Human T-lymphotropic virus type-1 (HTLV-1) is a complex retrovirus that causes adult T-cell leukemia/lymphoma (ATL) and is implicated in a variety of lymphocyte-mediated disorders. HTLV-1 pX ORF II encodes two proteins, p13 II  and p30 II  whose roles are beginning to be defined in the virus life cycle. Previous studies indicate the importance of these viral proteins in the ability of the virus to maintain viral loads and persist in an animal model of HTLV-1 infection. Intriguing new studies indicate that p30 II  is a multifunctional regulator that differentially modulates CREB and Tax-responsive element-mediated transcription through its interaction with CREB-binding protein (CBP)/p300 and specifically binds and represses  tax/rex  mRNA nuclear export. A new study characterized the role of p30 II  in regulation of cellular gene expression using comprehensive human gene arrays. Interestingly, p30 II  is an overall repressor of cellular gene expression, while selectively favoring the expression of regulatory gene pathways important to T lymphocytes. These new findings suggest that HTLV-1, which is associated with lymphoproliferative diseases, uses p30 II  to selectively repress cellular and viral gene expression to favor the survival of cellular targets ultimately resulting in leukemogenesis.tax/rex

The complex sequence of events set in motion by human T-lymphotropic virus type 1 (HTLV-1) to cause proliferation and ultimately transformation of T lymphocytes is beginning to be unraveled. Only recently has it become clear that viral encoded proteins, the so-called "accessory" gene products of this complex retrovirus, play an integral role in the pathogenic process. In addition to the structural and enzymatic gene products, HTLV-1 encodes regulatory and accessory proteins from four open reading frames (ORF) in the pX region between  env  and the 3' long terminal repeat (LTR) of the provirus [ 1 , 2 ]. The well studied Rex and Tax positive regulators are encoded in the ORF III and IV, respectively. Rex plays a critical role in nuclear export of unspliced or singly spliced viral mRNA [ 3 , 4 ]. Tax orchestrates multiple interactions with cellular transcription factors and activates transcription from the viral promoter and modulates the transcription or activity of numerous cellular genes involved in cell growth and differentiation, cell cycle control, and DNA repair [ 5 , 6 ]. Recent studies have indicated novel roles for pX ORF I and II gene products in the replication of HTLV-1 [ 7 - 9 ]. Although the study of these gene products were largely by-passed by virologists until the mid 1990's, they intensified when infectious molecular clones provided the tools to better understand their role  in vivo . Both HTLV-1 pX ORF I and II mRNAs have been detected in infected cell lines and blood leukocytes from HTLV-1-infected subjects including ATL and HAM/TSP patients [ 10 , 11 ]. Also, immune responses of HTLV-1 infected patients and asymptomatic carriers indicate that these proteins are expressed in vivo [ 12 - 14 ]. Molecular clones of HTLV-1 with selective mutations of ORF I and II have revealed the requirement of p12 I  and p13 II /p30 II  in the establishment of infection and maintenance of viral loads in a rabbit model of infection [ 15 - 17 ]. The nuclear and nucleolar localizing p30 II  has minimal homology to transcription factors Oct-1 and -2, Pit-1, and POU-M1 [ 18 - 21 ]. In addition, the protein co-localizes with p300 in the nucleus and physically interacts with CREB binding protein (CBP)/p300 and differentially modulates cAMP responsive element (CRE) and Tax response element-mediated transcription [ 21 , 22 ]. Intriguing recent reports also indicate a post-transcriptional role of HTLV-1 p30 II  and HTLV-2 p28 II (homologous protein encoded in the HTLV-2 pX ORF II region), in repressing the export of  tax/rex  mRNA from the nucleus [ 23 , 24 ]. Thus, it appears that HTLV-1 has yet another multifunctional protein with transcriptional and post-transcriptional roles in regulating viral gene expression. Microarrays are important tools to gain insight into changes in gene expression profiles of virus-infected cells. This approach has been primarily used to investigate gene expression in HTLV-1-immortalized/transformed cell lines or in cells from ATL patients [ 25 - 29 ]. In the report by Michael et al. [ 30 ] the authors used the Affymetrix U133A human gene chip to test the role of HTLV-1 p30 II  as a regulator of gene expression in Jurkat T cells. They identified alterations in gene expression profiles unique to cell cycle regulation, apoptosis, and T lymphocyte signaling/activation. Although p30 II  expression, as might be expected from earlier reports, resulted in a general repressive pattern of gene expression, their data indicated that the viral protein selectively spared or enhanced NFAT, NFκB, and AP-1 mediated transcription in T cells undergoing co-stimulation. Signaling pathways primarily affected by p30 II  as measured by luciferase reporters included both NFAT and NFκB, which increased from approximately 3 to 11 fold, depending on co-stimulatory treatment. Overall, this study supports earlier reports on the repressive role of HTLV-1 p30 II  in gene expression [ 21 - 24 ] and reveals new potential mechanisms by which p30 II  may play a role in HTLV-1 replication (figure  1 ). The effects of p30 II  appear to overlap or counteract the influence of other HTLV-1 regulatory proteins like Tax or other accessory proteins such as p12 I . Further studies to test if these proteins act coordinately or synergistically will undoubtedly shed light on this issue. It is possible that HTLV-1 employs selective use of these viral proteins during various stages of the infection to promote cell proliferation, a hallmark of the diseases associated with the deltaretrovirus family. Whatever the outcome of these studies, it is clear that "accessory" proteins, like p30 II , may have "essential" roles in the life cycle of HTLV-1.

The complex sequence of events set in motion by human T-lymphotropic virus type 1 (HTLV-1) to cause proliferation and ultimately transformation of T lymphocytes is beginning to be unraveled. Only recently has it become clear that viral encoded proteins, the so-called "accessory" gene products of this complex retrovirus, play an integral role in the pathogenic process. In addition to the structural and enzymatic gene products, HTLV-1 encodes regulatory and accessory proteins from four open reading frames (ORF) in the pX region between  env  and the 3' long terminal repeat (LTR) of the provirus [ 1 , 2 ]. The well studied Rex and Tax positive regulators are encoded in the ORF III and IV, respectively. Rex plays a critical role in nuclear export of unspliced or singly spliced viral mRNA [ 3 , 4 ]. Tax orchestrates multiple interactions with cellular transcription factors and activates transcription from the viral promoter and modulates the transcription or activity of numerous cellular genes involved in cell growth and differentiation, cell cycle control, and DNA repair [ 5 , 6 ]. Recent studies have indicated novel roles for pX ORF I and II gene products in the replication of HTLV-1 [ 7 - 9 ]. Although the study of these gene products were largely by-passed by virologists until the mid 1990's, they intensified when infectious molecular clones provided the tools to better understand their role  in vivo . Both HTLV-1 pX ORF I and II mRNAs have been detected in infected cell lines and blood leukocytes from HTLV-1-infected subjects including ATL and HAM/TSP patients [ 10 , 11 ]. Also, immune responses of HTLV-1 infected patients and asymptomatic carriers indicate that these proteins are expressed in vivo [ 12 - 14 ].envin vivoMolecular clones of HTLV-1 with selective mutations of ORF I and II have revealed the requirement of p12 I  and p13 II /p30 II  in the establishment of infection and maintenance of viral loads in a rabbit model of infection [ 15 - 17 ]. The nuclear and nucleolar localizing p30 II  has minimal homology to transcription factors Oct-1 and -2, Pit-1, and POU-M1 [ 18 - 21 ]. In addition, the protein co-localizes with p300 in the nucleus and physically interacts with CREB binding protein (CBP)/p300 and differentially modulates cAMP responsive element (CRE) and Tax response element-mediated transcription [ 21 , 22 ]. Intriguing recent reports also indicate a post-transcriptional role of HTLV-1 p30 II  and HTLV-2 p28 II (homologous protein encoded in the HTLV-2 pX ORF II region), in repressing the export of  tax/rex  mRNA from the nucleus [ 23 , 24 ]. Thus, it appears