The hagfish genome and the evolution of vertebrates

As the only surviving lineages of jawless fishes, hagfishes and lampreys provide a crucial window into early vertebrate evolution1-3. Here we investigate the complex history, timing and functional role of genome-wide duplications4-7 and programmed DNA elimination8,9 in vertebrates in the light of a chromosome-scale genome sequence for the brown hagfish Eptatretus atami. Combining evidence from syntenic and phylogenetic analyses, we establish a comprehensive picture of vertebrate genome evolution, including an auto-tetraploidization (1RV) that predates the early Cambrian cyclostome-gnathostome split, followed by a mid-late Cambrian allo-tetraploidization (2RJV) in gnathostomes and a prolonged Cambrian-Ordovician hexaploidization (2RCY) in cyclostomes. Subsequently, hagfishes underwent extensive genomic changes, with chromosomal fusions accompanied by the loss of genes that are essential for organ systems (for example, genes involved in the development of eyes and in the proliferation of osteoclasts); these changes account, in part, for the simplification of the hagfish body plan1,2. Finally, we characterize programmed DNA elimination in hagfish, identifying protein-coding genes and repetitive elements that are deleted from somatic cell lineages during early development. The elimination of these germline-specific genes provides a mechanism for resolving genetic conflict between soma and germline by repressing germline and pluripotency functions, paralleling findings in lampreys10,11. Reconstruction of the early genomic history of vertebrates provides a framework for further investigations of the evolution of cyclostomes and jawed vertebrates.

Effects of empagliflozin on progression of chronic kidney disease: a prespecified secondary analysis from the empa-kidney trial

BACKGROUND

Sodium-glucose co-transporter-2 (SGLT2) inhibitors reduce progression of chronic kidney disease and the risk of cardiovascular morbidity and mortality in a wide range of patients. However, their effects on kidney disease progression in some patients with chronic kidney disease are unclear because few clinical kidney outcomes occurred among such patients in the completed trials. In particular, some guidelines stratify their level of recommendation about who should be treated with SGLT2 inhibitors based on diabetes status and albuminuria. We aimed to assess the effects of empagliflozin on progression of chronic kidney disease both overall and among specific types of participants in the EMPA-KIDNEY trial.

METHODS

EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA), and included individuals aged 18 years or older with an estimated glomerular filtration rate (eGFR) of 20 to less than 45 mL/min per 1·73 m2, or with an eGFR of 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher. We explored the effects of 10 mg oral empagliflozin once daily versus placebo on the annualised rate of change in estimated glomerular filtration rate (eGFR slope), a tertiary outcome. We studied the acute slope (from randomisation to 2 months) and chronic slope (from 2 months onwards) separately, using shared parameter models to estimate the latter. Analyses were done in all randomly assigned participants by intention to treat. EMPA-KIDNEY is registered at ClinicalTrials.gov, NCT03594110.

FINDINGS

Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and then followed up for a median of 2·0 years (IQR 1·5-2·4). Prespecified subgroups of eGFR included 2282 (34·5%) participants with an eGFR of less than 30 mL/min per 1·73 m2, 2928 (44·3%) with an eGFR of 30 to less than 45 mL/min per 1·73 m2, and 1399 (21·2%) with an eGFR 45 mL/min per 1·73 m2 or higher. Prespecified subgroups of uACR included 1328 (20·1%) with a uACR of less than 30 mg/g, 1864 (28·2%) with a uACR of 30 to 300 mg/g, and 3417 (51·7%) with a uACR of more than 300 mg/g. Overall, allocation to empagliflozin caused an acute 2·12 mL/min per 1·73 m2 (95% CI 1·83-2·41) reduction in eGFR, equivalent to a 6% (5-6) dip in the first 2 months. After this, it halved the chronic slope from -2·75 to -1·37 mL/min per 1·73 m2 per year (relative difference 50%, 95% CI 42-58). The absolute and relative benefits of empagliflozin on the magnitude of the chronic slope varied significantly depending on diabetes status and baseline levels of eGFR and uACR. In particular, the absolute difference in chronic slopes was lower in patients with lower baseline uACR, but because this group progressed more slowly than those with higher uACR, this translated to a larger relative difference in chronic slopes in this group (86% [36-136] reduction in the chronic slope among those with baseline uACR <30 mg/g compared with a 29% [19-38] reduction for those with baseline uACR ≥2000 mg/g; ptrend<0·0001).

INTERPRETATION

Empagliflozin slowed the rate of progression of chronic kidney disease among all types of participant in the EMPA-KIDNEY trial, including those with little albuminuria. Albuminuria alone should not be used to determine whether to treat with an SGLT2 inhibitor.

FUNDING

Boehringer Ingelheim and Eli Lilly.

