Subpopulations of sensorless bacteria drive fitness in fluctuating environments.

Populations of bacteria often undergo a lag in growth when switching conditions. Because growth lags can be large compared to typical doubling times, variations in growth lag are an important but often overlooked component of bacterial fitness in fluctuating environments. We here explore how growth lag variation is determined for the archetypical switch from glucose to lactose as a carbon source in Escherichia coli. First, we show that single-cell lags are bimodally distributed and controlled by a single-molecule trigger. That is, gene expression noise causes the population before the switch to divide into subpopulations with zero and nonzero lac operon expression. While "sensorless" cells with zero preexisting lac expression at the switch have long lags because they are unable to sense the lactose signal, any nonzero lac operon expression suffices to ensure a short lag. Second, we show that the growth lag at the population level depends crucially on the fraction of sensorless cells and that this fraction in turn depends sensitively on the growth condition before the switch. Consequently, even small changes in basal expression can significantly affect the fraction of sensorless cells, thereby population lags and fitness under switching conditions, and may thus be subject to significant natural selection. Indeed, we show that condition-dependent population lags vary across wild E. coli isolates. Since many sensory genes are naturally low expressed in conditions where their inducer is not present, bimodal responses due to subpopulations of sensorless cells may be a general mechanism inducing phenotypic heterogeneity and controlling population lags in switching environments. This mechanism also illustrates how gene expression noise can turn even a simple sensory gene circuit into a bet hedging module and underlines the profound role of gene expression noise in regulatory responses.

The predictability of molecular evolution during functional innovation.

Determining the molecular changes that give rise to functional innovations is a major unresolved problem in biology. The paucity of examples has served as a significant hindrance in furthering our understanding of this process. Here we used experimental evolution with the bacterium Escherichia coli to quantify the molecular changes underlying functional innovation in 68 independent instances ranging over 22 different metabolic functions. Using whole-genome sequencing, we show that the relative contribution of regulatory and structural mutations depends on the cellular context of the metabolic function. In addition, we find that regulatory mutations affect genes that act in pathways relevant to the novel function, whereas structural mutations affect genes that act in unrelated pathways. Finally, we use population genetic modeling to show that the relative contributions of regulatory and structural mutations during functional innovation may be affected by population size. These results provide a predictive framework for the molecular basis of evolutionary innovation, which is essential for anticipating future evolutionary trajectories in the face of rapid environmental change.

The role of attachment style and depression in patients with hepatitis C.

Patients infected with chronic hepatitis C virus (HCV) commonly suffer from the triad of depression, pain and fatigue. This symptom triad in HCV is likely influenced by additional psychological and interpersonal factors, although the relationship is not clearly understood. This retrospective study aimed to characterize the relationship between attachment style and depressive and physical symptoms in the HCV-infected population. Over 18 months, 99 consecutively referred HCV infected patients were assessed with the Hamilton Depression Rating Scale (HDRS), Fatigue Severity Scale, Patient Health Questionnaire-15 for physical symptoms and the Relationship Questionnaire for attachment style. An ANOVA was used to identify differences between attachment styles and Pearson correlations were used to evaluate the association between depression, fatigue and physical symptoms. Approximately 15 % of patients in the sample had a fearful attachment style. Patients with fearful attachment style had significantly higher depressive symptoms compared to a secure attachment style (p = .025). No differences in physical and fatigue symptoms were observed between attachment styles. Further, HDRS scores were significantly associated with fatigue scores (p < .001) and physical symptoms (p < .001), reinforcing the relationship between these symptom domains in HCV-infected patients. Although depressive, physical and fatigue symptoms are inter-related in HCV-infected patients, our study results suggest that only depressive symptoms were influenced by the extremes of attachment style. Screening of relationship styles may identify at-risk HCV-infected individuals for depression who may have difficulty engaging in care and managing physical symptoms.