that HTLV-1 has yet another multifunctional protein with transcriptional and post-transcriptional roles in regulating viral gene expression.tax/rexMicroarrays are important tools to gain insight into changes in gene expression profiles of virus-infected cells. This approach has been primarily used to investigate gene expression in HTLV-1-immortalized/transformed cell lines or in cells from ATL patients [ 25 - 29 ]. In the report by Michael et al. [ 30 ] the authors used the Affymetrix U133A human gene chip to test the role of HTLV-1 p30 II  as a regulator of gene expression in Jurkat T cells. They identified alterations in gene expression profiles unique to cell cycle regulation, apoptosis, and T lymphocyte signaling/activation. Although p30 II  expression, as might be expected from earlier reports, resulted in a general repressive pattern of gene expression, their data indicated that the viral protein selectively spared or enhanced NFAT, NFκB, and AP-1 mediated transcription in T cells undergoing co-stimulation. Signaling pathways primarily affected by p30 II  as measured by luciferase reporters included both NFAT and NFκB, which increased from approximately 3 to 11 fold, depending on co-stimulatory treatment. Overall, this study supports earlier reports on the repressive role of HTLV-1 p30 II  in gene expression [ 21 - 24 ] and reveals new potential mechanisms by which p30 II  may play a role in HTLV-1 replication (figure  1 ). The effects of p30 II  appear to overlap or counteract the influence of other HTLV-1 regulatory proteins like Tax or other accessory proteins such as p12 I . Further studies to test if these proteins act coordinately or synergistically will undoubtedly shed light on this issue. It is possible that HTLV-1 employs selective use of these viral proteins during various stages of the infection to promote cell proliferation, a hallmark of the diseases associated with the deltaretrovirus family. Whatever the outcome of these studies, it is clear that "accessory" proteins, like p30 II , may have "essential" roles in the life cycle of HTLV-1.Abbreviations HTLV-1, human T cell lymphotropic virus type-1 ATL, adult T cell leukemia HAM/TSP, HTLV associated myelopathy/tropical spastic paraparesis ORF II, open reading frame II LTR, long terminal repeat CRE, cAMP responsive element CREB, cAMP response element binding protein NFAT, nuclear factor of activated T cells NFκB, nuclear factor kappa B AP-1, activator protein 1
Abbreviations
HTLV-1, human T cell lymphotropic virus type-1ATL, adult T cell leukemiaHAM/TSP, HTLV associated myelopathy/tropical spastic paraparesisORF II, open reading frame IILTR, long terminal repeatCRE, cAMP responsive elementCREB, cAMP response element binding proteinNFAT, nuclear factor of activated T cellsNFκB, nuclear factor kappa BAP-1, activator protein 1Competing Interests The author(s) declare that they have no competing interests. Figure 1 Model for HTLV-1 p30 II  transcriptional and posttranscriptional gene regulation. The cell nucleus surrounded by the nuclear membrane and key components are shown. p30 II  can directly interact with CBP/p300 and modulate transcription of viral and/or cellular genes. At low concentration p30 II  may stabilize the transcription complex and potentiate transcription, whereas a high concentration it may compete for limited amounts of CBP/p300 and repress gene expression. p30 II  (as well as the homologous p28 II  of HTLV-2) specifically binds  tax/rex  mRNA and block its export, reducing Tax and Rex and ultimately repressing viral gene expression. This interaction may be directly linked to splicing factors and splicing and/or the juxtaposition of specific exon/exon junction sequences. Thus, p30 II  is a multifunctional protein with transcriptional and post-transcriptional roles in regulating viral and/or cellular gene expression.
Competing Interests
The author(s) declare that they have no competing interests.


Background Depression is frequently occurring during and after psychosis. The aim of this study was to analyze if the psychosocial characteristics associated with depression/depressive symptoms in the late phase of a first episode psychosis (FEP) population were different compared to persons from the general population.
Background
Depression is frequently occurring during and after psychosis. The aim of this study was to analyze if the psychosocial characteristics associated with depression/depressive symptoms in the late phase of a first episode psychosis (FEP) population were different compared to persons from the general population.Methods A questionnaire was sent out to all individuals six years after their FEP and to a general population sample. Depressive symptoms were recorded using a self-rating scale, the Major Depression Inventory.
Methods
A questionnaire was sent out to all individuals six years after their FEP and to a general population sample. Depressive symptoms were recorded using a self-rating scale, the Major Depression Inventory.Results Formerly FEP persons had a higher representation of depressive symptoms/depression, unemployment, financial problems and insufficient social network. Depressive symptoms/depression were found to be associated with psychosocial problems. An age and gender effect was found in the general population, but not in the FEP sample. When the psychosocial characteristics were taken into account there were no association between having had FEP and depressive symptoms.
Results
Formerly FEP persons had a higher representation of depressive symptoms/depression, unemployment, financial problems and insufficient social network. Depressive symptoms/depression were found to be associated with psychosocial problems. An age and gender effect was found in the general population, but not in the FEP sample. When the psychosocial characteristics were taken into account there were no association between having had FEP and depressive symptoms.Conclusions The association between having been a FEP patient and depressive symptoms/depression disappeared when negative social aspects were taken into account.
Conclusions
The association between having been a FEP patient and depressive symptoms/depression disappeared when negative social aspects were taken into account.

Background Major Depression is the one of the most common psychiatric disorders and is frequently occurring in persons with psychotic disorders. Up to 25% of individuals with psychosis have this condition at some point during the course of their illness [ 1 ]. Insufficient social network, unemployment, living alone, financial problems and low social class are among the reported risk factors for depression in prospective studies [ 2 - 5 ]. Studies of characteristics associated with depression in psychosis have reported various results. Associations have been reported with negative as well as positive symptoms, medications and neuroleptic induced movement disorders [ 6 - 9 ]. In a study by Baynes et al, depressive symptoms were explored in a population of 120 patients with stable, chronic schizophrenia living in the community [ 10 ]. Patients who perceived themselves to have poor social support were more likely to be depressed. They proposed that a similar mechanism for the etiology of depression might exist in schizophrenia as in non-schizophrenic persons. The most commonly used depression self-rating scales in population studies were developed before the introduction of DSM-III, e.g. the Beck Depression Inventory (BDI) and the Zung Self-rating Depression Scale (Zung-SDS) [ 11 , 12 ]. The Major Depression Inventory (MDI) used in the present study was developed by Bech et al based on the DSM-IV symptoms of Major Depression and ICD-10 moderate to severe depression [ 13 , 14 ]. The MDI includes symptom thresholds as well as duration criteria. The internal and external validity has been reported to be higher than for Zung-SDS [ 14 ]. In order to evaluate screening scales there is a need for a "golden standard" and several studies has used Schedules for Clinical Assessment in Neuropsychiatry (SCAN) [ 15 , 16 ]. SCAN incorporates the 10 th  edition of the Present State Examination and the reliability has been reported to be good [ 17 ]. The authors of the scale have reported the sensitivity to be 0.90 and the specificity 0.82 when validating the MDI versus SCAN in a clinical setting [ 18 ]. The aim of the present study was to analyze if the psychosocial characteristics associated with depressive symptoms in persons six year after a first episode of psychosis (FEP) differed from the associations found in a population sample.