Impact of primary kidney disease on the effects of empagliflozin in patients with chronic kidney disease: secondary analyses of the EMPA-KIDNEY trial

BACKGROUND

The EMPA-KIDNEY trial showed that empagliflozin reduced the risk of the primary composite outcome of kidney disease progression or cardiovascular death in patients with chronic kidney disease mainly through slowing progression. We aimed to assess how effects of empagliflozin might differ by primary kidney disease across its broad population.

METHODS

EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA). Patients were eligible if their estimated glomerular filtration rate (eGFR) was 20 to less than 45 mL/min per 1·73 m2, or 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher at screening. They were randomly assigned (1:1) to 10 mg oral empagliflozin once daily or matching placebo. Effects on kidney disease progression (defined as a sustained ≥40% eGFR decline from randomisation, end-stage kidney disease, a sustained eGFR below 10 mL/min per 1·73 m2, or death from kidney failure) were assessed using prespecified Cox models, and eGFR slope analyses used shared parameter models. Subgroup comparisons were performed by including relevant interaction terms in models. EMPA-KIDNEY is registered with ClinicalTrials.gov, NCT03594110.

FINDINGS

Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and followed up for a median of 2·0 years (IQR 1·5-2·4). Prespecified subgroupings by primary kidney disease included 2057 (31·1%) participants with diabetic kidney disease, 1669 (25·3%) with glomerular disease, 1445 (21·9%) with hypertensive or renovascular disease, and 1438 (21·8%) with other or unknown causes. Kidney disease progression occurred in 384 (11·6%) of 3304 patients in the empagliflozin group and 504 (15·2%) of 3305 patients in the placebo group (hazard ratio 0·71 [95% CI 0·62-0·81]), with no evidence that the relative effect size varied significantly by primary kidney disease (pheterogeneity=0·62). The between-group difference in chronic eGFR slopes (ie, from 2 months to final follow-up) was 1·37 mL/min per 1·73 m2 per year (95% CI 1·16-1·59), representing a 50% (42-58) reduction in the rate of chronic eGFR decline. This relative effect of empagliflozin on chronic eGFR slope was similar in analyses by different primary kidney diseases, including in explorations by type of glomerular disease and diabetes (p values for heterogeneity all >0·1).

INTERPRETATION

In a broad range of patients with chronic kidney disease at risk of progression, including a wide range of non-diabetic causes of chronic kidney disease, empagliflozin reduced risk of kidney disease progression. Relative effect sizes were broadly similar irrespective of the cause of primary kidney disease, suggesting that SGLT2 inhibitors should be part of a standard of care to minimise risk of kidney failure in chronic kidney disease.

FUNDING

Boehringer Ingelheim, Eli Lilly, and UK Medical Research Council.

The prevalence of emotional abuse in children living in Sub-Saharan Africa - A systematic review

OBJECTIVES

This study is meant to put a focus on the prevalence of emotional abuse in low-income states like the Sub-Saharan region.

METHODOLOGY

Searching PubMed, Google scholar, and web of science during February and April 2021 a total of 2264 articles were identified, 27 met the inclusion criteria. We added the results of 13 VAC (Violence Against Children and Youth) studies, conducted by UNICEF capturing information about experienced sexual, physical, or emotional violence in 13-24-year-olds, as well as 56 MIC (Multiple Indicator Cluster) studies, conducted by the CDC to research the disciplinary methods used with children aged 1-14 years in the past month by older household members. Finally, in a meta-analytic approach, we aimed to calculate a pooled estimate of the prevalence.

RESULTS

The included studies depicted a wide range in prevalence rates across countries. For example, while the VAC study in Lesotho in 2018 showed low incidence rates of emotional violence (6.9 % Females, 3.8 % Males), the average prevalence recorded by the MIC study was as high as 57.8 % for females and 59.2 % for males. On average, the MIC studies displayed a higher incidence and the discrepancy of prevalence of emotional abuse between females and males was small. Calculating a pooled estimate of the prevalence was not possible, due to the heterogeneity of the data.

CONCLUSIONS

In general countries displayed a high prevalence. A standardized use of a uniform definition of emotional abuse might help to display a more homogenous data set in the future, giving the opportunity for pooled estimates of prevalence.

The hagfish genome and the evolution of vertebrates

As the only surviving lineages of jawless fishes, hagfishes and lampreys provide a critical window into early vertebrate evolution. Here, we investigate the complex history, timing, and functional role of genome-wide duplications in vertebrates in the light of a chromosome-scale genome of the brown hagfish Eptatretus atami. Using robust chromosome-scale (paralogon-based) phylogenetic methods, we confirm the monophyly of cyclostomes, document an auto-tetraploidization (1RV) that predated the origin of crown group vertebrates ~517 Mya, and establish the timing of subsequent independent duplications in the gnathostome and cyclostome lineages. Some 1RV gene duplications can be linked to key vertebrate innovations, suggesting that this early genomewide event contributed to the emergence of pan-vertebrate features such as neural crest. The hagfish karyotype is derived by numerous fusions relative to the ancestral cyclostome arrangement preserved by lampreys. These genomic changes were accompanied by the loss of genes essential for organ systems (eyes, osteoclast) that are absent in hagfish, accounting in part for the simplification of the hagfish body plan; other gene family expansions account for hagfishes' capacity to produce slime. Finally, we characterise programmed DNA elimination in somatic cells of hagfish, identifying protein-coding and repetitive elements that are deleted during development. As in lampreys, the elimination of these genes provides a mechanism for resolving genetic conflict between soma and germline by repressing germline/pluripotency functions. Reconstruction of the early genomic history of vertebrates provides a framework for further exploration of vertebrate novelties.

