Expression Evolution of Ancestral XY Gametologs across All Major Groups of Placental Mammals

Placental mammals present 180 million-year-old Y chromosomes that have retained a handful of dosage-sensitive genes. However, the expression evolution of Y-linked genes across placental groups has remained largely unexplored. Here, we expanded the number of Y gametolog sequences by analyzing ten additional species from previously unexplored groups. We detected seven remarkably conserved genes across 25 placental species with known Y repertoires. We then used RNA-seq data from 17 placental mammals to unveil the expression evolution of XY gametologs. We found that Y gametologs followed, on average, a 3-fold expression loss and that X gametologs also experienced some expression reduction, particularly in primates. Y gametologs gained testis specificity through an accelerated expression decay in somatic tissues. Moreover, despite the substantial expression decay of Y genes, the combined expression of XY gametologs in males is higher than that of both X gametologs in females. Finally, our work describes several features of the Y chromosome in the last common mammalian ancestor.

Repurposing of promoters and enhancers during mammalian evolution

Promoters and enhancers-key controllers of gene expression-have long been distinguished from each other based on their function. However, recent work suggested that common architectural and functional features might have facilitated the conversion of one type of element into the other during evolution. Here, based on cross-mammalian analyses of epigenome and transcriptome data, we provide support for this hypothesis by detecting 445 regulatory elements with signatures of activity turnover (termed P/E elements). Most events represent transformations of putative ancestral enhancers into promoters, leading to the emergence of species-specific transcribed loci or 5' exons. Distinct GC sequence compositions and stabilizing 5' splicing (U1) regulatory motif patterns may have predisposed P/E elements to regulatory repurposing, and changes in the U1 and polyadenylation signal densities and distributions likely drove the evolutionary activity switches. Our work suggests that regulatory repurposing facilitated regulatory innovation and the origination of new genes and exons during evolution.

Convergent origination of a Drosophila-like dosage compensation mechanism in a reptile lineage

Sex chromosomes differentiated from different ancestral autosomes in various vertebrate lineages. Here, we trace the functional evolution of the XY Chromosomes of the green anole lizard (Anolis carolinensis), on the basis of extensive high-throughput genome, transcriptome and histone modification sequencing data and revisit dosage compensation evolution in representative mammals and birds with substantial new expression data. Our analyses show that Anolis sex chromosomes represent an ancient XY system that originated at least ≈160 million years ago in the ancestor of Iguania lizards, shortly after the separation from the snake lineage. The age of this system approximately coincides with the ages of the avian and two mammalian sex chromosomes systems. To compensate for the almost complete Y Chromosome degeneration, X-linked genes have become twofold up-regulated, restoring ancestral expression levels. The highly efficient dosage compensation mechanism of Anolis represents the only vertebrate case identified so far to fully support Ohno's original dosage compensation hypothesis. Further analyses reveal that X up-regulation occurs only in males and is mediated by a male-specific chromatin machinery that leads to global hyperacetylation of histone H4 at lysine 16 specifically on the X Chromosome. The green anole dosage compensation mechanism is highly reminiscent of that of the fruit fly, Drosophila melanogaster. Altogether, our work unveils the convergent emergence of a Drosophila-like dosage compensation mechanism in an ancient reptilian sex chromosome system and highlights that the evolutionary pressures imposed by sex chromosome dosage reductions in different amniotes were resolved in fundamentally different ways.

Fever in the returning child traveller: approach to diagnosis and management

During the last half century there has been an exponential increase in international travel including to more exotic and long-haul destinations. The assessment of febrile returning child travellers presents diagnostic challenges and is often performed poorly. A detailed travel and medical history, clinical examination and appropriate first-line investigations are essential. While the majority of children will have a common self-limiting or easily treatable infection, it is important to consider other causes, including imported infections, which may be life-threatening or highly contagious. In this article, we provide guidance on the initial assessment and management of such children with a focus on some of the more important imported infections, including malaria, dengue, typhoid fever, travellers' diarrhoea, respiratory infections, tuberculosis, schistosomiasis and rickettsial diseases.

Conserved microRNA editing in mammalian evolution, development and disease

Background

Mammalian microRNAs (miRNAs) are sometimes subject to adenosine-to-inosine RNA editing, which can lead to dramatic changes in miRNA target specificity or expression levels. However, although a few miRNAs are known to be edited at identical positions in human and mouse, the evolution of miRNA editing has not been investigated in detail. In this study, we identify conserved miRNA editing events in a range of mammalian and non-mammalian species.

Results

We demonstrate deep conservation of several site-specific miRNA editing events, including two that date back to the common ancestor of mammals and bony fishes some 450 million years ago. We also find evidence of a recent expansion of an edited miRNA family in placental mammals and show that editing of these miRNAs is associated with changes in target mRNA expression during primate development and aging. While global patterns of miRNA editing tend to be conserved across species, we observe substantial variation in editing frequencies depending on tissue, age and disease state: editing is more frequent in neural tissues compared to heart, kidney and testis; in older compared to younger individuals; and in samples from healthy tissues compared to tumors, which together suggests that miRNA editing might be associated with a reduced rate of cell proliferation.