Background
Major Depression is the one of the most common psychiatric disorders and is frequently occurring in persons with psychotic disorders. Up to 25% of individuals with psychosis have this condition at some point during the course of their illness [ 1 ].Insufficient social network, unemployment, living alone, financial problems and low social class are among the reported risk factors for depression in prospective studies [ 2 - 5 ]. Studies of characteristics associated with depression in psychosis have reported various results. Associations have been reported with negative as well as positive symptoms, medications and neuroleptic induced movement disorders [ 6 - 9 ]. In a study by Baynes et al, depressive symptoms were explored in a population of 120 patients with stable, chronic schizophrenia living in the community [ 10 ]. Patients who perceived themselves to have poor social support were more likely to be depressed. They proposed that a similar mechanism for the etiology of depression might exist in schizophrenia as in non-schizophrenic persons.The most commonly used depression self-rating scales in population studies were developed before the introduction of DSM-III, e.g. the Beck Depression Inventory (BDI) and the Zung Self-rating Depression Scale (Zung-SDS) [ 11 , 12 ]. The Major Depression Inventory (MDI) used in the present study was developed by Bech et al based on the DSM-IV symptoms of Major Depression and ICD-10 moderate to severe depression [ 13 , 14 ]. The MDI includes symptom thresholds as well as duration criteria. The internal and external validity has been reported to be higher than for Zung-SDS [ 14 ]. In order to evaluate screening scales there is a need for a "golden standard" and several studies has used Schedules for Clinical Assessment in Neuropsychiatry (SCAN) [ 15 , 16 ]. SCAN incorporates the 10 th  edition of the Present State Examination and the reliability has been reported to be good [ 17 ]. The authors of the scale have reported the sensitivity to be 0.90 and the specificity 0.82 when validating the MDI versus SCAN in a clinical setting [ 18 ].The aim of the present study was to analyze if the psychosocial characteristics associated with depressive symptoms in persons six year after a first episode of psychosis (FEP) differed from the associations found in a population sample.Methods Population from the Parachute project The Parachute project is a Swedish multi center study of FEP. It includes all persons from the catchment area who for the first time sought psychiatric help for psychotic symptoms during 1996–1997. Persons who were 18–45 years old and without a dominating substance abuse or diagnosed brain disorder were included in the study. The catchment area covers approximately 20% of the Swedish population. The project integrates an epidemiological approach with intensive psychosocial and medical treatment of a cohort of first episode psychotic patients. It includes a large-scale system of "need adapted treatment" [ 19 ], which includes high degree of psychosocial support, lowest optimal antipsychotic medication, participation of families and treatment in normalized and integrated settings. The participating patients were followed for a period of six years with assessments of psychiatric, psychological, social and economic aspects. The project, which is a controlled study, is described in detail in a previous paper [ 20 ]. Of the 175 patients included in the project from the start 133 were followed during the complete six-year period. The questionnaire included in this study was sent out to the 133 persons six years after their first psychotic episode and 57.1% (76 persons) participated. Those who participated did not differ in age, gender, country of origin or psychiatric diagnosis from those who did not participate. Population from the PART study The PART study is a longitudinal population study of risk factors and social consequences of mental ill health in the Stockholm County. 19 744 Swedish citizens aged 20–64 years registered as living in the county of Stockholm were randomly selected in 1998–2000. This represents 1.8% of the population in this age group in this area. 10 442 persons (53%) participated in the study. The personal identification number (that all Swedish citizens have) of participants as well as non-participants were linked to the following official registers: income and wealth, sick leave, hospital discharge register (including diagnoses) and disability pension. Participation was related to female gender, higher age, higher income and education, being born in Sweden, and having no psychiatric diagnoses in the hospital discharge register or in the disability pension register. The odds ratios for associations between gender, income, country of origin, education and having a psychiatric diagnosis previously according to the registers, were similar among participants and non-participants (Lundberg et al, manuscript). Participants having had a diagnosis of psychotic disorder in the hospital discharge register were excluded from this study (n = 20). Questionnaire A questionnaire was sent out to the population included in the PART study. The questions included risk and protective factors for mental illness as well as psychiatric symptoms scales [ 21 ]. The same questionnaire was replicated in the follow up of the FEP group. The following variables were used in the present study • Demographic characteristics: age, gender and country of origin (Sweden/other). • Financial problems included the availability to get 14 000 SEK (1 797 USD) within a week, if necessary. • Working life: The persons were divided in the following two groups: employed/students and unemployed/disability pension/sick leave/early retirement pension. • Social network: An instrument developed by Unden & Orth-Gomer [ 22 ] was used. This instrument is developed from ISSI, the Interview Schedule for Social Interaction [ 23 ] Two sub scales were used, AVAT-availability of attachment and AVSI-availability of social integration. The score was calculated according to the authors of the scale. • Depressive symptoms: The Major depression Inventory was used strictly according to the authors of the scale [ 13 , 14 ]. The scale covers the ICD-10 as well as the DSM-IV symptoms of depression. It contains 12 items, but functionally it has 10 items since two of them contain sub items (restless/subdued and reduced/increased appetite). Each item gives a score from 0–5 based on the following answers: at no time, some of the time, slightly less than half of the time, slightly more than half of the time, most of the time and always. The MDI can be used as a scale for measuring the severity in which the total score is calculated giving a theoretical score from 0–50. A score of 26 is considered pathological according to the authors of the scale. Statistical analysis Simple factorial ANOVA'S were performed using being in the PART population or not as the dependent variable and age, gender and country of origin as covariates. Pearson's correlation was used to see if the demographic and psychosocial variables correlated with depressive symptoms. These analyses were performed separately in the PART and FEP populations. Additionally multiple regression analyses were performed with the scores on the Major Depression Inventory and a cut off score of 26 or more as the dependent variables. All variables were entered simultaneously. Being in the PART population or not was entered as a variable.
Methods
Population from the Parachute project The Parachute project is a Swedish multi center study of FEP. It includes all persons from the catchment area who for the first time sought psychiatric help for psychotic symptoms during 1996–1997. Persons who were 18–45 years old and without a dominating substance abuse or diagnosed brain disorder were included in the study. The catchment area covers approximately 20% of the Swedish population. The project integrates an epidemiological approach with intensive psychosocial and medical treatment of a cohort of first episode psychotic patients. It includes a large-scale system of "need adapted treatment" [ 19 ], which includes high degree of psychosocial support, lowest optimal antipsychotic medication, participation of families and treatment in normalized and integrated settings. The participating patients were followed for a period of six years with assessments of psychiatric, psychological, social and economic aspects. The project, which is a controlled study, is described in detail in a previous paper [ 20 ]. Of the 175 patients included in the project from the start 133 were followed during the complete six-year period. The questionnaire included in this study was sent out to the 133 persons six years after their first psychotic episode and 57.1% (76 persons) participated. Those who participated did not differ in age, gender, country of origin or psychiatric diagnosis from those who did not participate.
Population from the Parachute project
The Parachute project is a Swedish multi center study of FEP. It includes all persons from the catchment area who for the first time sought psychiatric help for psychotic symptoms during 1996–1997. Persons who were 18–45 years old and without a dominating substance abuse or diagnosed brain disorder were included in the study. The catchment area covers approximately 20% of the Swedish population. The project integrates an epidemiological approach with intensive psychosocial and medical treatment of a cohort of first episode psychotic patients. It includes a large-scale system of "need adapted treatment" [ 19 ], which includes high degree of psychosocial support, lowest optimal antipsychotic medication, participation of families and treatment in normalized and integrated settings. The participating patients were followed for a period of six years with assessments of psychiatric, psychological, social and economic aspects. The project, which is a controlled study, is described in detail in a previous paper [ 20 ].Of the 175 patients included in the project from the start 133 were followed during the complete six-year period. The questionnaire included in this study was sent out to the 133 persons six years after their first psychotic episode and 57.1% (76 persons) participated. Those who participated did not differ in age, gender, country of origin or psychiatric diagnosis from those who did not participate.Population from the PART study The PART study is a longitudinal population study of risk factors and social consequences of mental ill health in the Stockholm County. 19 744 Swedish citizens aged 20–64 years registered as living in the county of Stockholm were randomly selected in 1998–2000. This represents 1.8% of the population in this age group in this area. 10 442 persons (53%) participated in the study. The personal identification number (that all Swedish citizens have) of participants as well as non-participants were linked to the following official registers: income and wealth, sick leave, hospital discharge register (including diagnoses) and disability pension. Participation was related to female gender, higher age, higher income and education, being born in Sweden, and having no psychiatric diagnoses in the hospital discharge register or in the disability pension register. The odds ratios for associations between gender, income, country of origin, education and having a psychiatric diagnosis previously according to the registers, were similar among participants and non-participants (Lundberg et al, manuscript). Participants having had a diagnosis of psychotic disorder in the hospital discharge register were excluded from this study (n = 20).
