Genomic charting of ribosomally synthesized natural product chemical space facilitates targeted mining.

Microbial natural products are an evolved resource of bioactive small molecules, which form the foundation of many modern therapeutic regimes. Ribosomally synthesized and posttranslationally modified peptides (RiPPs) represent a class of natural products which have attracted extensive interest for their diverse chemical structures and potent biological activities. Genome sequencing has revealed that the vast majority of genetically encoded natural products remain unknown. Many bioinformatic resources have therefore been developed to predict the chemical structures of natural products, particularly nonribosomal peptides and polyketides, from sequence data. However, the diversity and complexity of RiPPs have challenged systematic investigation of RiPP diversity, and consequently the vast majority of genetically encoded RiPPs remain chemical "dark matter." Here, we introduce an algorithm to catalog RiPP biosynthetic gene clusters and chart genetically encoded RiPP chemical space. A global analysis of 65,421 prokaryotic genomes revealed 30,261 RiPP clusters, encoding 2,231 unique products. We further leverage the structure predictions generated by our algorithm to facilitate the genome-guided discovery of a molecule from a rare family of RiPPs. Our results provide the systematic investigation of RiPP genetic and chemical space, revealing the widespread distribution of RiPP biosynthesis throughout the prokaryotic tree of life, and provide a platform for the targeted discovery of RiPPs based on genome sequencing.

Polyketide and nonribosomal peptide retro-biosynthesis and global gene cluster matching.

Polyketides (PKs) and nonribosomal peptides (NRPs) are profoundly important natural products, forming the foundations of many therapeutic regimes. Decades of research have revealed over 11,000 PK and NRP structures, and genome sequencing is uncovering new PK and NRP gene clusters at an unprecedented rate. However, only ∼10% of PK and NRPs are currently associated with gene clusters, and it is unclear how many of these orphan gene clusters encode previously isolated molecules. Therefore, to efficiently guide the discovery of new molecules, we must first systematically de-orphan emergent gene clusters from genomes. Here we provide to our knowledge the first comprehensive retro-biosynthetic program, generalized retro-biosynthetic assembly prediction engine (GRAPE), for PK and NRP families and introduce a computational pipeline, global alignment for natural products cheminformatics (GARLIC), to uncover how observed biosynthetic gene clusters relate to known molecules, leading to the identification of gene clusters that encode new molecules.

Assembly and clustering of natural antibiotics guides target identification.

Antibiotics are essential for numerous medical procedures, including the treatment of bacterial infections, but their widespread use has led to the accumulation of resistance, prompting calls for the discovery of antibacterial agents with new targets. A majority of clinically approved antibacterial scaffolds are derived from microbial natural products, but these valuable molecules are not well annotated or organized, limiting the efficacy of modern informatic analyses. Here, we provide a comprehensive resource defining the targets, chemical origins and families of the natural antibacterial collective through a retrobiosynthetic algorithm. From this we also detail the directed mining of biosynthetic scaffolds and resistance determinants to reveal structures with a high likelihood of having previously unknown modes of action. Implementing this pipeline led to investigations of the telomycin family of natural products from Streptomyces canus, revealing that these bactericidal molecules possess a new antibacterial mode of action dependent on the bacterial phospholipid cardiolipin.

Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM).

Microbial natural products are an invaluable source of evolved bioactive small molecules and pharmaceutical agents. Next-generation and metagenomic sequencing indicates untapped genomic potential, yet high rediscovery rates of known metabolites increasingly frustrate conventional natural product screening programs. New methods to connect biosynthetic gene clusters to novel chemical scaffolds are therefore critical to enable the targeted discovery of genetically encoded natural products. Here, we present PRISM, a computational resource for the identification of biosynthetic gene clusters, prediction of genetically encoded nonribosomal peptides and type I and II polyketides, and bio- and cheminformatic dereplication of known natural products. PRISM implements novel algorithms which render it uniquely capable of predicting type II polyketides, deoxygenated sugars, and starter units, making it a comprehensive genome-guided chemical structure prediction engine. A library of 57 tailoring reactions is leveraged for combinatorial scaffold library generation when multiple potential substrates are consistent with biosynthetic logic. We compare the accuracy of PRISM to existing genomic analysis platforms. PRISM is an open-source, user-friendly web application available at http://magarveylab.ca/prism/.

The use of a new indirect method to estimate ethnic-group fertility rates for subnational projections for England.

