promoter regions of the genes encoding these proteins strongly suggest that they are involved in copper homeostasis. Induction of this system is thought to assist in avoiding indirect damage that could result from medium acidification.

The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution.

Lactobacillus delbrueckii ssp. bulgaricus (L. bulgaricus) is a representative of the group of lactic acid-producing bacteria, mainly known for its worldwide application in yogurt production. The genome sequence of this bacterium has been determined and shows the signs of ongoing specialization, with a substantial number of pseudogenes and incomplete metabolic pathways and relatively few regulatory functions. Several unique features of the L. bulgaricus genome support the hypothesis that the genome is in a phase of rapid evolution. (i) Exceptionally high numbers of rRNA and tRNA genes with regard to genome size may indicate that the L. bulgaricus genome has known a recent phase of important size reduction, in agreement with the observed high frequency of gene inactivation and elimination; (ii) a much higher GC content at codon position 3 than expected on the basis of the overall GC content suggests that the composition of the genome is evolving toward a higher GC content; and (iii) the presence of a 47.5-kbp inverted repeat in the replication termination region, an extremely rare feature in bacterial genomes, may be interpreted as a transient stage in genome evolution. The results indicate the adaptation of L. bulgaricus from a plant-associated habitat to the stable protein and lactose-rich milk environment through the loss of superfluous functions and protocooperation with Streptococcus thermophilus.

Lactococcus lactis and stress.

It is now generally recognized that cell growth conditions in nature are often suboptimal compared to controlled conditions provided in the laboratory. Natural stresses like starvation and acidity are generated by cell growth itself. Other stresses like temperature or osmotic shock, or oxygen, are imposed by the environment. It is now clear that defense mechanisms to withstand different stresses must be present in all organisms. The exploration of stress responses in lactic acid bacteria has just begun. Several stress response genes have been revealed through homologies with known genes in other organisms. While stress response genes appear to be highly conserved, however, their regulation may not be. Thus, search of the regulation of stress response in lactic acid bacteria may reveal new regulatory circuits. The first part of this report addresses the available information on stress response in Lactococcus lactis. Acid stress response may be particularly important in lactic acid bacteria, whose growth and transition to stationary phase is accompanied by the production of lactic acid, which results in acidification of the media, arrest of cell multiplication, and possible cell death. The second part of this report will focus on progress made in acid stress response, particularly in L. lactis and on factors which may affect its regulation. Acid tolerance is presently under study in L. lactis. Our results with strain MG1363 show that it survives a lethal challenge at pH 4.0 if adapted briefly (5 to 15 minutes) at a pH between 4.5 and 6.5. Adaptation requires protein synthesis, indicating that acid conditions induce expression of newly synthesized genes. These results show that L. lactis possesses an inducible response to acid stress in exponential phase. To identify possible regulatory genes involved in acid stress response, we determined low pH conditions in which MG1363 is unable to grow, and selected at 37 degrees C for transposition insertional mutants which were able to survive. About thirty mutants resistant to low pH conditions were characterized. The interrupted genes were identified by sequence homology with known genes. One insertion interrupts ahrC, the putative regulator of arginine metabolism; possibly, increased arginine catabolism in the mutant produces metabolites which increase the pH. Several other mutations putatively map at some step in the pathway of (p)ppGpp synthesis. Our results suggest that the stringent response pathway, which is involved in starvation and stationary phase survival, may also be implicated in acid pH tolerance.

Identification of stress-inducible proteins in Lactobacillus delbrueckii subsp. bulgaricus.

Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus) is a homofermentative bacterium that produces lactic acid during growth. We adapted the two-dimensional electrophoresis (2-DE) technique to study the response of this bacterium to acidity. De novo protein synthesis was monitored by [35S]methionine labeling of exponentially growing cultures under standard (pH 6) and acidic (pH 4.75) conditions. After 2-DE separation, the protein patterns were compared. The protein spots showing increased radioactivity levels under acid conditions were considered acid-induced. We determined the N-terminal amino acid sequence of three highly induced proteins; comparing these proteins to databases we identified them to be the well-known heat shock proteins GroES, GroEL, and DnaK. Their induction levels were measured and compared. This is the first study by 2-DE of stress response in L. bulgaricus. We established the method and present a protein map which will be useful for future studies.

Physiological study of Lactobacillus delbrueckii subsp. bulgaricus strains in a novel chemically defined medium.