Population from the PART study
The PART study is a longitudinal population study of risk factors and social consequences of mental ill health in the Stockholm County. 19 744 Swedish citizens aged 20–64 years registered as living in the county of Stockholm were randomly selected in 1998–2000. This represents 1.8% of the population in this age group in this area. 10 442 persons (53%) participated in the study. The personal identification number (that all Swedish citizens have) of participants as well as non-participants were linked to the following official registers: income and wealth, sick leave, hospital discharge register (including diagnoses) and disability pension. Participation was related to female gender, higher age, higher income and education, being born in Sweden, and having no psychiatric diagnoses in the hospital discharge register or in the disability pension register. The odds ratios for associations between gender, income, country of origin, education and having a psychiatric diagnosis previously according to the registers, were similar among participants and non-participants (Lundberg et al, manuscript). Participants having had a diagnosis of psychotic disorder in the hospital discharge register were excluded from this study (n = 20).Questionnaire A questionnaire was sent out to the population included in the PART study. The questions included risk and protective factors for mental illness as well as psychiatric symptoms scales [ 21 ]. The same questionnaire was replicated in the follow up of the FEP group.
Questionnaire
A questionnaire was sent out to the population included in the PART study. The questions included risk and protective factors for mental illness as well as psychiatric symptoms scales [ 21 ]. The same questionnaire was replicated in the follow up of the FEP group.The following variables were used in the present study • Demographic characteristics: age, gender and country of origin (Sweden/other). • Financial problems included the availability to get 14 000 SEK (1 797 USD) within a week, if necessary. • Working life: The persons were divided in the following two groups: employed/students and unemployed/disability pension/sick leave/early retirement pension. • Social network: An instrument developed by Unden & Orth-Gomer [ 22 ] was used. This instrument is developed from ISSI, the Interview Schedule for Social Interaction [ 23 ] Two sub scales were used, AVAT-availability of attachment and AVSI-availability of social integration. The score was calculated according to the authors of the scale. • Depressive symptoms: The Major depression Inventory was used strictly according to the authors of the scale [ 13 , 14 ]. The scale covers the ICD-10 as well as the DSM-IV symptoms of depression. It contains 12 items, but functionally it has 10 items since two of them contain sub items (restless/subdued and reduced/increased appetite). Each item gives a score from 0–5 based on the following answers: at no time, some of the time, slightly less than half of the time, slightly more than half of the time, most of the time and always. The MDI can be used as a scale for measuring the severity in which the total score is calculated giving a theoretical score from 0–50. A score of 26 is considered pathological according to the authors of the scale.
The following variables were used in the present study
• Demographic characteristics: age, gender and country of origin (Sweden/other).• Financial problems included the availability to get 14 000 SEK (1 797 USD) within a week, if necessary.• Working life: The persons were divided in the following two groups: employed/students and unemployed/disability pension/sick leave/early retirement pension.• Social network: An instrument developed by Unden & Orth-Gomer [ 22 ] was used. This instrument is developed from ISSI, the Interview Schedule for Social Interaction [ 23 ] Two sub scales were used, AVAT-availability of attachment and AVSI-availability of social integration. The score was calculated according to the authors of the scale.• Depressive symptoms: The Major depression Inventory was used strictly according to the authors of the scale [ 13 , 14 ]. The scale covers the ICD-10 as well as the DSM-IV symptoms of depression. It contains 12 items, but functionally it has 10 items since two of them contain sub items (restless/subdued and reduced/increased appetite). Each item gives a score from 0–5 based on the following answers: at no time, some of the time, slightly less than half of the time, slightly more than half of the time, most of the time and always. The MDI can be used as a scale for measuring the severity in which the total score is calculated giving a theoretical score from 0–50. A score of 26 is considered pathological according to the authors of the scale.Statistical analysis Simple factorial ANOVA'S were performed using being in the PART population or not as the dependent variable and age, gender and country of origin as covariates. Pearson's correlation was used to see if the demographic and psychosocial variables correlated with depressive symptoms. These analyses were performed separately in the PART and FEP populations. Additionally multiple regression analyses were performed with the scores on the Major Depression Inventory and a cut off score of 26 or more as the dependent variables. All variables were entered simultaneously. Being in the PART population or not was entered as a variable.
Statistical analysis
Simple factorial ANOVA'S were performed using being in the PART population or not as the dependent variable and age, gender and country of origin as covariates. Pearson's correlation was used to see if the demographic and psychosocial variables correlated with depressive symptoms. These analyses were performed separately in the PART and FEP populations. Additionally multiple regression analyses were performed with the scores on the Major Depression Inventory and a cut off score of 26 or more as the dependent variables. All variables were entered simultaneously. Being in the PART population or not was entered as a variable.Results The demographic and psychosocial characteristics of the two populations are presented and compared in table  1 . Persons in the FEP population more often had unemployment/disability pension/sick leave/early retirement pension (F = 110.26, df 1, p < 0.001) and financial problems (F = 30.06, p < 0.001). Additionally fewer of them had a sufficient social network ((AVSI; F = 52.26, df 1, p < 0.001) and (AVAT; F = 39.18, df 1, p < 0.001)). They also had higher score on the Major Depression Inventory (F = 25.69, df 1, p < 0.001). The symptoms within the Major Depression Inventory were also analyzed separately. The only symptom that was equally distributed was sleep disturbances; all other symptoms were more common in the FEP population. Table 1 Demographic and psychosocial variables in the FEP population and in the general population sample. The statistical analyses were controlled for age, gender and country of origin (Sweden/other). General pop. sample, n = 10 425, %(n) FEP pop. n = 76, %(n) Female gender 55.5(5 798) 50.0(38) Not born in Sweden 10.7(1 120) 15.8(12) Unemployed † 9.7(1 009) 38.2(29)* Financial difficulties 14.9(1 553) 40.8(31)* Mean (95%CI) Mean (95%CI) Age 41.4 (41.2–41.7) 28.5 (26.8–30.3) AVAT (availability of attachment) 17.7 (17.6–17.7) 16.0 (15.1–16.9)* AVSI (availability of social integration) 16.2 (16.2–16.3) 12.4 (11.4–13.4)* Major Depression Inventory 8.8 (8.6–9.0) 15.8 (12.7–18.9)* † Including disability pension/early retirement pension/sick leave, *p < 0.001 When using a MDI cut-off score of 26, 25.8% (17 persons) had a score above the cut-off in the FEP population and 8.0% (783 persons) in the general population sample. Table  2  presents the correlations between the demographic and psychosocial characteristics and the total score of the MDI. In the general population sample all demographic and psychosocial variables were found to be associated with the total score of the MDI. In the FEP population not born in Sweden and being younger were not associated. The gender associations were different in the two samples, while female gender was associated in the general population sample male gender was associated in the FEP population. Table 2 Correlations between the demographic, psychosocial characteristics and total score of the Major Depression Inventory in the FEP population and in the general population sample. General pop. sample N = 10 425 FEP pop. N = 76 Not born in Sweden 0.11*** 0.12 Age -0.13*** -0.01 Female gender 0.13*** -0.21* Unemployment 0.14*** 0.23* Financial problems 0.27*** 0.35** AVAT (availability of attachment) -0.32*** -0.48*** AVSI (availability of social integration) -0.31*** -0.41*** *p < 0.1, **p < 0.01,***p < 0.001 Separate multiple regression analyses were performed in the two samples with the Major Depression Inventory total score as the dependent variable. In the general population sample the adjusted R square was 0.21 (SE 8.7) and in the FEP population 0.28 (SE 11.4). In addition an analysis was made were general population/FEP population was inserted as a variable. The result is presented in table  3 , and shows that the correlation between being a person having had a FEP and higher scores on the Major Depression Inventory no longer was present when the other variables were taken into account. Adjusted R square for this analysis was 0.21 (SE 8.7). A similar regression was performed entering depressed/not depressed using a cut-off score of 26 and the result is also presented in table  3 . Adjusted R square for this analysis was 0.12 (SE 25.5) Table 3 Multiple regression analyses with total score on the Major Depression Inventory and a MDI cut off at 26 as the dependent variables. MDI Score Beta  Stand. MDI Cut-off Beta  Stand. FEP pop. vs. General pop. sample 0.00 0.00 Not born in Sweden 0.04* 0.04* Age -0.16* -0.07* Female gender 0.13* 0.08* Unemployed 0.10* 0.09* Financial problems 0.10* 0.09* AVAT (availability of attachment) -0.15* -0.19* AVSI (availability of social integration) -0.24* -0.09* *p < 0.001
