Improving Cell-Free Expression of Model Membrane Proteins by Tuning Ribosome Cotranslational Membrane Association and Nascent Chain Aggregation

Cell-free gene expression (CFE) systems are powerful tools for transcribing and translating genes outside of a living cell. Synthesis of membrane proteins is of particular interest, but their yield in CFE is substantially lower than that for soluble proteins. In this paper, we study the CFE of membrane proteins and develop a quantitative kinetic model. We identify that ribosome stalling during the translation of membrane proteins is a strong predictor of membrane protein synthesis due to aggregation between the ribosome nascent chains. Synthesis can be improved by the addition of lipid membranes, which incorporate protein nascent chains and, therefore, kinetically compete with aggregation. We show that the balance between peptide-membrane association and peptide aggregation rates determines the yield of the synthesized membrane protein. We define a membrane protein expression score that can be used to rationalize the engineering of lipid composition and the N-terminal domain of a native and computationally designed membrane proteins produced through CFE.

Phospholipid dependency of membrane protein insertion by the Sec translocon

Membrane protein insertion into and translocation across the bacterial cytoplasmic membrane are essential processes facilitated by the Sec translocon. Membrane insertion occurs co-translationally whereby the ribosome nascent chain is targeted to the translocon via signal recognition particle and its receptor FtsY. The phospholipid dependence of membrane protein insertion has remained mostly unknown. Here we assessed in vitro the dependence of the SecA independent insertion of the mannitol permease MtlA into the membrane on the main phospholipid species present in Escherichia coli. We observed that insertion depends on the presence of phosphatidylglycerol and is due to the anionic nature of the polar headgroup, while insertion is stimulated by the zwitterionic phosphatidylethanolamine. We found an optimal insertion efficiency at about 30 mol% DOPG and 50 mol% DOPE which approaches the bulk membrane phospholipid composition of E. coli.

The complex relationship between diet, symptoms, and intestinal inflammation in persons with inflammatory bowel disease: The Manitoba Living With IBD Study

BACKGROUND

We aimed to examine whether an association exists between diet quality, based on the Prospective Urban Rural Epidemiology (PURE) Healthy Diet Score (HDS), and active inflammatory bowel disease (IBD).

METHODS

Participants were drawn from the Manitoba Living With IBD Study cohort. The Harvard Food Frequency Questionnaire (FFQ) was used to calculate the HDS at two time points: baseline and 1-year follow-up. Using generalized estimating equations (GEE) logistic regression, we assessed the association between the HDS and (1) the IBD Symptom Inventory (IBDSI); (2) intestinal inflammation, measured by fecal calprotectin (FCAL); and (3) self-reported IBD flares.

RESULTS

There were 294 completed FFQs among 153 people. Of these, 100% had completed data about an IBD flare, 98% had FCAL measurements, and 96% had completed IBDSI scores. On a HDS scoring method of 0-8, the odds of FCAL >250 mcg/g were lower for participants with a HDS of 4 vs 0-3 (adjusted odds ratio [OR], 0.38; 95% CI, 0.19-0.77). When applying a second HDS scoring method (8-40), the odds of having an IBD flare were 3.6 times greater with a HDS between 21 and 24 compared with an HDS ≤20 (adjusted OR, 3.63; 95% CI, 1.03-12.78).

CONCLUSIONS

We found that active inflammation was less likely among those with a moderate HDS , whereas symptomatic IBD flares were more likely. People may choose to consume a moderate amount of healthy foods such as fruits and vegetables, even knowing that those foods may cause a symptomatic flare.