Supply-side contribution to the lack of PBF impact on unmet need for family planning in Burkina Faso

Background

In 2020, about one in four women in Burkina Faso faced an unmet need for family planning (FP). Between 2013 and 2017, Burkina Faso implemented a performance-based financing (PBF) program to improve primary health care service provision (including FP) at rural health centers. Our prior work revealed that PBF did not lead to a reduction in unmet need for FP, in spite of FP being an explicitly targeted service. Our current study assesses supply-side factors that have likely contributed towards this lack of effect at population level, by examining changes in facility-based indicators relevant to the provision of FP induced by PBF.

Methods

We used facility-based survey data from 406 PBF and 117 control facilities collected before and after the PBF implementation. To compare changes in FP service provision, we examined changes in a number of relevant indicators including: a. the types of FP methods offered by facilities; b. trainings received by different FP providers; and c. available stocks of modern contraceptives. We relied on a difference-in-differences (DID) regression model to estimate the impact of PBF on these indicators.

Results

We observed a significant positive impact on the number of staff qualified to provide injectables, implants and IUDs (effect size 0.47, p 0.003) as well as the number of facilities offering IUDs (effect size 0.28, p 0.016) and a significant reduction in the number of facilities experiencing stock-outs of female condoms (effect size -0.09, p 0.007) and implants (effect size -0.03, p 0.042).

Conclusions

Given the significant positive impacts on the number of qualified staff, facilities providing IUDs and a reduction in stock-outs of female condoms and implants attributable to the PBF intervention without showing signs of negative effects on the indicators measured supply-side factors might not have been the main reason for the lack of effect of the PBF program on unmet need for FP.

Key messages

• Supply-side factors might not have been the main reason for the lack of effect of the PBF program on unmet need for FP.

• Further research is needed to explore other potential underlying reasons.

The economic burden of treating uncomplicated hypertension in Sub-Saharan Africa: a systematic literature review

Background and Objectives

Hypertension is one of the leading cardiovascular risk factors with high numbers of undiagnosed and untreated patients in Sub Saharan Africa (SSA). The health systems and affected people are often overwhelmed by the social and economic burden that comes with the disease. However, the research on the economic burden and consequences of hypertension treatment remains scare in SSA. The objective of our review was to compare different hypertension treatment costs across the continent and identify major cost drivers.

Material and Methods

Systematic literature searches were conducted in multiple databases (e.g., PubMed, Web of Science, Google Scholar) for peer reviewed articles written in English language with a publication date from inception to Jan. 2022. We included studies assessing direct and indirect costs of hypertension therapy in SSA from a provider or user perspective. The search and a quality assessment were independently executed by two researchers. All results were converted to 2021 US Dollar.

Results

Of 3999 results identified in the initial search, 33 were selected for data extraction. Costs differed between countries, costing perspectives and cost categories. Only 25% of the SSA countries were mentioned in the studies, with Nigeria dominating the research with a share of 27% of the studies. We identified 15 results each from a user or provider perspective. Medication costs were accountable for the most part of the expenditures with a range from 1.70$ to 97.06$ from a patient perspective and 0.09$ to 193.55$ from a provider perspective per patient per month. Major cost drivers were multidrug treatment, inpatient or hospital care and having a comorbidity like diabetes.

Conclusion

Hypertension poses a significant economic burden for patients and governments in SSA. Interpreting and comparing the results from different countries and studies is difficult as there are different financing methods and cost items are defined in different ways. However, our results identify medication costs as one of the biggest cost contributors. When fighting the economic burden in SSA, reducing medication costs in form of subsidies or special interventions needs to be considered.

Trial registration

Registration: PROSPERO, ID CRD42020220957.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12889-022-13877-4.

Long-term safety and efficacy of anacetrapib in patients with atherosclerotic vascular disease

AIMS

REVEAL was the first randomized controlled trial to demonstrate that adding cholesteryl ester transfer protein inhibitor therapy to intensive statin therapy reduced the risk of major coronary events. We now report results from extended follow-up beyond the scheduled study treatment period.