Results
The demographic and psychosocial characteristics of the two populations are presented and compared in table  1 . Persons in the FEP population more often had unemployment/disability pension/sick leave/early retirement pension (F = 110.26, df 1, p < 0.001) and financial problems (F = 30.06, p < 0.001). Additionally fewer of them had a sufficient social network ((AVSI; F = 52.26, df 1, p < 0.001) and (AVAT; F = 39.18, df 1, p < 0.001)). They also had higher score on the Major Depression Inventory (F = 25.69, df 1, p < 0.001). The symptoms within the Major Depression Inventory were also analyzed separately. The only symptom that was equally distributed was sleep disturbances; all other symptoms were more common in the FEP population.Demographic and psychosocial variables in the FEP population and in the general population sample. The statistical analyses were controlled for age, gender and country of origin (Sweden/other).† Including disability pension/early retirement pension/sick leave, *p < 0.001When using a MDI cut-off score of 26, 25.8% (17 persons) had a score above the cut-off in the FEP population and 8.0% (783 persons) in the general population sample.Table  2  presents the correlations between the demographic and psychosocial characteristics and the total score of the MDI. In the general population sample all demographic and psychosocial variables were found to be associated with the total score of the MDI. In the FEP population not born in Sweden and being younger were not associated. The gender associations were different in the two samples, while female gender was associated in the general population sample male gender was associated in the FEP population.Correlations between the demographic, psychosocial characteristics and total score of the Major Depression Inventory in the FEP population and in the general population sample.*p < 0.1, **p < 0.01,***p < 0.001Separate multiple regression analyses were performed in the two samples with the Major Depression Inventory total score as the dependent variable. In the general population sample the adjusted R square was 0.21 (SE 8.7) and in the FEP population 0.28 (SE 11.4). In addition an analysis was made were general population/FEP population was inserted as a variable. The result is presented in table  3 , and shows that the correlation between being a person having had a FEP and higher scores on the Major Depression Inventory no longer was present when the other variables were taken into account. Adjusted R square for this analysis was 0.21 (SE 8.7). A similar regression was performed entering depressed/not depressed using a cut-off score of 26 and the result is also presented in table  3 . Adjusted R square for this analysis was 0.12 (SE 25.5)Multiple regression analyses with total score on the Major Depression Inventory and a MDI cut off at 26 as the dependent variables.*p < 0.001Discussion The main finding of this study was that the association between having suffered a FEP and self-reported depressive symptoms/depression six years later disappeared when a negative social situation was taken into account. Not surprisingly, persons with a previous FEP had a higher representation of unemployment, financial problems and insufficient social network, which have been reported in other studies [ 24 - 26 ]. In the general population there was an age and gender effect, females and younger age had an overrepresentation of depressive symptoms. This was not seen in the FEP follow up group where age had no effect and being a male was slightly over represented. This is in agreement with a study by Zisook et al [ 9 ]. Not born in Sweden was associated with depressive symptoms in the general population sample, but not in the FEP population. This could have been due to low numbers in the FEP population. The non-participation rate was high in the general population and persons with severe psychiatric disorders most likely did not respond to the enquiry. However, the associations between gender, income, country of origin, education and having a previous psychiatric diagnosis was similar among participants and non-participants. The FEP group also had a high non-participation rate, although the distribution of age, gender, country of origin and psychiatric diagnoses were similar among participants and non-participants. The general population sample was an urban population while the FEP population was from areas all over Sweden, which might have affected the result. The strengths of the study were that the FEP group was a total population, followed over six years and having received treatment according to a "need-adapted approach". Moreover, the instrument in use, the MDI has been reported to have a higher internal validity than Ham-D 17  and Zung-SDS [ 13 , 14 ]. The sensitivity and specificity have been above 0.80 when the MDI was compared to clinical interviews using SCAN [ 18 ]. The results of this study fully agree with the goals of WHO [ 27 ]: Links need to be established between mental health services and various community agencies at the local level so that appropriate housing, income support, disability benefits, employment and other social service supports are mobilized on behalf of patients and in order that prevention and rehabilitation strategies can be more effectively implemented. Following these recommendations would most likely decrease the rates of depressive symptoms in former FEP person with a secondary positive effect on their quality of life in general.
Discussion
The main finding of this study was that the association between having suffered a FEP and self-reported depressive symptoms/depression six years later disappeared when a negative social situation was taken into account.Not surprisingly, persons with a previous FEP had a higher representation of unemployment, financial problems and insufficient social network, which have been reported in other studies [ 24 - 26 ]. In the general population there was an age and gender effect, females and younger age had an overrepresentation of depressive symptoms. This was not seen in the FEP follow up group where age had no effect and being a male was slightly over represented. This is in agreement with a study by Zisook et al [ 9 ]. Not born in Sweden was associated with depressive symptoms in the general population sample, but not in the FEP population. This could have been due to low numbers in the FEP population.The non-participation rate was high in the general population and persons with severe psychiatric disorders most likely did not respond to the enquiry. However, the associations between gender, income, country of origin, education and having a previous psychiatric diagnosis was similar among participants and non-participants. The FEP group also had a high non-participation rate, although the distribution of age, gender, country of origin and psychiatric diagnoses were similar among participants and non-participants. The general population sample was an urban population while the FEP population was from areas all over Sweden, which might have affected the result.The strengths of the study were that the FEP group was a total population, followed over six years and having received treatment according to a "need-adapted approach". Moreover, the instrument in use, the MDI has been reported to have a higher internal validity than Ham-D 17  and Zung-SDS [ 13 , 14 ]. The sensitivity and specificity have been above 0.80 when the MDI was compared to clinical interviews using SCAN [ 18 ].The results of this study fully agree with the goals of WHO [ 27 ]: Links need to be established between mental health services and various community agencies at the local level so that appropriate housing, income support, disability benefits, employment and other social service supports are mobilized on behalf of patients and in order that prevention and rehabilitation strategies can be more effectively implemented. Following these recommendations would most likely decrease the rates of depressive symptoms in former FEP person with a secondary positive effect on their quality of life in general.Conclusions Having had a first episode psychosis six years earlier had no association with depressive symptoms/depression when a negative social situation was taken into account.
Conclusions
Having had a first episode psychosis six years earlier had no association with depressive symptoms/depression when a negative social situation was taken into account.Competing interests The authors declare that they have no competing interests.
Competing interests
The authors declare that they have no competing interests.Authors' contributions YF, SL and JC participated in the data collection. YF performed the statistical analysis. All three authors wrote and approved the final manuscript.