Identifying opportunities to improve management of autoimmune hepatitis: evaluation of drug adherence and psychosocial factors.

BACKGROUND & AIMS: Recognizing the importance of adherence to therapy in autoimmune hepatitis (AIH) is critical for patient care and avoidance of unnecessary intervention. The influence of psychosocial factors on treatment adherence needs better understanding and prominence. We sought to determine the association between anxiety, depressive symptoms, and avoidant relationship style on self-reported immunosuppressant medication adherence and treatment response in patients with AIH. METHODS: Fifty two patients with AIH were assessed using the Patient Health Questionnaire-9, the Generalized Anxiety Disorder-7, the Experiences in Close Relationship Scale (ECR) and a visual analogue scale to measure self-reported adherence. Laboratory markers of adherence and immunosuppressant treatment response were recorded. Chi-square Fisher's exact or Wilcox rank sum tests were used for comparison between groups. RESULTS: Treatment responders compared to non-responders were older (p=0.035), had normal or mild score ranges for anxiety and depression (p=0.025) and were significantly more likely to report >80% treatment adherence (p=0.007). Non-responders had higher anxiety symptoms (p=0.025), and significantly higher ECR-avoidance scores (p=0.023), suggestive of a tendency towards a more avoidant relationship style. CONCLUSIONS: We formally document that patients with AIH who have higher depressive and anxiety symptoms and avoidant relationship styles are more likely to be non-adherent to AIH therapy. We reiterate the need for early recognition and treatment of anxiety and depression in patients with AIH, stress the need for treatment adherence and highlight the need for formal evaluation of these factors in trials of therapy targeting apparent treatment non-responders.

Arginine methylation in subunits of mammalian pre-mRNA cleavage factor I.

Mammalian cleavage factor I (CF I(m)) is composed of two polypeptides of 25 kDa and either a 59 or 68 kDa subunit (CF I(m)25, CF I(m)59, CF I(m)68). It is part of the cleavage and polyadenylation complex responsible for processing the 3' ends of messenger RNA precursors. To investigate post-translational modifications in factors of the 3' processing complex, we systematically searched for enzymes that modify arginines by the addition of methyl groups. Protein arginine methyltransferases (PRMTs) are such enzymes that transfer methyl groups from S-adenosyl methionine to arginine residues within polypeptide chains resulting in mono- or dimethylated arginines. We found that CF I(m)68 and the nuclear poly(A) binding protein 1 (PABPN1) were methylated by HeLa cell extracts in vitro. By fractionation of these extracts followed by mass spectral analysis, we could demonstrate that the catalytic subunit PRMT5, together with its cofactor WD45, could symmetrically dimethylate CF I(m)68, whereas pICln, the third polypeptide of the complex, was stimulatory. As sites of methylation in CF I(m)68 we could exclusively identify arginines in a GGRGRGRF or "GAR" motif that is conserved in vertebrates. Further in vitro assays revealed a second methyltransferase, PRMT1, which modifies CF I(m)68 by asymmetric dimethylation of the GAR motif and also weakly methylates the C-termini of both CF I(m)59 and CF I(m)68. The results suggest that native-as compared with recombinant-protein substrates may contain additional determinants for methylation by specific PRMTs. A possible involvement of CF I(m) methylation in the context of RNA export is discussed.

Distinct roles of non-canonical poly(A) polymerases in RNA metabolism.