METHODS AND RESULTS

A total of 30 449 adults with prior atherosclerotic vascular disease were randomly allocated to anacetrapib 100 mg daily or matching placebo, in addition to open-label atorvastatin therapy. After stopping the randomly allocated treatment, 26 129 survivors entered a post-trial follow-up period, blind to their original treatment allocation. The primary outcome was first post-randomization major coronary event (i.e. coronary death, myocardial infarction, or coronary revascularization) during the in-trial and post-trial treatment periods, with analysis by intention-to-treat. Allocation to anacetrapib conferred a 9% [95% confidence interval (CI) 3-15%; P = 0.004] proportional reduction in the incidence of major coronary events during the study treatment period (median 4.1 years). During extended follow-up (median 2.2 years), there was a further 20% (95% CI 10-29%; P < 0.001) reduction. Overall, there was a 12% (95% CI 7-17%, P < 0.001) proportional reduction in major coronary events during the overall follow-up period (median 6.3 years), corresponding to a 1.8% (95% CI 1.0-2.6%) absolute reduction. There were no significant effects on non-vascular mortality, site-specific cancer, or other serious adverse events. Morbidity follow-up was obtained for 25 784 (99%) participants.

CONCLUSION

The beneficial effects of anacetrapib on major coronary events increased with longer follow-up, and no adverse effects emerged on non-vascular mortality or morbidity. These findings illustrate the importance of sufficiently long treatment and follow-up duration in randomized trials of lipid-modifying agents to assess their full benefits and potential harms.

TRIAL REGISTRATION

International Standard Randomized Controlled Trial Number (ISRCTN) 48678192; ClinicalTrials.gov No. NCT01252953; EudraCT No. 2010-023467-18.

CaRdiac Arrest Survival Score (CRASS) - A tool to predict good neurological outcome after out-of-hospital cardiac arrest

AIM

The aim of this study was to develop a score to predict the outcome for patients brought to hospital following out-of-hospital cardiac arrest (OHCA).

METHODS

All patients recorded in the German Resuscitation Registry (GRR) who suffered OHCA 2010-2017, who had ROSC or ongoing CPR at hospital admission were included. The study population was divided into development (2010-2016: 7985) and validation dataset (2017: 1806). Binary logistic regression analysis was used to derive the score. The probability of hospital discharge with good neurological outcome was defined as 1/(1 + e^-X), where X is the weighted sum of independent variables.

RESULTS

The following variables were found to have a significant positive (+) or negative (-) impact: age 61-70 years (-0·5), 71-80 (-0·9), 81-90 (-1·3) and > = 91 (-2·3); initial PEA (-0·9) and asystole (-1·4); presumable trauma (-1·1); mechanical CPR (-0·3); application of adrenalin > 0 - < 2 mg (-1·1), 2 - <4 mg (-1·6), 4 - < 6 mg (-2·1), 6 - < 8 mg (-2·5) and > = 8 mg (-2·8); pre emergency status without previous disease (+0·5) or minor disease (+0·2); location at nursing home (-0·6), working place/school (+0·7), doctor's office (+0·7) and public place (+0·3); application of amiodarone (+0·4); hospital admission with ongoing CPR (-1·9) or normotension (+0·4); witnessed arrest (+0·6); time from collapse until start CPR 2 - < 10 min (-0·3) and > = 10 min (-0·5); duration of CPR <5 min (+0·6). The AUC in the development dataset was 0·88 (95% CI 0·87-0·89) and in the validation dataset 0·88 (95% CI 0·86-0·90).

CONCLUSION

The CaRdiac Arrest Survival Score (CRASS) represents a tool for calculating the probability of survival with good neurological function for patients brought to hospital following OHCA.

A novel molecular rotor facilitates detection of p53-DNA interactions using the Fluorescent Intercalator Displacement Assay

We have investigated the use of fluorescent molecular rotors as probes for detection of p53 binding to DNA. These are a class of fluorophores that undergo twisted intramolecular charge transfer (TICT). They are non-fluorescent in a freely rotating conformation and experience a fluorescence increase when restricted in the planar conformation. We hypothesized that intercalation of a molecular rotor between DNA base pairs would result in a fluorescence turn-on signal. Upon displacement by a DNA binding protein, measurable loss of signal would facilitate use of the molecular rotor in the fluorescent intercalator displacement (FID) assay. A panel of probes was interrogated using the well-established p53 model system across various DNA response elements. A novel, readily synthesizable molecular rotor incorporating an acridine orange DNA intercalating group (AO-R) outperformed other conventional dyes in the FID assay. It enabled relative measurement of p53 sequence-specific DNA interactions and study of the dominant-negative effects of cancer-associated p53 mutants. In a further application, AO-R also proved useful for staining apoptotic cells in live zebrafish embryos.