Authors' contributions
YF, SL and JC participated in the data collection. YF performed the statistical analysis. All three authors wrote and approved the final manuscript.Pre-publication history The pre-publication history for this paper can be accessed here:
Pre-publication history
The pre-publication history for this paper can be accessed here:


Lactic acid bacteria (LAB) are essential for the manufacture of fermented dairy products. Studies on the physiology, biochemistry and genetics of these microorganisms over the last century have contributed considerably to the improvement of fermentation processes and have resulted in better and safer products. Nevertheless, the potential of LAB is far from being maximized. The sophistication of biotechnologies and the availability of complete genome sequences have opened the door to the metabolic engineering of LAB. In this regard, the recent publication of the complete genome sequences of two  Streptococcus thermophilus  strains will provide a key tool to facilitate the genetic manipulation of this important dairy species.Streptococcus thermophilus

Introduction The souring of milk by microorganisms has been used for thousand of years as a natural preservation procedure [ 1 ]. The method was domesticated to manufacture man-made edible fermented products such as cheese, which appeared in the human diet some 8,000–10,000 years ago. However, up to the beginning of the 20th century, milk fermentation was by no means a controlled process, and the search for improvements was strictly empiric and based on trial and error. The discovery and characterization of lactic acid bacteria (LAB) has tremendously modified the way fermented milk products are made. Considerable efforts have been devoted over the last fifty years to increase our knowledge about the genetics, biochemistry, and physiology of LAB. In addition to enhancing our understanding of microbial life, these studies have allowed dairy microbiologists and cheesemakers to select better strains and improve the productivity, quality, and safety of the final products. The characterization of LAB has promoted the rational development of blends of defined bacterial strains, now known as starter cultures, which are increasingly replacing the undefined blends traditionally used by the dairy industry. This strategy makes it easier to control acid production and, to some extent, phage problems. Unfortunately, it is also widely perceived that this approach reduces the much sought-after rich, complex flavour of fermented products made with undefined cultures. Thus, the search for LAB strains that produce characteristic aroma and flavours remains an attractive challenge for the dairy industry. The increasing awareness of the population of the importance of a healthy diet has led scientists to revisit the century-old hypothesis that some specific fermented dairy products may provide health benefits. A plethora of studies are underway to evaluate this concept and to improve the health benefits of LAB. Also, the long history of the safe use of these bacteria has made them very attractive candidates as vaccine delivery vehicles [ 2 , 3 ]. Lastly, thanks to their relatively small genome and simple metabolism, LAB can be exploited as food-grade cell factories to produce molecules of industrial and therapeutic interest. To meet some of these challenges and promises, it became apparent that metabolic engineering was the best approach. Owing to the industrial interest, the sound knowledge of its genetic and the availability of genetic tools, metabolic engineering of LAB has been carried out mainly with  Lactococcus lactis . The publication of the complete genome sequence of  L. lactis  in 2001 [ 4 ] was a boost to speed up achievements in rerouting metabolic fluxes with this LAB. For instances, it became possible to increase the production of diacetyl and to transform this mesophilic bacterium from homolactic fermenter to homoalanine fermenter. The innovative production of vitamins by  L. lactis  via genetic manipulation [ 5 , 6 ] is a convincing example of how metabolic engineering of LAB can be beneficial for consumers. A number of reviews [ 7 - 12 ] provide a more comprehensive discussion of the metabolic engineering of  L. lactis . Recently, the complete genome sequence of two  Streptococcus thermophilus  strains were published [ 13 ] and a third one is nearing completion [ 14 ].  S. thermophilus  is a thermophilic LAB species widely used for the manufacture of yogurt and cheeses that require elevated cooking temperatures such as Swiss and Italian types. The availability of these genome sequences will make it possible to apply genomic-related analytic methods such as functional and comparative genomics, microarray technologies, proteomics, and bioinformatics to this species. These genomic-based technologies will undoubtedly accelerate the metabolic engineering of  S. thermophilus , which is still at its infancy. We will briefly discuss current studies that will greatly benefit from these  S. thermophilus  genomic sequences: food-grade vectors, optimization of lactose metabolism and exopolysaccharide (EPS) production, and resistance to bacteriophages.
Introduction
The souring of milk by microorganisms has been used for thousand of years as a natural preservation procedure [ 1 ]. The method was domesticated to manufacture man-made edible fermented products such as cheese, which appeared in the human diet some 8,000–10,000 years ago. However, up to the beginning of the 20th century, milk fermentation was by no means a controlled process, and the search for improvements was strictly empiric and based on trial and error.The discovery and characterization of lactic acid bacteria (LAB) has tremendously modified the way fermented milk products are made. Considerable efforts have been devoted over the last fifty years to increase our knowledge about the genetics, biochemistry, and physiology of LAB. In addition to enhancing our understanding of microbial life, these studies have allowed dairy microbiologists and cheesemakers to select better strains and improve the productivity, quality, and safety of the final products. The characterization of LAB has promoted the rational development of blends of defined bacterial strains, now known as starter cultures, which are increasingly replacing the undefined blends traditionally used by the dairy industry. This strategy makes it easier to control acid production and, to some extent, phage problems. Unfortunately, it is also widely perceived that this approach reduces the much sought-after rich, complex flavour of fermented products made with undefined cultures. Thus, the search for LAB strains that produce characteristic aroma and flavours remains an attractive challenge for the dairy industry.The increasing awareness of the population of the importance of a healthy diet has led scientists to revisit the century-old hypothesis that some specific fermented dairy products may provide health benefits. A plethora of studies are underway to evaluate this concept and to improve the health benefits of LAB. Also, the long history of the safe use of these bacteria has made them very attractive candidates as vaccine delivery vehicles [ 2 , 3 ]. Lastly, thanks to their relatively small genome and simple metabolism, LAB can be exploited as food-grade cell factories to produce molecules of industrial and therapeutic interest.To meet some of these challenges and promises, it became apparent that metabolic engineering was the best approach. Owing to the industrial interest, the sound knowledge of its genetic and the availability of genetic tools, metabolic engineering of LAB has been carried out mainly with  Lactococcus lactis . The publication of the complete genome sequence of  L. lactis  in 2001 [ 4 ] was a boost to speed up achievements in rerouting metabolic fluxes with this LAB. For instances, it became possible to increase the production of diacetyl and to transform this mesophilic bacterium from homolactic fermenter to homoalanine fermenter. The innovative production of vitamins by  L. lactis  via genetic manipulation [ 5 , 6 ] is a convincing example of how metabolic engineering of LAB can be beneficial for consumers. A number of reviews [ 7 - 12 ] provide a more comprehensive discussion of the metabolic engineering of  L. lactis .Lactococcus lactisL. lactisL. lactisL. lactisRecently, the complete genome sequence of two  Streptococcus thermophilus  strains were published [ 13 ] and a third one is nearing completion [ 14 ].  S. thermophilus  is a thermophilic LAB species widely used for the manufacture of yogurt and cheeses that require elevated cooking temperatures such as Swiss and Italian types. The availability of these genome sequences will make it possible to apply genomic-related analytic methods such as functional and comparative genomics, microarray technologies, proteomics, and bioinformatics to this species. These genomic-based technologies will undoubtedly accelerate the metabolic engineering of  S. thermophilus , which is still at its infancy. We will briefly discuss current studies that will greatly benefit from these  S. thermophilus  genomic sequences: food-grade vectors, optimization of lactose metabolism and exopolysaccharide (EPS) production, and resistance to bacteriophages.Streptococcus thermophilusS. thermophilusS. thermophilusS. thermophilusDiscussion Food-grade vectors Metabolic engineering often involves inactivation or overexpression of relevant chromosomal genes or stringent control of an extrachromosomal foreign gene borne by a plasmid artificially introduced into the host. Plasmids thus play a central role in these studies because they are the primary vehicles used to manipulate target DNA sequences. However, these extrachromosomal genetic elements are naturally but infrequently observed in  S. thermophilus  strains[ 15 ]. Understandably, very few cloning tools are at hand, and those that are available are based on similar replication machinery. This lack of diversity poses significant problems for many genetic studies. While several types of transformation methods have been developed to introduce foreign DNA into  S. thermophilus , an