We developed a chemically defined medium called milieu proche du lait (MPL), in which 22 Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus) strains exhibited growth rates ranging from 0.55 to 1 h(-1). MPL can also be used for cultivation of other lactobacilli and Streptococcus thermophilus. The growth characteristics of L. bulgaricus in MPL containing different carbon sources were determined, including an initial characterization of the phosphotransferase system transporters involved. For the 22 tested strains, growth on lactose was faster than on glucose, mannose, and fructose. Lactose concentrations below 0.4% were limiting for growth. We isolated 2-deoxyglucose-resistant mutants from strains CNRZ397 and ATCC 11842. CNRZ397-derived mutants were all deficient for glucose, fructose, and mannose utilization, indicating that these three sugars are probably transported via a unique mannose-specific-enzyme-II-like transporter. In contrast, mutants of ATCC 11842 exhibited diverse phenotypes, suggesting that multiple transporters may exist in that strain. We also developed a protein labeling method and verified that exopolysaccharide production and phage infection can occur in MPL. The MPL medium should thus be useful in conducting physiological studies of L. bulgaricus and other lactic acid bacteria under well controlled nutritional conditions.

A 7-base-pair sequence protects DNA from exonucleolytic degradation in Lactococcus lactis.

Linear DNA molecules are subject to degradation by various exonucleases in vivo unless their ends are protected. It has been demonstrated that a specific 8-bp sequence, 5'-GCTGGTGG-3', named Chi, can protect linear double-stranded DNA from the major Escherichia coli exonuclease RecBCD. Chi protects linear replication products of rolling-circle plasmids from RecBCD degradation in vivo, in agreement with observations in vitro. A unique 7-bp sequence, 5'-GCGCGTG-3', is shown to protect similar replication products from degradation in Lactococcus lactis strains but not in more distantly related Gram-positive bacteria. The properties of this sequence in L. lactis correspond to those of a Chi site. Linear plasmid replication products have been detected in numerous prokaryotes, suggesting the widespread existence of short species-specific sequences that preserve linear DNA from extensive degradation by host cell exonucleases.

Efficient insertional mutagenesis in lactococci and other gram-positive bacteria.

In lactococci, the study of chromosomal genes and their regulation is limited by the lack of an efficient transposon mutagenesis system. We associated the insertion sequence ISS1 with the thermosensitive replicon pG+ host to generate a mutagenic tool that can be used even in poorly transformable strains. ISS1 transposition is random in different lactococcal strains as well as in Enterococcus faecalis and Streptococcus thermophilus. High-frequency random insertion (of about 1%) obtained with this system in Lactococcus lactis allows efficient mutagenesis, with typically one insertion per cell. After ISS1 replicative transposition, the chromosome contains duplicated ISS1 sequences flanking pG+ host. This structure allows cloning of the interrupted gene. In addition, efficient excision of the plasmid leaves a single ISS1 copy at the mutated site, thus generating a stable mutant strain with no foreign markers. Mutants obtained by this transposition system are food grade and can thus be used in fermentation processes.

High-efficiency gene inactivation and replacement system for gram-positive bacteria.

A system for high-efficiency single- and double-crossover homologous integration in gram-positive bacteria has been developed, with Lactococcus lactis as a model system. The system is based on a thermosensitive broad-host-range rolling-circle plasmid, pG+host5, which contains a pBR322 replicon for propagation in Escherichia coli at 37 degrees C. A nested set of L. lactis chromosomal fragments cloned onto pG+host5 were used to show that the single-crossover integration frequency was logarithmically proportional to the length of homology for DNA fragments between 0.35 and 2.5 kb. Using random chromosomal 1-kb fragments, we showed that homologous integration can occur along the entire chromosome. We made use of the reported stimulatory effect of rolling-circle replication on intramolecular recombination to develop a protocol for gene replacement. Cultures were first maintained at 37 degrees C to select for a bacterial population enriched for plasmid integrants; activation of the integrated rolling-circle plasmid by a temperature shift to 28 degrees C resulted in efficient plasmid excision by homologous recombination and replacement of a chromosomal gene by the plasmid-carried modified copy. More than 50% of cells underwent replacement recombination when selection was applied for the replacing gene. Between 1 and 40% of cells underwent replacement recombination when no selection was applied. Chromosomal insertions and deletions were obtained in this way. These results show that gene replacement can be obtained at an extremely high efficiency by making use of the thermosensitive rolling-circle nature of the delivery vector. This procedure is applicable to numerous gram-positive bacteria.