[Use of cognitive aids in pediatric emergency care : Interdisciplinary consensus statement]

Preclinical pediatric emergencies are rare events and are therefore often associated with stress and uncertainty for emergency medical service personnel. To ensure adequate treatment of pediatric patients a variety of different cognitive aids exist (e.g. books, apps, rulers, weight-adapted bag systems). Especially the size specifications of the medical equipment and the dosage of emergency medication are individually very different in children and are dependent on parameters, such as body height and weight. Therefore, cognitive aids often enable length measurement whereby it is possible to draw conclusions on body weight for calculating the child's medication dosage. These aids may help to avoid the wrong medication dose or the wrong therapy of children but uncritical and untrained usage of these aids carries a potential risk of mistakes. This recommendation gives an overview of the general requirements and different problems of cognitive aids and should help improve the general framework and the rational basis for the use and further development of cognitive aids in emergency medicine.

[Recommendation on temperature management after cardiopulmonary arrest and severe traumatic brain injury in childhood beyond the neonatal period : Statement of the German Society for Neonatology and Pediatric Intensive Care Medicine (GNPI) and the scientific Working Group for Paediatric Anaesthesia (WAKKA) of the German Society of Anaesthesiology and Intensive Care (DGAI)]

The available data on the effectiveness of therapeutic hypothermia in different patient groups are heterogeneous. Although the benefits have been proven for some collectives, recommendations for the use of hypothermia treatment in other groups are based on less robust data and conclusions by analogy. This article gives a review of the current evidence of temperature management in all age groups and based on this state of knowledge, recommends active temperature management with the primary aim of strict normothermia (36-36.5 °C) for 72 hours after cardiopulmonary arrest or severe traumatic brain injury for children beyond the neonatal period.

The genome of the largest bony fish, ocean sunfish (Mola mola), provides insights into its fast growth rate

BACKGROUND

The ocean sunfish (Mola mola), which can grow up to a length of 2.7 m and weigh 2.3 tons, is the world's largest bony fish. It has an extremely fast growth rate and its endoskeleton is mainly composed of cartilage. Another unique feature of the sunfish is its lack of a caudal fin, which is replaced by a broad and stiff lobe that results in the characteristic truncated appearance of the fish.

RESULTS

To gain insights into the genomic basis of these phenotypic traits, we sequenced the sunfish genome and performed a comparative analysis with other teleost genomes. Several sunfish genes involved in the growth hormone and insulin-like growth factor 1 (GH/IGF1) axis signalling pathway were found to be under positive selection or accelerated evolution, which might explain its fast growth rate and large body size. A number of genes associated with the extracellular matrix, some of which are involved in the regulation of bone and cartilage development, have also undergone positive selection or accelerated evolution. A comparison of the sunfish genome with that of the pufferfish (fugu), which has a caudal fin, revealed that the sunfish contains more homeobox (Hox) genes although both genomes contain seven Hox clusters. Thus, caudal fin loss in sunfish is not associated with the loss of a specific Hox gene.

CONCLUSIONS

Our analyses provide insights into the molecular basis of the fast growth rate and large size of the ocean sunfish. The high-quality genome assembly generated in this study should facilitate further studies of this 'natural mutant'.

Attitudes towards prenatal HIV testing and treatment among pregnant women in southern India

During June and July 1999, oral interviews were conducted on 666 women seeking prenatal care at 9 medical facilities in Chennai and Mysore, India, to assess their attitudes towards prenatal HIV testing and antiretroviral prophylaxis for preventing perinatal HIV transmission if needed. Seventy-eight per cent were aware of the risk of perinatal HIV transmission and 36% knew that intervention could reduce the chances of such transmission. Eighty-six per cent would agree to undergo prenatal HIV testing but only 21% of all respondents would make this decision independently while 46% said their husband would have to decide. Of those women who would not agree to testing, 21% would agree if testing were compulsory. Ninety-seven per cent of respondents would undergo antiretroviral prophylaxis to prevent vertical transmission, and 94% would consider alternatives to breastfeeding if HIV positive. Considering its widespread acceptability, prenatal voluntary counselling and testing may be an affordable method of HIV prevention for this population.

The p53-Mdm2 interaction and the E3 ligase activity of Mdm2/Mdm4 are conserved from lampreys to humans

Here, Coffill et al. characterize Tp53, Tp63, and Tp73 in a jawless vertebrate, the Japanese lamprey, as well as the Mdm2 and Mdm4 genes using genome analysis. Functional analysis reveals conservation of p63 and p73 compared with p53, which shows substantial variability within the C-terminal and N-terminal domains, and that lamprey Mdm2 degrades human p53 with great efficiency; however, this interaction is not inhibited by currently available small molecule inhibitors of the human HDM2 protein.