Trf4p and Trf5p are non-canonical poly(A) polymerases and are part of the heteromeric protein complexes TRAMP4 and TRAMP5 that promote the degradation of aberrant and short-lived RNA substrates by interacting with the nuclear exosome. To assess the level of functional redundancy between the paralogous Trf4 and Trf5 proteins and to investigate the role of the Trf4-dependent polyadenylation in vivo, we used DNA microarrays to compare gene expression of the wild-type yeast strain of S. cerevisiae with either that of trf4Delta or trf5Delta mutant strains or the trf4Delta mutant expressing the polyadenylation-defective Trf4(DADA) protein. We found little overlap between the sets of transcripts with altered expression in the trf4Delta or the trf5Delta mutants, suggesting that Trf4p and Trf5p target distinct groups of RNAs for degradation. Surprisingly, most RNAs the expression of which was altered by the trf4 deletion were restored to wild-type levels by overexpression of TRF4(DADA), showing that the polyadenylation activity of Trf4p is dispensable in vivo. Apart from previously reported Trf4p and Trf5p target RNAs, this analysis along with in vivo cross-linking and RNA immunopurification-chip experiments revealed that both the TRAMP4 and the TRAMP5 complexes stimulate the degradation of spliced-out introns via a mechanism that is independent of the polyadenylation activity of Trf4p. In addition, we show that disruption of trf4 causes severe shortening of telomeres suggesting that TRF4 functions in the maintenance of telomere length. Finally, our study demonstrates that TRF4, the exosome, and TRF5 participate in antisense RNA-mediated regulation of genes involved in phosphate metabolism. In conclusion, our results suggest that paralogous TRAMP complexes have distinct RNA selectivities with functional implications in RNA surveillance as well as other RNA-related processes. This indicates widespread and integrative functions of TRAMP complexes for the coordination of different gene expression regulatory processes.

A comparison of depression screening instruments in hepatitis C and the impact of depression on somatic symptoms.

OBJECTIVE: Treatment of hepatitis C (HCV) with pegylated interferon-alpha (IFNα) can cause depression in approximately 30% of patients and underscores the need for effective detection of depression prior to and during IFNα treatment. Elevated rates of depression in untreated HCV can be a barrier to initiating HCV therapy and can impact fatigue and physical symptoms. In this preliminary study, we examined the accuracy of the seven-item Hamilton Depression Rating Scale (HAM-7) and Patient Health Questionnairre-9 (PHQ-9) in detecting depression in HCV-infected patients and determined the effect of major depression on somatic symptoms. METHODS: We conducted a preliminary comparison of operating characteristics of the PHQ-9 and HAM-7 to the MINI International Neuropsychiatric Interview for major depression in 116 individuals with chronic HCV assessed in an ambulatory office setting. We also examined the differences in fatigue and somatic symptoms in depressed HCV-infected patients. RESULTS: Currently depressed chronic hepatitis C patients had significantly higher scores on all the scales compared with nondepressed patients. HAM-7 and PHQ-9 scores were significantly correlated with somatic and physical symptoms scales. Both the PHQ-9 and HAM-7 demonstrated comparable accuracy in detecting depression in comparison to the MINI. CONCLUSIONS: Our results suggest that the HAM-7 and PHQ-9 both have good operating characteristics compared with a criterion standard measure. Given that depression was associated with fatigue and increased somatic complaints, improved detection and treatment of depression could reduce disability and facilitate treatment for depressed HCV-infected patients.

Using alternative statistical formats for presenting risks and risk reductions.