Conclusions

Our results show that site-specific miRNA editing is an evolutionarily conserved mechanism, which increases the functional diversity of mammalian miRNA transcriptomes. Furthermore, we find that although miRNA editing is rare compared to editing of long RNAs, miRNAs are greatly overrepresented among conserved editing targets.

Regulation of Plasmodium falciparum development by calcium-dependent protein kinase 7 (PfCDPK7)

Second messengers such as phosphoinositides and calcium are known to control diverse processes involved in the development of malaria parasites. However, the underlying molecular mechanisms and pathways need to be unraveled, which may be achieved by understanding the regulation of effectors of these second messengers. Calcium-dependent protein kinase (CDPK) family members regulate diverse parasitic processes. Because CDPKs are absent from the host, these kinases are considered as potential drug targets. We have dissected the function of an atypical CDPK from Plasmodium falciparum, PfCDPK7. The domain architecture of PfCDPK7 is very different from that of other CDPKs; it has a pleckstrin homology domain adjacent to the kinase domain and two calcium-binding EF-hands at its N terminus. We demonstrate that PfCDPK7 interacts with PI(4,5)P2 via its pleckstrin homology domain, which may guide its subcellular localization. Disruption of PfCDPK7 caused a marked reduction in the growth of the blood stage parasites, as maturation of rings to trophozoites was markedly stalled. In addition, parasite proliferation was significantly attenuated. These findings shed light on an important role for PfCDPK7 in the erythrocytic asexual cycle of malaria parasites.

Expression in yeast links field polymorphisms in PfATP6 to in vitro artemisinin resistance and identifies new inhibitor classes

BACKGROUND

The mechanism of action of artemisinins against malaria is unclear, despite their widespread use in combination therapies and the emergence of resistance.

RESULTS

Here, we report expression of PfATP6 (a SERCA pump) in yeast and demonstrate its inhibition by artemisinins. Mutations in PfATP6 identified in field isolates (such as S769N) and in laboratory clones (such as L263E) decrease susceptibility to artemisinins, whereas they increase susceptibility to unrelated inhibitors such as cyclopiazonic acid. As predicted from the yeast model, Plasmodium falciparum with the L263E mutation is also more susceptible to cyclopiazonic acid. An inability to knockout parasite SERCA pumps provides genetic evidence that they are essential in asexual stages of development. Thaperoxides are a new class of potent antimalarial designed to act by inhibiting PfATP6. Results in yeast confirm this inhibition.

CONCLUSIONS

The identification of inhibitors effective against mutated PfATP6 suggests ways in which artemisinin resistance may be overcome.

Two nucleus-localized CDK-like kinases with crucial roles for malaria parasite erythrocytic replication are involved in phosphorylation of splicing factor

The kinome of the human malaria parasite Plasmodium falciparum comprises representatives of most eukaryotic protein kinase groups, including kinases which regulate proliferation and differentiation processes. Despite extensive research on most plasmodial enzymes, little information is available regarding the four identified members of the cyclin-dependent kinase-like kinase (CLK) family. In other eukaryotes, CLKs regulate mRNA splicing through phosphorylation of Serine/Arginine-rich proteins. Here, we investigate two of the PfCLKs, the Lammer kinase homolog PfCLK-1, and PfCLK-2. Both PfCLKs show homology with the yeast Serine/Arginine protein kinase Sky1p and are transcribed throughout the asexual blood stages and in gametocytes. PfCLK-1/Lammer possesses two nuclear localization signal sites and PfCLK-2 possesses one of these signal sites upstream of the C-terminal catalytic domains. Indirect immunofluorescence, Western blot, and electron microscopy data confirm that the kinases are primarily localized in the parasite nucleus, and PfCLK-2 is further present in the cytoplasm. The two kinases are important for completion of the asexual replication cycle of P. falciparum, as demonstrated by reverse genetics approaches. In vitro kinase assays show substrate phosphorylation by the PfCLKs, including the Sky1p substrate, splicing factor Npl3p, and the plasmodial alternative splicing factor PfASF-1. Mass spectrometric analysis of co-immunoprecipitated proteins indicates assembly of the two PfCLKs with proteins with predicted nuclease, phosphatase, or helicase functions. Our data indicate a crucial role of PfCLKs for malaria blood stage parasites, presumably by participating in gene regulation through the post-transcriptional modification of mRNA.