The extant jawless vertebrates, represented by lampreys and hagfish, are the oldest group of vertebrates and provide an interesting genomic evolutionary pivot point between invertebrates and jawed vertebrates. Through genome analysis of one of these jawless vertebrates, the Japanese lamprey (Lethenteron japonicum), we identified all three members of the important p53 transcription factor family—Tp53, Tp63, and Tp73—as well as the Mdm2 and Mdm4 genes. These genes and their products are significant cellular regulators in human cancer, and further examination of their roles in this most distant vertebrate relative sheds light on their origin and coevolution. Their important role in response to DNA damage has been highlighted by the discovery of multiple copies of the Tp53 gene in elephants. Expression of lamprey p53, Mdm2, and Mdm4 proteins in mammalian cells reveals that the p53–Mdm2 interaction and the Mdm2/Mdm4 E3 ligase activity existed in the common ancestor of vertebrates and have been conserved for >500 million years of vertebrate evolution. Lamprey Mdm2 degrades human p53 with great efficiency, but this interaction is not blocked by currently available small molecule inhibitors of the human HDM2 protein, suggesting utility of lamprey Mdm2 in the study of the human p53 signaling pathway.

Successful thrombolytic treatment of neonatal arterial thromboses

Compared to children of other age groups neonates show an increased thrombotic risk. The acute therapy depends on thrombus age, the localisation of vascular occlusion and the severity of the underlying disease. The treatment of choice is represented by the administration of unfractionated (UFH) or low molecular weight heparin (LMWH). If loss of limbs or organs is imminent, the application of thrombolytic treatment with recombinant tissue-type plasminogen activator (rt-PA) should be considered whilst taking into account the associated bleeding risk. We report on two patients in which thrombolytic therapy has been conducted successfully.

The patient with dyspnea. Rational diagnostic evaluation

Dyspnea is the uncomfortable awareness of difficult breathing. It is a common symptom in primary and nonprimary care settings. Although multiple disorders and diseases may cause breathlessness, the majority of the conditions are of cardiac or pulmonary origin. The challenge is to establish the diagnosis timely and with minimized investigations. Frequently, information about onset, progression, and circumstances of occurrence considerably narrow the underlying etiology. In most cases, a carefully taken history and a comprehensive physical examination lead to the correct diagnosis. Nevertheless, one should be aware of concomitant conditions and not be satisfied with a diagnosis if comorbidity may still be a candidate in causing dyspnea. Otherwise, it has been observed that chronic obstructive pulmonary disease was over-diagnosed in patients with systolic heart failure and dyspnea. A prudential use of investigating modalities for confirmation and exclusion of a questionable diagnosis is the key for allocating the correct therapy and achieving fast symptom relief in patients with dyspnea.

Characterization of the Runx gene family in a jawless vertebrate, the Japanese lamprey (Lethenteron japonicum)

The cyclostomes (jawless vertebrates), comprising lampreys and hagfishes, are the sister group of jawed vertebrates (gnathostomes) and are hence an important group for the study of vertebrate evolution. In mammals, three Runx genes, Runx1, Runx2 and Runx3, encode transcription factors that are essential for cell proliferation and differentiation in major developmental pathways such as haematopoiesis, skeletogenesis and neurogenesis and are frequently associated with diseases. We describe here the characterization of Runx gene family members from a cyclostome, the Japanese lamprey (Lethenteron japonicum). The Japanese lamprey contains three Runx genes, RunxA, RunxB, and RunxC. However, phylogenetic and synteny analyses suggest that they are not one-to-one orthologs of gnathostome Runx1, Runx2 and Runx3. The major protein domains and motifs found in gnathostome Runx proteins are highly conserved in the lamprey Runx proteins. Although all gnathostome Runx genes each contain two alternative promoters, P1 (distal) and P2 (proximal), only lamprey RunxB possesses the alternative promoters; lamprey RunxA and RunxC contain only P2 and P1 promoter, respectively. Furthermore, the three lamprey Runx genes give rise to fewer alternative isoforms than the three gnathostome Runx genes. The promoters of the lamprey Runx genes lack the tandem Runx-binding motifs that are highly conserved among the P1 promoters of gnathostome Runx1, Runx2 and Runx3 genes; instead these promoters contain dispersed single Runx-binding motifs. The 3'UTR of lamprey RunxB contains binding sites for miR-27 and miR-130b/301ab, which are conserved in mammalian Runx1 and Runx3, respectively. Overall, the Runx genes in lamprey seem to have experienced a different evolutionary trajectory from that of gnathostome Runx genes which are highly conserved all the way from cartilaginous fishes to mammals.

Expression of Wnt signaling skeletal development genes in the cartilaginous fish, elephant shark (Callorhinchus milii)

Jawed vertebrates (Gnasthostomes) are broadly separated into cartilaginous fishes (Chondricthyes) and bony vertebrates (Osteichthyes). Cartilaginous fishes are divided into chimaeras (e.g. ratfish, rabbit fish and elephant shark) and elasmobranchs (e.g. sharks, rays and skates). Both cartilaginous fish and bony vertebrates are believed to have a common armoured bony ancestor (Class Placodermi), however cartilaginous fish are believed to have lost bone. This study has identified and investigated genes involved in skeletal development in vertebrates, in the cartilaginous fish, elephant shark (Callorhinchus milii). Ctnnb1 (β-catenin), Sfrp (secreted frizzled protein) and a single Sost or Sostdc1 gene (sclerostin or sclerostin domain-containing protein 1) were identified in the elephant shark genome and found to be expressed in a number of tissues, including cartilage. β-catenin was also localized in several elephant shark tissues. The expression of these genes, which belong to the Wnt/β-catenin pathway, is required for normal bone formation in mammals. These findings in the cartilaginous skeleton of elephant shark support the hypothesis that the common ancestor of cartilaginous fishes and bony vertebrates had the potential for making bone.