Patterns of Alcohol Consumption in the PURE Poland Cohort Study and Their Relationship with Health Problems

(1) Background: Alcohol is a leading risk factor of premature morbidity and mortality. The objective of this study was to investigate the patterns of alcohol consumption in the PURE Poland cohort study baseline. (2) Methods: A Polish cohort was enrolled in the baseline study in 2007–2010. The study group consisted of 2021 adult participants of urban and rural areas from the Lower Silesia voivodeship in Poland (747 men and 1274 women). (3) Results: In the overall study population, 67.3% were current drinkers, 10.3% were former drinkers, and 22.4% were abstainers. Current use of alcohol products was more prevalent in men (77.2%), people living in urban areas (73.0%), and people with a higher level of education (78.0%). The percentage of current drinkers decreased with increasing age (from 73.4% in 30- to 44-year-olds to 48.8% in participants aged 64 and more). The majority of participants (89.2%) declared a low level of alcohol intake. The chance of high level of intake of alcohol was four times higher in men than in women (OR 4.17; CI 1.64–10.6). The majority of participants (54.6%) declared most frequent consumption of low-alcohol drinks (beer, wine) and 21% declared most frequent consumption of spirits. Current drinkers had almost 1.5-fold higher odds of diabetes and cardiovascular diseases (CVD) than never drinkers (OR 1.49, CI 1.03–2.17; OR 1.66, CI 1.27–2.18, respectively). Former drinkers had higher odds for hypertension and CVD than never drinkers (1.73, CI 1.05–2.85; OR 1.76, CI 1.22–2.53, respectively). (4) Conclusions: In our cohort study, we observed several socio-demographic factors differentiating the patterns of alcohol consumption. The preventive programs should focus predominantly on men, people aged <45 years, and those with a higher level of education.

Changes in diabetes prevalence and corresponding risk factors - findings from 3- and 6-year follow-up of PURE Poland cohort study

Background

Diabetes mellitus (DM) is one of the greatest challenges for public health worldwide. The aim of the study was the analysis of diabetes development in participants with normoglycemia and Impaired Fasting Glucose (IFG) in 3-year and 6-year follow-up of PURE Poland cohort study.

Methods

The analysis was conducted in Polish cohort enrolled into Prospective Urban and Rural Epidemiology (PURE) Study. The following study presents results of 1330 participants that have partaken both in the baseline study, in 3-year and in the 6-year follow up. The analysis of the impact of risk factors on diabetes development was performed using multivariate Cox frailty analysis. Population Attributable Risk (PAR) was computed individually for every risk factor.

Results

Diabetes prevalence increased from 17.7% at baseline to 23.98% in 3-year- and 28.27% in 6-year follow-up. The risk of diabetes was higher in participants with obesity [HR = 5.7, 95%Cl 2,56-12,82], overweight [HR = 3.4, 95%Cl 1,56-7,54] and IFG [HR = 2.7, 95%Cl 1,87-3,85]. The risk of diabetes development was almost 2-fold higher in men than in women [HR = 1.826; 95%CI =1,24 - 2,69]. In 6 years, diabetes developed in 23.8% of participants with IFG and 7.9% of participants with normoglycemia. According to PAR, overweight and obesity accounted for 80.8%, hypertension for 67.6% and IFG for 38.3% of diabetes cases in our population.

Conclusions

Our study reveals alarming increase in prevalence of diabetes during 6 years of observation. In our population, most diabetes cases can be attributed to overweight, obesity, hypertension and IFG. Findings add strong rationale to implement targeted preventive measures in population of high risk.

Replication and expansion of epigenome-wide association literature in a black South African population

Background

DNA methylation is associated with non-communicable diseases (NCDs) and related traits. Methylation data on continental African ancestries are currently scarce, even though there are known genetic and epigenetic differences between ancestral groups and a high burden of NCDs in Africans. Furthermore, the degree to which current literature can be extrapolated to the understudied African populations, who have limited resources to conduct independent large-scale analysis, is not yet known. To this end, this study examines the reproducibility of previously published epigenome-wide association studies of DNA methylation conducted in different ethinicities, on factors related to NCDs, by replicating findings in 120 South African Batswana men aged 45 to 88 years. In addition, novel associations between methylation and NCD-related factors are investigated using the Illumina EPIC BeadChip.

Results

Up to 86% of previously identified epigenome-wide associations with NCD-related traits (alcohol consumption, smoking, body mass index, waist circumference, C-reactive protein, blood lipids and age) overlapped with those observed here and a further 13% were directionally consistent. Only 1% of the replicated associations presented with effects opposite to findings in other ancestral groups. The majority of these inconcistencies were associated with population-specific genomic variance. In addition, we identified eight new 450K array CpG associations not previously reported in other ancestries, and 11 novel EPIC CpG associations with alcohol consumption.