BACKGROUND: The success of evidence-based practice depends on the clear and effective communication of statistical information. OBJECTIVES: To evaluate the effects of using alternative statistical presentations of the same risks and risk reductions on understanding, perception, persuasiveness and behaviour of health professionals, policy makers, and consumers. SEARCH STRATEGY: We searched Ovid MEDLINE (1966 to October 2007), EMBASE (1980 to October 2007), PsycLIT (1887 to October 2007), and the Cochrane Central Register of Controlled Trials (The Cochrane Library, 2007, Issue 3). We reviewed the reference lists of relevant articles, and contacted experts in the field. SELECTION CRITERIA: We included randomized and non-randomized controlled parallel and cross-over studies. We focused on four comparisons: a comparison of statistical presentations of a risk (eg frequencies versus probabilities) and three comparisons of statistical presentation of risk reduction: relative risk reduction (RRR) versus absolute risk reduction (ARR), RRR versus number needed to treat (NNT), and ARR versus NNT. DATA COLLECTION AND ANALYSIS: Two authors independently selected studies for inclusion, extracted data, and assessed risk of bias. We contacted investigators to obtain missing information. We graded the quality of evidence for each outcome using the GRADE approach. We standardized the outcome effects using adjusted standardized mean difference (SMD). MAIN RESULTS: We included 35 studies reporting 83 comparisons. None of the studies involved policy makers. Participants (health professionals and consumers) understood natural frequencies better than probabilities (SMD 0.69 (95% confidence interval (CI) 0.45 to 0.93)). Compared with ARR, RRR had little or no difference in understanding (SMD 0.02 (95% CI -0.39 to 0.43)) but was perceived to be larger (SMD 0.41 (95% CI 0.03 to 0.79)) and more persuasive (SMD 0.66 (95% CI 0.51 to 0.81)). Compared with NNT, RRR was better understood (SMD 0.73 (95% CI 0.43 to 1.04)), was perceived to be larger (SMD 1.15 (95% CI 0.80 to 1.50)) and was more persuasive (SMD 0.65 (95% CI 0.51 to 0.80)). Compared with NNT, ARR was better understood (SMD 0.42 (95% CI 0.12 to 0.71)), was perceived to be larger (SMD 0.79 (95% CI 0.43 to 1.15)).There was little or no difference for persuasiveness (SMD 0.05 (95% CI -0.04 to 0.15)). The sensitivity analyses including only high quality comparisons showed consistent results for persuasiveness for all three comparisons. Overall there were no differences between health professionals and consumers. The overall quality of evidence was rated down to moderate because of the use of surrogate outcomes and/or heterogeneity. None of the comparisons assessed behaviourbehaviour. AUTHORS' CONCLUSIONS: Natural frequencies are probably better understood than probabilities. Relative risk reduction (RRR), compared with absolute risk reduction (ARR) and number needed to treat (NNT), may be perceived to be larger and is more likely to be persuasive. However, it is uncertain whether presenting RRR is likely to help people make decisions most consistent with their own values and, in fact, it could lead to misinterpretation. More research is needed to further explore this question.

Framing of health information messages.