Reflex: intramolecular barcoding of long-range PCR products for sequencing multiple pooled DNAs

We present an intramolecular reaction, Reflex™, to derive shorter, sequencer-ready, daughter polymerase chain reaction products from a pooled population of barcoded long-range polymerase chain reaction products, whilst still preserving the cognate DNA barcodes. Our Reflex workflow needs only a small number of primer extension steps to rapidly enable uniform sequence coverage of long contiguous sequence targets in large numbers of samples at low cost on desktop next-generation sequencers.

Sequencing of Pax6 loci from the elephant shark reveals a family of Pax6 genes in vertebrate genomes, forged by ancient duplications and divergences

Pax6 is a developmental control gene essential for eye development throughout the animal kingdom. In addition, Pax6 plays key roles in other parts of the CNS, olfactory system, and pancreas. In mammals a single Pax6 gene encoding multiple isoforms delivers these pleiotropic functions. Here we provide evidence that the genomes of many other vertebrate species contain multiple Pax6 loci. We sequenced Pax6-containing BACs from the cartilaginous elephant shark (Callorhinchus milii) and found two distinct Pax6 loci. Pax6.1 is highly similar to mammalian Pax6, while Pax6.2 encodes a paired-less Pax6. Using synteny relationships, we identify homologs of this novel paired-less Pax6.2 gene in lizard and in frog, as well as in zebrafish and in other teleosts. In zebrafish two full-length Pax6 duplicates were known previously, originating from the fish-specific genome duplication (FSGD) and expressed in divergent patterns due to paralog-specific loss of cis-elements. We show that teleosts other than zebrafish also maintain duplicate full-length Pax6 loci, but differences in gene and regulatory domain structure suggest that these Pax6 paralogs originate from a more ancient duplication event and are hence renamed as Pax6.3. Sequence comparisons between mammalian and elephant shark Pax6.1 loci highlight the presence of short- and long-range conserved noncoding elements (CNEs). Functional analysis demonstrates the ancient role of long-range enhancers for Pax6 transcription. We show that the paired-less Pax6.2 ortholog in zebrafish is expressed specifically in the developing retina. Transgenic analysis of elephant shark and zebrafish Pax6.2 CNEs with homology to the mouse NRE/Pα internal promoter revealed highly specific retinal expression. Finally, morpholino depletion of zebrafish Pax6.2 resulted in a "small eye" phenotype, supporting a role in retinal development. In summary, our study reveals that the pleiotropic functions of Pax6 in vertebrates are served by a divergent family of Pax6 genes, forged by ancient duplication events and by independent, lineage-specific gene losses.

Evolution and functional characterisation of melanopsins in a deep-sea chimaera (elephant shark, Callorhinchus milii)

Non-visual photoreception in mammals is primarily mediated by two splice variants that derive from a single melanopsin (OPN4M) gene, whose expression is restricted to a subset of retinal ganglion cells. Physiologically, this sensory system regulates the photoentrainment of many biological rhythms, such as sleep via the melatonin endocrine system and pupil constriction. By contrast, melanopsin exists as two distinct lineages in non-mammals, opn4m and opn4x, and is broadly expressed in a wide range of tissue types, including the eye, brain, pineal gland and skin. Despite these findings, the evolution and function of melanopsin in early vertebrates are largely unknown. We, therefore, investigated the complement of opn4 classes present in the genome of a model deep-sea cartilaginous species, the elephant shark (Callorhinchus milii), as a representative vertebrate that resides at the base of the gnathostome (jawed vertebrate) lineage. We reveal that three melanopsin genes, opn4m1, opn4m2 and opn4x, are expressed in multiple tissues of the elephant shark. The two opn4m genes are likely to have arisen as a result of a lineage-specific duplication, whereas “long” and “short” splice variants are generated from a single opn4x gene. By using a heterologous expression system, we suggest that these genes encode functional photopigments that exhibit both “invertebrate-like” bistable and classical “vertebrate-like” monostable biochemical characteristics. We discuss the evolution and function of these melanopsin pigments within the context of the diverse photic and ecological environments inhabited by this chimaerid holocephalan, as well as the origin of non-visual sensory systems in early vertebrates.