efficient, stable, food grade expression system is still lacking. The recent discovery of a novel theta-type replicating plasmid [ 15 ] as well as suitable selection markers effective in  S. thermophilus , such as galactokinase [ 16 ] and alpha-galactosidase [ 17 ], suggest that help is on the way. The complete  S. thermophilus  genome sequences also provide crucial information on transcription and translation initiation signals and the codon usage of this bacterium. This may help in the design of efficient expression systems. Lactose metabolism The ability of  S. thermophilus  to rapidly take up and metabolize lactose is crucial in several fermentation processes. While  S. thermophilus  readily metabolizes the glucose moiety of lactose, it is unable to metabolize galactose, which is expelled into the external medium. The presence of galactose in yogurt and other dairy products might be unwanted for different reasons. Notably, galactose is poorly metabolized by humans and may cause, under certain conditions, health problems [ 18 , 19 ]. The release of galactose by  S. thermophilus  results either from poor expression of the  gal  operon [ 20 ] or inefficient translation of the  galK  gene coding for galactokinase [ 16 , 21 ]. The finding that the inability to grow on galactose was a consequence of poor  galK  translation was first suggested by a comparative analysis of the  S. thermophilus gal - lac  operons with the homologous genes from the phylogenetically related oral bacterium  Streptococcus salivarius . This is a convincing example of how comparative genome analysis may help to decipher specific metabolic pathways of LAB. While the introduction of a functional extrachromosomal  S. salivarius galK  allele in  S. thermophilus  allows it to grow on galactose, it does not prevent the expulsion of galactose during growth on lactose [ 16 ]. In this context, it is noteworthy that 10% of  S. thermophilus  genes are not functional (pseudogenes) and that one third of these pseudogenes are dedicated to sugar metabolism [ 13 ]. It would be interesting to determine whether reactivation of one or several pseudogenes that were originally involved in sugar metabolism could prevent or decrease galactose expulsion during growth on lactose. In this context, the availability of the complete sequence of the  S. salivarius  genome would be welcome since many  S. thermophilus  pseudogenes involved in sugar transport are functional in  S. salivarius  [ 13 ]. Exopolysacharides Some strains of  S. thermophilus  are widely used for the commercial manufacture of yogurt because they produce exopolysaccharides (EPS), which give a viscous texture to the fermented dairy product. Other EPS-producing  S. thermophilus  strains can also enhance the functional properties of some cheeses such as Mozzarella. The organoleptic properties of these products are largely due to the amount and types of exopolysaccharide produced during the fermentation process. The yield and sugar constituents of EPS are influenced by several factors and vary from strain to strain [ 22 ].  S. thermophilus  does not naturally produce large amounts of EPS, which explains why considerable efforts are being directed toward understanding the cellular mechanisms of EPS biosynthesis. Since low levels of sugar precursors may limit EPS synthesis, a better understanding of  S. thermophilus  metabolic flux during sugar metabolism may lead to new strategies to enhance EPS production [ 22 ]. Levander et al. [ 23 ] showed that such knowledge can be used to enhance EPS production in  S. thermophilus  by metabolic engineering of central carbon metabolism. Moreover, because EPS yields are growth associated, efforts to increase production levels are likely to require novel strategies to enhance biomass production. This task clearly requires a comprehensive view of the cell machinery. The sequencing of a whole genome is a mandatory step to achieve this goal. As our knowledge of  S. thermophilus  continues to improve, novel EPS and/or applications for EPS +  cultures are likely to emerge. Phage resistance Bacteriophages are the most significant cause of fermentation failures in the dairy industry worldwide. Dairy microbiologists have attempted for more than 70 years to eliminate, or at least bring under better control, the bacteriophages that interfere with the manufacture of many fermented milk products [ 24 ]. The publication of the complete genomes of two  S. thermophilus  hosts should provide new insights in several areas of phage research. The development of bacteriophage-insensitive  S. thermophilus  mutants is generally the first approach used to transform a phage-sensitive strain into a phage-resistant mutant, most likely following spontaneous chromosomal mutation in the gene encoding the phage receptor. Although progress has been made in identifying phage proteins involved in  S. thermophilus  host recognition [ 25 ], the identification of the phage receptors on the cell surface has remained elusive. Based on the results of genome data mining [ 26 ], a number of potential receptors can now be experimentally verified. At least eight complete  S. thermophilus  phage genomes are now available [ 27 , 28 ]. Phage research has thus already entered into the post-genomic era. Microarrays covering the two main groups of  S. thermophilus  phages are already available[ 29 ], meaning that it is now possible to design a complete array containing host and phage genes to study phage-host interactions on a novel and global scale during the infection process.
Discussion
Food-grade vectors Metabolic engineering often involves inactivation or overexpression of relevant chromosomal genes or stringent control of an extrachromosomal foreign gene borne by a plasmid artificially introduced into the host. Plasmids thus play a central role in these studies because they are the primary vehicles used to manipulate target DNA sequences. However, these extrachromosomal genetic elements are naturally but infrequently observed in  S. thermophilus  strains[ 15 ]. Understandably, very few cloning tools are at hand, and those that are available are based on similar replication machinery. This lack of diversity poses significant problems for many genetic studies. While several types of transformation methods have been developed to introduce foreign DNA into  S. thermophilus , an efficient, stable, food grade expression system is still lacking. The recent discovery of a novel theta-type replicating plasmid [ 15 ] as well as suitable selection markers effective in  S. thermophilus , such as galactokinase [ 16 ] and alpha-galactosidase [ 17 ], suggest that help is on the way. The complete  S. thermophilus  genome sequences also provide crucial information on transcription and translation initiation signals and the codon usage of this bacterium. This may help in the design of efficient expression systems.
Food-grade vectors
Metabolic engineering often involves inactivation or overexpression of relevant chromosomal genes or stringent control of an extrachromosomal foreign gene borne by a plasmid artificially introduced into the host. Plasmids thus play a central role in these studies because they are the primary vehicles used to manipulate target DNA sequences. However, these extrachromosomal genetic elements are naturally but infrequently observed in  S. thermophilus  strains[ 15 ].S. thermophilusUnderstandably, very few cloning tools are at hand, and those that are available are based on similar replication machinery. This lack of diversity poses significant problems for many genetic studies. While several types of transformation methods have been developed to introduce foreign DNA into  S. thermophilus , an efficient, stable, food grade expression system is still lacking. The recent discovery of a novel theta-type replicating plasmid [ 15 ] as well as suitable selection markers effective in  S. thermophilus , such as galactokinase [ 16 ] and alpha-galactosidase [ 17 ], suggest that help is on the way. The complete  S. thermophilus  genome sequences also provide crucial information on transcription and translation initiation signals and the codon usage of this bacterium. This may help in the design of efficient expression systems.S. thermophilusS. thermophilusS. thermophilusLactose metabolism The ability of  S. thermophilus  to rapidly take up and metabolize lactose is crucial in several fermentation processes. While  S. thermophilus  readily metabolizes the glucose moiety of lactose, it is unable to metabolize galactose, which is expelled into the external medium. The presence of galactose in yogurt and other dairy products might be unwanted for different reasons. Notably, galactose is poorly metabolized by humans and may cause, under certain conditions, health problems [ 18 , 19 ]. The release of galactose by  S. thermophilus  results either from poor expression of the  gal  operon [ 20 ] or inefficient translation of the  galK  gene coding for galactokinase [ 16 , 21 ]. The finding that the inability to grow on galactose was a consequence of poor  galK  translation was first suggested by a comparative analysis of the  S. thermophilus gal - lac  operons with the homologous genes from the phylogenetically related oral bacterium  Streptococcus salivarius . This is a convincing example of how comparative genome analysis may help to decipher specific metabolic pathways of LAB. While the introduction of a functional extrachromosomal  S. salivarius galK  allele in  S. thermophilus  allows it to grow on galactose, it does not prevent the expulsion of galactose during growth on lactose [ 16 ]. In this context, it is noteworthy that 10% of  S. thermophilus  genes are not functional (pseudogenes) and that one third of these pseudogenes are dedicated to sugar metabolism [ 13 ]. It would be interesting to determine whether reactivation of one or several pseudogenes that were originally involved in sugar metabolism could prevent or decrease galactose expulsion during growth on lactose. In this context, the availability of the complete sequence of the  S. salivarius  genome would be welcome since many  S. thermophilus  pseudogenes involved in sugar transport are functional in  S. salivarius  [ 13 ].