To project the ethnic-group populations of local authorities in England to 2051, estimates of ethnic-specific fertility rates were needed. In the absence of ethnic information on birth records, we developed indirect estimation methods that use a combination of vital statistics, the census (both microdata and aggregate tables), and survey data (Labour Force Survey). We estimated age-specific and total fertility rates successively for five broad ethnic groups encompassed by all data-sets, and for eight ethnic groups encompassed by the 1991 and 2001 Censuses for England. We then used census data to disaggregate the estimates to the 16 ethnic groups required for the subnational projections and the Hadwiger function to estimate single-year-of-age estimates. We estimated the uncertainty around the fertility estimates and used a logistic model to project rates to 2021, after which we assumed rates would remain constant.

Positive pretransplantation cytomegalovirus serology is a risk factor for cardiac allograft vasculopathy in children.

BACKGROUND: Cytomegalovirus (CMV) infection has been implicated as a cause of posttransplantation coronary artery disease in adults. The purpose of this retrospective observational study was to evaluate the effect of CMV on outcome after heart transplantation in children. METHODS AND RESULTS: Risk factors tested were recipient age, sex, and pretransplantation CMV serology; use of anti-CMV prophylaxis; posttransplantation evidence of CMV infection; and donor CMV serology. Transplantations were stratified traditionally according to CMV risk as low risk (recipient negative/donor negative), intermediate risk (recipient positive), and high risk (recipient negative/donor positive). Primary outcome measures were (1) development of coronary artery vasculopathy, (2) mortality (or graft loss) that occurred outside the early postoperative period, and (3) death (or graft loss) due to vasculopathy. Analysis was by proportional hazards modeling. A total of 165 children underwent heart transplantation, with a mean age at transplantation of 7.8 (SD 5.6) years. Thirty-two children had laboratory evidence of CMV infection after transplantation, but only 6 developed CMV disease or syndrome. Traditional CMV risk stratification correlated well with CMV infection but did not predict mortality, coronary artery disease, or coronary death. In contrast, positive recipient CMV was the only independent predictor of all 3 outcome measures: coronary artery disease (hazard ratio=3.6), all-cause mortality (partial hazard ratio=4.1), and coronary death (hazard ratio=4.6). CONCLUSIONS: In children, pretransplantation recipient CMV status is a more powerful predictor for the development of clinically significant vasculopathy and subsequent death than traditional risk stratification. This phenomenon warrants further investigation.

Endocrine predictors of mortality in canine babesiosis caused by Babesia canis rossi.

This prospective, cross-sectional, observational study was designed to determine the association between the hormones of the pituitary-adrenal and pituitary-thyroid axes and outcome in dogs with naturally occurring Babesia canis rossi babesiosis. Ninety-five dogs with canine babesiosis were studied and blood samples were obtained from the jugular vein in each dog prior to treatment at admission to hospital. Serum cortisol, adrenocorticotrophic hormone (ACTH), thyroxine, free thyroxine and thyrotropin (TSH) concentrations were measured. Diagnosis was confirmed by polymerase chain reaction and reverse line blot and dogs infected with Babesia canis vogeli or Ehrlichia canis were excluded. Three outcomes were defined: hospitalization with subsequent death (n=7); hospitalization followed by recovery (n=56); and treatment as an outpatient (n=32). Serum cortisol and ACTH concentrations were significantly higher in the dogs that died, compared to hospitalized dogs that survived and compared to dogs treated as outpatients. Serum T4 and free T4 concentrations were significantly lower in the dogs that died, compared to the hospitalized dogs that survived and compared to dogs treated as outpatients. Serum TSH concentrations were not significantly different between any of the groups. Mortality was significantly associated with high cortisol and high ACTH concentrations and with low T4 and fT4 concentrations in dogs suffering from B. canis rossi babesiosis.

Selective migration, health and deprivation: a longitudinal analysis.