Update on the pfam5000 strategy for selection of structural genomics targets

Structural Genomics is an international effort to determine the three-dimensional shapes of all important biological macromolecules, with a primary focus on proteins. Target proteins should be selected according to a strategy that is medically and biologically relevant, of good financial value, and tractable. In 2003, we presented the "Pfam5000" strategy, which involves selecting the 5,000 most important families from the Pfam database as sources for targets. In this update, we show that although both the Pfam database and the number of sequenced genomes have increased in size, the expected benefits of the Pfam5000 strategy have not changed substantially. Solving the structures of proteins from the 5,000 largest Pfam families would allow accurate fold assignment for approximately 65% of all prokaryotic proteins (covering 54% of residues) and 63% of eukaryotic proteins (42% of residues). Fewer than 2,300 of the largest families on this list remain to be solved, making the project feasible in the next five years given the expected throughput to be achieved in the production phase of the Protein Structure Initiative.

Peripartum cardiomyopathy. An update

Peripartum cardiomyopathy (PPCM) is a rare disease of the heart muscle that affects women with previously unknown heart diseases during pregnancy or in the first months after delivery. Cardinal symptoms are dyspnoea and fluid retention. However, tachycardia, cardiogenic thromboembolism and other clinical signs of cardiac dysfunction may also herald this uncommon cause of heart failure. The estimated incidence of PPCM shows large regional variations: in Europe and the United States it is between 1:2000 and 1:4000. The markedly higher incidence rates observed in Haitian or South African women (up to 1:300) suggest that genetic or environmental factors may play a pathogenetic role. However, the underlying aetiology of PPCM still is unclear. Besides genetic susceptibility an abnormal autoimmune response against cardiac tissue components, viral infections or an irregular activity of cathepsin D generating a potentially cardio-toxic splice variant of prolactin have been discussed. New therapeutic strategies as immune modulation or prolactin inhibition were therefore suggested, but are not yet established. Treatment strategies focus on the standard therapies for heart failure and its complications. During pregnancy heart failure therapy is limited to substances without fetotoxic effects. But even with optimal heart failure therapy the course of the disease exhibits large variations ranging from full recovery to deterioration of heart function and even early cardiac death. This review cumulates the current knowledge on PPCM and aims to raise awareness for this rare and potentially life-threatening disorder amongst all medical professionals involved in the care for pregnant women.

The fifth neurohypophysial hormone receptor is structurally related to the V2-type receptor but functionally similar to V1-type receptors

The neurohypophysial peptides of the vasopressin (VP) and oxytocin (OT) families regulate salt and water homeostasis and reproduction through distinct G protein-coupled receptors. The current thinking is that there are four neurohypophysial hormone receptors (V1aR, V1bR, V2R, and OTR) in vertebrates, and their evolutionary history is still debated. We report the identification of a fifth neurohypophysial hormone receptor (V2bR) from the holocephalan elephant fish. This receptor is similar to conventional V2R (V2aR) in sequence, but induced Ca(2+) signaling in response to vasotocin (VT), the non-mammalian VP ortholog; such signaling is typical of V1-type receptors. In addition, V1aR, V1bR and OTR were also isolated from the elephant fish. Further screening revealed that orthologous V2bRs are widely distributed throughout the jawed vertebrates, and that the V2bR family is subdivided into two subfamilies: the fish specific type-1, and a type-2 that is characteristically found in tetrapods. Analysis suggested that the mammalian V2bR may have lost its function. Based on molecular phylogenetic, synteny and functional analyses, we propose a new evolutionary history for the neurohypophysial hormone receptors in vertebrates as follows: the first duplication generated V1aR/V1bR/OTR and V2aR/V2bR lineages; after divergence from the V2bR lineage, the V2aRs evolved to use cAMP as a second messenger, while the V2bRs retained the original Ca(2+) signaling system. Future studies on the role of V2bR in the brain, heart, kidney and reproductive organs, in which it is highly expressed, will open a new research field in VP/VT physiology and evolution.

Basal vertebrates clarify the evolutionary history of ciliopathy-associated genes Tmem138 and Tmem216

Recently, Lee et al. (Lee JH, Silhavy JL, Lee JE, et al. (30 co-authors). 2012. Evolutionarily assembled cis-regulatory module at a human ciliopathy locus. Science (335:966-969.) demonstrated that mutation in either of the transmembrane protein encoding genes, TMEM138 or TMEM216, causes phenotypically indistinguishable ciliopathy. Furthermore, on the basis of the observation that their orthologs are linked in a head-to-tail configuration in other mammals and Anolis, but present on different scaffolds or chromosomes in Xenopus tropicalis and zebrafish, the authors concluded that the two genes were joined by chromosomal rearrangement at the evolutionary amphibian-to-reptile transition to form a functional module. We have sequenced these gene loci in a cartilaginous fish, the elephant shark, and found that the two genes together with a related gene (Tmem80) constitute a tandem cluster. This suggests that the two genes were already linked in the vertebrate ancestor and then rearranged independently in Xenopus and zebrafish. Analyses of the coelacanth and lamprey genomes support this hypothesis. Our study highlights the importance of basal vertebrates as critical reference genomes.