Lactose metabolism
The ability of  S. thermophilus  to rapidly take up and metabolize lactose is crucial in several fermentation processes. While  S. thermophilus  readily metabolizes the glucose moiety of lactose, it is unable to metabolize galactose, which is expelled into the external medium. The presence of galactose in yogurt and other dairy products might be unwanted for different reasons. Notably, galactose is poorly metabolized by humans and may cause, under certain conditions, health problems [ 18 , 19 ]. The release of galactose by  S. thermophilus  results either from poor expression of the  gal  operon [ 20 ] or inefficient translation of the  galK  gene coding for galactokinase [ 16 , 21 ]. The finding that the inability to grow on galactose was a consequence of poor  galK  translation was first suggested by a comparative analysis of the  S. thermophilus gal - lac  operons with the homologous genes from the phylogenetically related oral bacterium  Streptococcus salivarius . This is a convincing example of how comparative genome analysis may help to decipher specific metabolic pathways of LAB. While the introduction of a functional extrachromosomal  S. salivarius galK  allele in  S. thermophilus  allows it to grow on galactose, it does not prevent the expulsion of galactose during growth on lactose [ 16 ]. In this context, it is noteworthy that 10% of  S. thermophilus  genes are not functional (pseudogenes) and that one third of these pseudogenes are dedicated to sugar metabolism [ 13 ]. It would be interesting to determine whether reactivation of one or several pseudogenes that were originally involved in sugar metabolism could prevent or decrease galactose expulsion during growth on lactose. In this context, the availability of the complete sequence of the  S. salivarius  genome would be welcome since many  S. thermophilus  pseudogenes involved in sugar transport are functional in  S. salivarius  [ 13 ].S. thermophilusS. thermophilusS. thermophilusgalgalKgalKS. thermophilus gallacStreptococcus salivariusS. salivarius galKS. thermophilusS. thermophilusS. salivariusS. thermophilusS. salivariusExopolysacharides Some strains of  S. thermophilus  are widely used for the commercial manufacture of yogurt because they produce exopolysaccharides (EPS), which give a viscous texture to the fermented dairy product. Other EPS-producing  S. thermophilus  strains can also enhance the functional properties of some cheeses such as Mozzarella. The organoleptic properties of these products are largely due to the amount and types of exopolysaccharide produced during the fermentation process. The yield and sugar constituents of EPS are influenced by several factors and vary from strain to strain [ 22 ].  S. thermophilus  does not naturally produce large amounts of EPS, which explains why considerable efforts are being directed toward understanding the cellular mechanisms of EPS biosynthesis. Since low levels of sugar precursors may limit EPS synthesis, a better understanding of  S. thermophilus  metabolic flux during sugar metabolism may lead to new strategies to enhance EPS production [ 22 ]. Levander et al. [ 23 ] showed that such knowledge can be used to enhance EPS production in  S. thermophilus  by metabolic engineering of central carbon metabolism. Moreover, because EPS yields are growth associated, efforts to increase production levels are likely to require novel strategies to enhance biomass production. This task clearly requires a comprehensive view of the cell machinery. The sequencing of a whole genome is a mandatory step to achieve this goal. As our knowledge of  S. thermophilus  continues to improve, novel EPS and/or applications for EPS +  cultures are likely to emerge.
Exopolysacharides
Some strains of  S. thermophilus  are widely used for the commercial manufacture of yogurt because they produce exopolysaccharides (EPS), which give a viscous texture to the fermented dairy product. Other EPS-producing  S. thermophilus  strains can also enhance the functional properties of some cheeses such as Mozzarella. The organoleptic properties of these products are largely due to the amount and types of exopolysaccharide produced during the fermentation process. The yield and sugar constituents of EPS are influenced by several factors and vary from strain to strain [ 22 ].  S. thermophilus  does not naturally produce large amounts of EPS, which explains why considerable efforts are being directed toward understanding the cellular mechanisms of EPS biosynthesis. Since low levels of sugar precursors may limit EPS synthesis, a better understanding of  S. thermophilus  metabolic flux during sugar metabolism may lead to new strategies to enhance EPS production [ 22 ]. Levander et al. [ 23 ] showed that such knowledge can be used to enhance EPS production in  S. thermophilus  by metabolic engineering of central carbon metabolism. Moreover, because EPS yields are growth associated, efforts to increase production levels are likely to require novel strategies to enhance biomass production. This task clearly requires a comprehensive view of the cell machinery. The sequencing of a whole genome is a mandatory step to achieve this goal. As our knowledge of  S. thermophilus  continues to improve, novel EPS and/or applications for EPS +  cultures are likely to emerge.S. thermophilusS. thermophilusS. thermophilusS. thermophilusS. thermophilusS. thermophilusPhage resistance Bacteriophages are the most significant cause of fermentation failures in the dairy industry worldwide. Dairy microbiologists have attempted for more than 70 years to eliminate, or at least bring under better control, the bacteriophages that interfere with the manufacture of many fermented milk products [ 24 ]. The publication of the complete genomes of two  S. thermophilus  hosts should provide new insights in several areas of phage research. The development of bacteriophage-insensitive  S. thermophilus  mutants is generally the first approach used to transform a phage-sensitive strain into a phage-resistant mutant, most likely following spontaneous chromosomal mutation in the gene encoding the phage receptor. Although progress has been made in identifying phage proteins involved in  S. thermophilus  host recognition [ 25 ], the identification of the phage receptors on the cell surface has remained elusive. Based on the results of genome data mining [ 26 ], a number of potential receptors can now be experimentally verified. At least eight complete  S. thermophilus  phage genomes are now available [ 27 , 28 ]. Phage research has thus already entered into the post-genomic era. Microarrays covering the two main groups of  S. thermophilus  phages are already available[ 29 ], meaning that it is now possible to design a complete array containing host and phage genes to study phage-host interactions on a novel and global scale during the infection process.
Phage resistance
Bacteriophages are the most significant cause of fermentation failures in the dairy industry worldwide. Dairy microbiologists have attempted for more than 70 years to eliminate, or at least bring under better control, the bacteriophages that interfere with the manufacture of many fermented milk products [ 24 ]. The publication of the complete genomes of two  S. thermophilus  hosts should provide new insights in several areas of phage research.S. thermophilusThe development of bacteriophage-insensitive  S. thermophilus  mutants is generally the first approach used to transform a phage-sensitive strain into a phage-resistant mutant, most likely following spontaneous chromosomal mutation in the gene encoding the phage receptor. Although progress has been made in identifying phage proteins involved in  S. thermophilus  host recognition [ 25 ], the identification of the phage receptors on the cell surface has remained elusive. Based on the results of genome data mining [ 26 ], a number of potential receptors can now be experimentally verified.S. thermophilusS. thermophilusAt least eight complete  S. thermophilus  phage genomes are now available [ 27 , 28 ]. Phage research has thus already entered into the post-genomic era. Microarrays covering the two main groups of  S. thermophilus  phages are already available[ 29 ], meaning that it is now possible to design a complete array containing host and phage genes to study phage-host interactions on a novel and global scale during the infection process.S. thermophilusS. thermophilusConclusions A thorough understanding of LAB metabolism and how it is regulated by external stimuli is a prerequisite for maximizing the potential of LAB. The availability of complete  S. thermophilus  genome sequences will obviously facilitate our understanding of the metabolic potential of  S. thermophilus . It will also make it easier to design rational genetic manipulations of this important dairy bacterium in order to produce added value cheeses and yogurts and to use it as a cell factory. In addition, knowing the complete genome sequences should lead to the development of new genetic tools that will provide insights into the evolution of microbial communities, shifts in metabolism, and how each member adapts to the environmental changes that occur during complex fermentation processes. The exciting biotechnological developments in LAB and studies that are already underway will benefit both consumers and the dairy industry. The availability of the complete  S. thermophilus  genome sequence have opened up exciting, new possibilities that will build on an already rich heritage.
Conclusions
A thorough understanding of LAB metabolism and how it is regulated by external stimuli is a prerequisite for maximizing the potential of LAB. The availability of complete  S. thermophilus  genome sequences will obviously facilitate our understanding of the metabolic potential of  S. thermophilus . It will also make it easier to design rational genetic manipulations of this important dairy bacterium in order to produce added value cheeses and yogurts and to use it as a cell factory. In addition, knowing the complete genome sequences should lead to the development of new genetic tools that will provide insights into the evolution of microbial communities, shifts in metabolism, and how each member adapts to the environmental changes that occur during complex fermentation processes.S. thermophilusS. thermophilusThe exciting biotechnological developments in LAB and studies that are already underway will benefit both consumers and the dairy industry. The availability of the complete  S. thermophilus  genome sequence have opened up exciting, new possibilities that will build on an already rich heritage.S. thermophilus