Population migration is a major determinant of an area's age-sex structure and socio-economic characteristics. The suggestion that migration can contribute to an increase or decrease in place-specific rates of illness is not new. However, differences in health status between small geographical locations that may be affected by the inter-relationships between health, area-based deprivation and migration are under-researched. Using the Office for National Statistics (ONS) England and Wales Longitudinal Study (LS) 1971-1991, this research tracks individuals to identify any systematic sorting of people that has contributed to the area-level relationships between health (limiting long-term illness and mortality) and deprivation (Carstairs quintiles). The results demonstrate that among the young, migrants are generally healthier than non-migrants. Migrants who move from more to less deprived locations are healthier than migrants who move from less to more deprived locations. Within less deprived areas migrants are healthier than non-migrants but within deprived areas migrants are less healthy than non-migrants. Over the 20 year period, the largest absolute flow is by relatively healthy migrants moving away from more deprived areas towards less deprived areas. The effect is to raise ill-health and mortality rates in the origins and lower them in the destinations. This is reinforced by a significant group of people in poor health who move from less to more deprived locations. In contrast, a small group of unhealthy people moved away from more deprived into less deprived areas. These countercurrents of less healthy people have a slight ameliorating effect on the health-deprivation relationship. Whilst health-deprivation relationships are more marked for migrants there are also health (dis-) benefits for non-migrants if their location becomes relatively more or less deprived over time. Overall we found that between 1971 and 1991, inequalities in health increased between the least and most deprived areas, compared with the health-deprivation relationship which would have existed if peoples' locations and deprivation patterns had stayed geographically constant. Migration, rather than changes in the deprivation of the area that non-migrants live in, accounts for the large majority of change.

Improved early outcome for end-stage dilated cardiomyopathy in children.

OBJECTIVE: To review the impact of management changes on the early outcomes of end-stage dilated cardiomyopathy in children. METHODS: We conducted a retrospective study of all consecutive children with end-stage dilated cardiomyopathy who received hospital treatment since 1992. Over the past 3 years the following management changes were made: (1) more aggressive use of mechanical cardiac assistance; (2) high priority listing for transplantation; and (3) ABO incompatible transplants for infants. Outcomes for 46 patients admitted between 1992 and 1999 (group I) were compared with 53 patients between 2000 and March 2003 (group II). RESULTS: In group I, 12 (26%) patients received mechanical support with recovery in 3 and transplantation in 5 (1 died). In group II, 19 (36%) patients received extracorporeal membrane oxygenation, with recovery in 5 and transplantation in 12 (all survived). The use of mechanical assistance was associated with high morbidity related to bleeding, end-organ failure, and long-term mechanical ventilation. Five patients in group II received ABO incompatible transplants and all survived. There have been no episodes of rejection or need for increased immunosuppressive therapy. Hospital mortality has been significantly reduced (group I, 37% vs group II, 11%; P <.05). CONCLUSIONS: Recent refinements in the management of end-stage dilated cardiomyopathy in children have significantly reduced early mortality. Identification of markers of early myocardial recovery and development of mechanical devices for longer term and more physiologic support are essential to achieve further improvements in outcome.

Changing places. Do changes in the relative deprivation of areas influence limiting long-term illness and mortality among non-migrant people living in non-deprived households?

Numerous studies have investigated the relative importance of contextual (place) and compositional (person) factors in explaining health and mortality variations. Commonly, these studies control for a range of individual characteristics before testing whether one or more contextual variables have a significant impact on the health or mortality outcome. The findings have been inconsistent, although the growing consensus is, first, that contextual effects are significant but are less important than compositional factors and, second, that contextual effects have a stronger impact in studies of morbidity than in studies of mortality. Here we use longitudinal data to examine a related, but rather different, question. Extracting a select group of people from the ONS Longitudinal Study for England and Wales who had not moved house between 1971 and 1991 and who were living in non-deprived households throughout the 20-year period, we tested whether a change in the relative deprivation of the area in which they were living influenced their health and mortality status. The results demonstrate that changes in the relative deprivation of areas are related to health and mortality outcomes in a consistent way for both outcomes, although the results were more significant for morbidity. These findings suggest that neighbourhood-based public health and regeneration programmes may have demonstrable effects on the health of the residents who live there.

Does migration exaggerate the relationship between deprivation and limiting long-term illness? A Scottish analysis.

Few epidemiological studies of the links between health and environmental variables account for the potentially confounding effects of population migration. Here we explore the relationship between self-reported limiting long-term illness and material deprivation, using individual-level 1991 census data extracted for Scotland. The aim is to investigate whether the migration patterns of ill individuals influences the relationship between limiting long-term illness and material deprivation. Specifically, we seek to determine whether individuals who are well are more likely to migrate away from deprived areas and whether ill individuals are more likely to migrate towards deprived areas. If true, this would suggest that the apparent relationship between deprivation and limiting long-term illness is exaggerated by the effects of migration. We then examine the issue controlling for individual-level characteristics expected to influence limiting long-term illness and pay special attention to the role of public housing in these relationships.