BACKGROUND: The same information about the evidence on health effects can be framed either in positive words or in negative words. Some research suggests that positive versus negative framing can lead to different decisions, a phenomenon described as the framing effect. Attribute framing is the positive versus negative description of a specific attribute of a single item or a state, for example, "the chance of survival with cancer is 2/3" versus "the chance of mortality with cancer is 1/3". Goal framing is the description of the consequences of performing or not performing an act as a gain versus a loss, for example, "if you undergo a screening test for cancer, your survival will be prolonged" versus "if you don't undergo screening test for cancer, your survival will be shortened". OBJECTIVES: To evaluate the effects of attribute (positive versus negative) framing and of goal (gain versus loss) framing of the same health information, on understanding, perception of effectiveness, persuasiveness, and behavior of health professionals, policy makers, and consumers. SEARCH METHODS: We searched the Cochrane Central Register of Controlled Trials (CENTRAL, The Cochrane Library, issue 3 2007), MEDLINE (Ovid) (1966 to October 2007), EMBASE (Ovid) (1980 to October 2007), PsycINFO (Ovid) (1887 to October 2007). There were no language restrictions. We reviewed the reference lists of related systematic reviews, included studies and of excluded but closely related studies. We also contacted experts in the field. SELECTION CRITERIA: We included randomized controlled trials, quasi-randomised controlled trials, and cross-over studies with health professionals, policy makers, and consumers evaluating one of the two types of framing. DATA COLLECTION AND ANALYSIS: Two review authors extracted data in duplicate and independently. We graded the quality of evidence for each outcome using the GRADE approach. We standardized the outcome effects using standardized mean difference (SMD). We stratified the analysis by the type of framing (attribute, goal) and conducted pre-planned subgroup analyses based on the type of message (screening, prevention, and treatment). The primary outcome was behaviour. We did not assess any adverse outcomes. MAIN RESULTS: We included 35 studies involving 16,342 participants (all health consumers) and reporting 51 comparisons.In the context of attribute framing, participants in one included study understood the message better when it was framed negatively than when it was framed positively (1 study; SMD -0.58 (95% confidence interval (CI) -0.94 to -0.22); moderate effect size; low quality evidence). Although positively-framed messages may have led to more positive perception of effectiveness than negatively-framed messages (2 studies; SMD 0.36 (95% CI -0.13 to 0.85); small effect size; low quality evidence), there was little or no difference in persuasiveness (11 studies; SMD 0.07 (95% CI -0.23 to 0.37); low quality evidence) and behavior (1 study; SMD 0.09 (95% CI -0.14 to 0.31); moderate quality evidence).In the context of goal framing, loss messages led to a more positive perception of effectiveness compared to gain messages for screening messages (5 studies; SMD -0.30 (95% CI -0.49 to -0.10); small effect size; moderate quality evidence) and may have been more persuasive for treatment messages (3 studies; SMD -0.50 (95% CI -1.04 to 0.04); moderate effect size; very low quality evidence). There was little or no difference in behavior (16 studies; SMD -0.06 (95% CI -0.15 to 0.03); low quality evidence). No study assessed the effect on understanding. AUTHORS' CONCLUSIONS: Contrary to commonly held beliefs, the available low to moderate quality evidence suggests that both attribute and goal framing may have little if any consistent effect on health consumers' behaviour. The unexplained heterogeneity between studies suggests the possibility of a framing effect under specific conditions. Future research needs to investigate these conditions.

A new yeast poly(A) polymerase complex involved in RNA quality control.

Eukaryotic cells contain several unconventional poly(A) polymerases in addition to the canonical enzymes responsible for the synthesis of poly(A) tails of nuclear messenger RNA precursors. The yeast protein Trf4p has been implicated in a quality control pathway that leads to the polyadenylation and subsequent exosome-mediated degradation of hypomethylated initiator tRNAMet (tRNAiMet). Here we show that Trf4p is the catalytic subunit of a new poly(A) polymerase complex that contains Air1p or Air2p as potential RNA-binding subunits, as well as the putative RNA helicase Mtr4p. Comparison of native tRNAiMet with its in vitro transcribed unmodified counterpart revealed that the unmodified RNA was preferentially polyadenylated by affinity-purified Trf4 complex from yeast, as well as by complexes reconstituted from recombinant components. These results and additional experiments with other tRNA substrates suggested that the Trf4 complex can discriminate between native tRNAs and molecules that are incorrectly folded. Moreover, the polyadenylation activity of the Trf4 complex stimulated the degradation of unmodified tRNAiMet by nuclear exosome fractions in vitro. Degradation was most efficient when coupled to the polyadenylation activity of the Trf4 complex, indicating that the poly(A) tails serve as signals for the recruitment of the exosome. This polyadenylation-mediated RNA surveillance resembles the role of polyadenylation in bacterial RNA turnover.

Bipolar disorder and suicide: research synthesis and clinical translation.

Attempted suicide and suicide are prevalent in individuals with bipolar disorder (BD). Extant evidence indicates that history of suicide attempts, percentage of time spent in a depressed state, and hostility are factors associated with suicide attempts and completed suicide. Childhood adversity (eg, sexual and physical abuse) is emerging as a risk factor for suicide attempts in adults with BD. The pertinacity of medical comorbidity (eg, obesity, metabolic syndrome) in the bipolar population is further underscored by its preliminary association with suicidality. Biomarkers such as cerebrospinal fluid monoamine metabolite levels may be predictive of suicide attempts and lethality in BD. Compelling evidence supports an antisuicide effect of long-term lithium prophylaxis; lithium's salutary effect is mediated primarily by reduced lethality of suicidal acts. Conventional unimodal antidepressants may engender or exacerbate suicidality in susceptible individuals with BD. A nascent database suggests that adjunctive psychosocial interventions may further reduce suicide risk in bipolar individuals.