Conclusions

The successful replication of existing EWAS findings in this African population demonstrates that blood-based 450K EWAS findings from commonly investigated ancestries can largely be extrapolated to ethnicities for which epigenetic data are not yet available. Possible population-specific differences in 14% of the tested associations do, however, motivate the need to include a diversity of ethnic groups in future epigenetic research. The novel associations found with the enhanced coverage of the Illumina EPIC array support its usefulness to expand epigenetic literature.

Loop-mediated isothermal amplification (LAMP): Expansion of its practical application as a tool to achieve universal health coverage

Since its invention in 2000, loop-mediated isothermal amplification (LAMP) has attracted great interest from researchers and has been used as a simple and rapid diagnostic tool for detection of infectious and non-infectious diseases. Here we review the recent circumstances and outcomes of these applications of LAMP to show the potential of LAMP as a tool for achieving universal health coverage (UHC). A future application of LAMP, such as in an automated multiplex format, is also discussed.

Sociodemographic characteristic of changes in smoking patterns in rural and urban population of PURE Poland study: findings from 6-year follow up

Background

Tobacco smoking is one of the most serious modern civilization threats. According to WHO identifying patterns of tobacco use is essential for implementing effective preventive policies. The aim of the paper was to assess changes in smoking patterns among the PURE study population over 6 years.

Methods

The study sample comprised of 1784 adult participants from PURE Poland study, who were assessed at baseline (2007–2010) and then at 6-year follow-up. Participants were classified into current smokers, ex-smokers and never smokers. Smoking patterns were analyzed according to sex, age/birth cohort, place of residence (urban vs rural setting), and education level.

Results

Overall, a significant decrease of 3.1% in current smokers was observed (from 20.0% in baseline to 16.9 at follow-up). However, 0.8% of never smokers and 6.2% of ex-smokers at baseline were classified as current smokers at 6-year follow-up. Despite overall decrease in percentage of current smokers in both rural and urban area, in fact significantly more ex-smokers from rural area became current smokers after 6 years. Living in the rural area was associated with nearly two-fold increase in current smoking, and almost two-fold decline in chances to quit smoking. The highest percentage of current smokers was observed in birth year cohort 1961–1979.

Conclusion

Despite a small but significant decline in overall smoking rates, important differences in smoking and quitting patterns emerged between rural and urban areas, as well as sexes. A less favorable smoking patterns were observed among women, and rural populations, suggesting that these are important targets of future tobacco control interventions in Poland.

Overview of Coronary Heart Disease Risk Initiatives in South Asia

PURPOSE OF REVIEW

Cardiovascular disease (CVD) is now the leading cause of morbidity and mortality worldwide. Industrialization and economic growth have led to an unprecedented increment in the burden of CVD and their risk factors in less industrialized regions of the world. While there are abundant data on CVD and their risk factors from longitudinal cohort studies done in the West, good-quality data from South Asia are lacking.

RECENT FINDINGS

Several multi-institutional, observational, prospective registries, and epidemiologic cohorts in South Asia have been established to systematically evaluate the burden of CVD and their risk factors. The PINNACLE (Practice Innovation and Clinical Excellence) India Quality Improvement Program (PIQIP), the Kerala Acute Coronary Syndrome (ACS), and Trivandrum Heart Failure registries have focused on secondary prevention of CVD and performance measurement in both outpatient and inpatient settings, respectively. The Prospective Urban and Rural Epidemiology (PURE), Centre for Cardiometabolic Risk Reduction in South Asia (CARRS), and other epidemiologic and genetic studies have focused on primary prevention of CVD and evaluated variables such as environment, smoking, physical activity, health systems, food and nutrition policy, dietary consumption patterns, socioeconomic factors, and healthy neighborhoods. The international cardiovascular community has been responsive to a burgeoning cardiovascular disease burden in South Asia. Several collaborations have formed between the West (North America in particular) and South Asia to catalyze evidence-based and data-driven changes in the federal health policy in this part of the world to promote cardiovascular health and mitigate cardiovascular risk.