Healthy life expectancy changes in Thailand, 2002-2007.

We investigate links between increasing longevity and health status in Thailand. Using data from 2002 and 2007 national surveys of the elderly, healthy life expectancies at older ages were estimated. Change depended on health indicator, gender and age. Self-reported health and self-care disability showed expansion of morbidity. Mobility disability change indicated compression but a wording change means this may be an artefact. We compare these findings with the 1990 and 2010 results of the Global Burden of Disease study. Using HLE based on disease prevalence, the GBD found that Thailand experienced small longevity gains and morbidity compression. Our findings suggest these results should be treated with caution, as, since 2000, Thailand has introduced universal health care.

European Regional Populations: Current Trends, Future Pathways, and Policy Options.

Europe is currently experiencing an ageing population and slowing population growth of both the total and working-age populations. These trends are likely to continue. Even though population ageing will affect all European regions, different regions will be affected in different ways. Even under favorable conditions, 35-40 % of all NUTS2 regions will face a labor force decline. If economic conditions are poor, some regions may continue to grow, but 55-70 % of the regions will see a labor force decline by 10 % or more. In most regions of Eastern Europe, the labor force may decrease by more than 30 %. To keep regions prosperous (maintaining competitiveness) and to avoid worse inequality (maintaining cohesion), policy-makers must find ways to cope with these challenges through new fiscal and social policies, though policies directly affecting demographic and migratory trends may also be needed.

Accuracy of algorithms to predict accessory pathway location in children with Wolff-Parkinson-White syndrome.

OBJECTIVE: The aim of this study was to examine the accuracy in predicting pathway location in children with Wolff-Parkinson-White syndrome for each of seven published algorithms. PATIENTS AND INTERVENTIONS: ECGs from 100 consecutive children with Wolff-Parkinson-White syndrome undergoing electrophysiological study were analysed by six investigators using seven published algorithms, six of which had been developed in adult patients. MAIN OUTCOME MEASURES: Accuracy and concordance of predictions were adjusted for the number of pathway locations. RESULTS: Accessory pathways were left-sided in 49, septal in 20 and right-sided in 31 children. Overall accuracy of prediction was 30-49% for the exact location and 61-68% including adjacent locations. Concordance between investigators varied between 41% and 86%. No algorithm was better at predicting septal pathways (accuracy 5-35%, improving to 40-78% including adjacent locations), but one was significantly worse. Predictive accuracy was 24-53% for the exact location of right-sided pathways (50-71% including adjacent locations) and 32-55% for the exact location of left-sided pathways (58-73% including adjacent locations). CONCLUSIONS: All algorithms were less accurate in our hands than in other authors' own assessment. None performed well in identifying midseptal or right anteroseptal accessory pathway locations.

Laboratory testing improves diagnosis and treatment outcomes in primary health care facilities.

OBJECTIVE: To determine if use of basic laboratory tests improves diagnosis and treatment outcomes in outpatients attending rural primary health care facilities. SETTING: Six rural health centres in Kenya. DESIGN: Cross-sectional study to observe change in diagnosis and treatment made by clinical officers after laboratory testing in outpatients attending six rural health centres in Kenya. SUBJECT: The diagnosis and treatment of 1134 patients attending outpatient services in six rural health centres were compared before and after basic laboratory testing. Essential clinical diagnostic equipment and laboratory tests were established at each health centre. Clinical officers and laboratory technicians received on-site refresher training in good diagnostic practices and laboratory procedures before the study began. RESULTS: Laboratory tests were ordered on 704 (62.1%) patients. Diagnosis and treatment were changed in 45% of tested patients who returned with laboratory results (21% of all patients attending the clinics). 166 (23.5%) patients did not return to the clinician for a final diagnosis and management decision after laboratory testing. Blood slide examination for malaria parasites, wet preparations, urine microscopy and stool microscopy resulted in most changes to diagnosis. There was no significant change in drug costs after laboratory testing. The greatest changes in numbers of recorded diseases following laboratory testing was for intestinal worms (53%) and malaria (21%). CONCLUSION: Effective use of basic laboratory tests at primary health care level significantly improves diagnosis and patient treatment. Use of laboratory testing can be readily incorporated into routine clinical practice. On-site refresher training is an effective means of improving the quality of patient care and communication between clinical and laboratory staff.