A novel program for treating patients with trimorbidity: hepatitis C, serious mental illness, and active substance use.

BACKGROUND: Advances in hepatitis C virus (HCV) treatment have yielded improved virological response rates, and yet, many individuals with psychiatric illness still fail to receive HCV therapy. Concerns about safety, adherence, and efficacy of HCV treatment are compounded and treatment is further deferred when substance use is also present. This is especially problematic given the disproportionately high rates of both mental health issues and substance use among individuals living with HCV. OBJECTIVE: This study sought to examine HCV treatment outcomes in clients with serious mental illness (SMI) and with high rates of active substance use who were participating in a community-based HCV treatment program. PATIENTS AND METHODS: A retrospective chart review of 129 clients was carried out. Patients were classified as having an SMI if they had a history of bipolar disorder, psychotic disorder, past suicide attempt or mental health related hospitalization. RESULTS: Fifty-one patients were defined as having an SMI. Among the 46 patients with SMI and a detectable HCV viral load, HCV antiviral therapy was initiated in nine (19.6%). A relapse or an increase in substance use was common (77.8% or n=7), as was the requirement for adjustment or initiation of psychotropic medications (66.7% or n=6) during HCV antiviral therapy. Despite these barriers, rates of adherence to antiviral therapy were high and overall sustained virological response rates were comparable with published trials. CONCLUSION: This study is the first to report HCV treatment outcomes in a population in which SMI and active polysubstance use was prevalent and suggests that with appropriate models of care, clients with trimorbidity can be treated safely and effectively.

Yhh1p/Cft1p directly links poly(A) site recognition and RNA polymerase II transcription termination.

RNA polymerase II (pol II) transcription termination requires co-transcriptional recognition of a functional polyadenylation signal, but the molecular mechanisms that transduce this signal to pol II remain unclear. We show that Yhh1p/Cft1p, the yeast homologue of the mammalian AAUAAA interacting protein CPSF 160, is an RNA-binding protein and provide evidence that it participates in poly(A) site recognition. Interestingly, RNA binding is mediated by a central domain composed of predicted beta-propeller-forming repeats, which occurs in proteins of diverse cellular functions. We also found that Yhh1p/Cft1p bound specifically to the phosphorylated C-terminal domain (CTD) of pol II in vitro and in a two-hybrid test in vivo. Furthermore, transcriptional run-on analysis demonstrated that yhh1 mutants were defective in transcription termination, suggesting that Yhh1p/Cft1p functions in the coupling of transcription and 3'-end formation. We propose that direct interactions of Yhh1p/Cft1p with both the RNA transcript and the CTD are required to communicate poly(A) site recognition to elongating pol II to initiate transcription termination.

A role for SSU72 in balancing RNA polymerase II transcription elongation and termination.

Interactions of pre-mRNA 3'end factors and the CTD of RNA polymerase II (RNAP II) are required for transcription termination and 3'end processing. Here, we demonstrate that Ssu72p is stably associated with yeast cleavage and polyadenylation factor CPF and provide evidence that it bridges the CPF subunits Pta1p and Ydh1p/Cft2p, the general transcription factor TFIIB, and RNAP II via Rpb2p. Analyses of ssu72-2 mutant cells in the absence and presence of the nuclear exosome component Rrp6p revealed defects in RNAP II transcription elongation and termination. 6-azauracil, that reduces transcription elongation rates, suppressed the ssu72-2 growth defect at 33 degrees C. The sum of our analyses suggests a negative influence of Ssu72p on RNAP II during transcription that affects the commitment to either elongation or termination.