Lung transplantation in children with idiopathic pulmonary arterial hypertension.

BACKGROUND: Despite improved medical therapy, transplantation (Tx) represents the only option for end-stage pulmonary vascular disease. METHODS: Clinical data of children with idiopathic pulmonary arterial hypertension (IPAH) referred for Tx assessment between January 2002 and June 2007 were related to listing decision and outcome. RESULTS: Seven of the 14 children assessed for Tx were listed. Five were transplanted (lung Tx, n = 3; heart-lung Tx, n = 2) and two died on the waiting list. Mean age at diagnosis was 3.7 (0.4-9.5) years. Time from diagnosis to listing was 3.6 years (range 1.4-9.3). Children listed were in a worse functional class (WHO 3.5 vs. 2.5; P = 0.0006), had a lower SpO(2) on exercise (76.5% vs. 89%; P = 0.0001) and a shorter 6-min walk distance (154 m vs. 330 m; P < 0.01) than those not listed. Right ventricular function was worse in those listed (P = 0.03), as was pulmonary vascular resistance index (PVRI) on vasodilator testing (34 U m(2) vs. 14.6 U m(2); P = 0.03). Age at diagnosis and at assessment, weight, height, mean pulmonary artery pressure, baseline PVRI, B-type natriuretic peptide, spirometry and resting-SO(2) did not differ between the two groups. For the five children transplanted, median waiting time was 81 days. Age at Tx was 5.4 years. After 2.8 years all transplanted children are alive with a good functional outcome. Two patients died on the active waiting list. All children considered too well for listing are still alive and stable on treatment. CONCLUSIONS: Outcome after transplantation in children with IPAH has been encouraging. Defining listing criteria for these patients remains a challenge.

Pre-implantation basiliximab reduces incidence of early acute rejection in pediatric heart transplantation.

BACKGROUND: Basiliximab is an anti-CD25 monoclonal antibody used as induction therapy in solid-organ transplantation. In this study we aim to determine whether pre-operative administration of basiliximab is beneficial in preventing early heart allograft rejection. METHODS: In this investigation we assess the effect of pre-implantation basiliximab on CD25 count and on acute rejection in children undergoing cardiothoracic transplantation. The notes of all children undergoing cardiothoracic transplantation at the Great Ormond Street Hospital between January 2000 and June 2007 were retrospectively reviewed. One hundred twenty-one heart transplant recipients were included: 29 patients did not receive basiliximab; 33 patients received basiliximab after coming off cardiopulmonary bypass (CPB); and 59 patients received basiliximab prior to organ implantation. RESULTS: All patients receiving basiliximab had an effectively suppressed CD25 count (<0.2%) on Days 1 and 10 post-transplant. Freedom from Grade 3A or greater rejection in the first year was significantly greater in the pre-implantation basiliximab group than in the post-implantation and no-basiliximab groups (95%, 70% and 72%, respectively; p = 0.02). Induction regimen was the only significant explanatory variable after multivariate Cox regression. CONCLUSIONS: The results of this study confirm that basiliximab is effective at suppressing CD25 count whether given pre- or post-CPB. Basiliximab before transplantation appeared to reduce acute rejection, whereas post-CPB administration did not suggest similar effects. These findings require independent validation in randomized trials and further studies should seek to mechanistically delineate these observations.

The estimation of mortality for ethnic groups at local scale within the United Kingdom.

As an input to projections of sub-national populations by ethnicity, this paper develops the first estimates of the mortality risks experienced by the UK ethnic groups. Two estimates were developed using alternative methods. In the first, UK 2001 Census data on limiting long-term illness to predict mortality levels and regression equations between local Standardized Illness and Mortality Ratios for all ethnicities are assumed to apply to individual ethnic groups. In the second, the geographical distribution of ethnic groups by local areas is combined with local mortality for all ethnicities to estimate national mortality rates by ethnicity, which are then employed to estimate local ethnic mortality. A comparison of the two estimates indicates that the method based on illness rates produces more plausible outcomes. The local SMRs produced for each ethnic group were used to generate ethnic group life tables for 432 UK local authority areas in 2001, which included estimates of survivorship probabilities by single year of age, gender and ethnic group for each local area for use in a projection model.