Malaria: targeting parasite and host cell kinomes

Malaria still remains one of the deadliest infectious diseases, and has a tremendous morbidity and mortality impact in the developing world. The propensity of the parasites to develop drug resistance, and the relative reluctance of the pharmaceutical industry to invest massively in the developments of drugs that would offer only limited marketing prospects, are major issues in antimalarial drug discovery. Protein kinases (PKs) have become a major family of targets for drug discovery research in a number of disease contexts, which has generated considerable resources such as kinase-directed libraries and high throughput kinase inhibition assays. The phylogenetic distance between malaria parasites and their human host translates into important divergences in their respective kinomes, and most Plasmodium kinases display atypical properties (as compared to mammalian PKs) that can be exploited towards selective inhibition. Here, we discuss the taxon-specific kinases possessed by malaria parasites, and give an overview of target PKs that have been validated by reverse genetics, either in the human malaria parasite Plasmodium falciparum or in the rodent model Plasmodium berghei. We also briefly allude to the possibility of attacking Plasmodium through the inhibition of human PKs that are required for survival of this obligatory intracellular parasite, and which are targets for other human diseases.

Functional characterization of both MAP kinases of the human malaria parasite Plasmodium falciparum by reverse genetics

The kinome of the human malaria parasite Plasmodium falciparum includes two genes encoding mitogen-activated protein kinase (MAPK) homologues, pfmap-1 and pfmap-2, but no clear orthologue of the MAPK kinase (MAPKK) family, raising the question of the mode of activation and function of the plasmodial MAPKs. Functional studies in the rodent malaria model Plasmodium berghei recently showed the map-2 gene to be dispensable for asexual growth and gametocytogenesis, but essential for male gametogenesis in the mosquito vector. Here, we demonstrate by using a reverse genetics approach that the map-2 gene is essential for completion of the asexual cycle of P. falciparum, an unexpected result in view of the non-essentiality of the orthologous gene for P. berghei erythrocytic schizogony. This validates Pfmap-2 as a potential target for chemotherapeutic intervention. In contrast, the other P. falciparum MAPK, Pfmap-1, is required neither for in vitro schizogony and gametocytogenesis in erythrocytes, nor for gametogenesis and sporogony in the mosquito vector. However, Pfmap-2 protein levels are elevated in pfmap-1(-) parasites, suggesting that Pfmap-1 fulfils an important function in asexual parasites that necessitates compensatory adaptation in parasites lacking this enzyme.

Host genotype by parasite genotype interactions underlying the resistance of anopheline mosquitoes to Plasmodium falciparum

Background

Most studies on the resistance of mosquitoes to their malaria parasites focus on the response of a mosquito line or colony against a single parasite genotype. In natural situations, however, it may be expected that mosquito-malaria relationships are based, as are many other host-parasite systems, on host genotype by parasite genotype interactions. In such systems, certain hosts are resistant to one subset of the parasite's genotypes, while other hosts are resistant to a different subset.

Methods

To test for genotype by genotype interactions between malaria parasites and their anopheline vectors, different genetic backgrounds (families consisting of the F1 offspring of individual females) of the major African vector Anopheles gambiae were challenged with several isolates of the human malaria parasite Plasmodium falciparum (obtained from naturally infected children in Kenya).

Results

Averaged across all parasites, the proportion of infected mosquitoes and the number of oocysts found in their midguts were similar in all mosquito families. Both indices of resistance, however, differed considerably among isolates of the parasite. In particular, no mosquito family was most resistant to all parasites, and no parasite isolate was most infectious to all mosquitoes.

Conclusions

These results suggest that the level of mosquito resistance depends on the interaction between its own and the parasite's genotype. This finding thus emphasizes the need to take into account the range of genetic diversity exhibited by mosquito and malaria field populations in ideas and studies concerning the control of malaria.

Does hydrotherapy improve strength and physical function in patients with osteoarthritis--a randomised controlled trial comparing a gym based and a hydrotherapy based strengthening programme

OBJECTIVE

To compare the effects of a hydrotherapy resistance exercise programme with a gym based resistance exercise programme on strength and function in the treatment of osteoarthritis (OA).

DESIGN

Single blind, three arm, randomised controlled trial.

SUBJECTS

105 community living participants aged 50 years and over with clinical OA of the hip or knee.

METHODS

Participants were randomised into one of three groups: hydrotherapy (n = 35), gym (n = 35), or control (n = 35). The two exercising groups had three exercise sessions a week for six weeks. At six weeks an independent physiotherapist unaware of the treatment allocation performed all outcome assessments (muscle strength dynamometry, six minute walk test, WOMAC OA Index, total drugs, SF-12 quality of life, Adelaide Activities Profile, and the Arthritis Self-Efficacy Scale).

RESULTS

In the gym group both left and right quadriceps significantly increased in strength compared with the control group, and right quadriceps strength was also significantly better than in the hydrotherapy group. The hydrotherapy group increased left quadriceps strength only at follow up, and this was significantly different from the control group. The hydrotherapy group was significantly different from the control group for distance walked and the physical component of the SF-12. The gym group was significantly different from the control group for walk speed and self efficacy satisfaction. Compliance rates were similar for both exercise groups, with 84% of hydrotherapy and 75% of gym sessions attended. There were no differences in drug use between groups over the study period.

CONCLUSION

Functional gains were achieved with both exercise programmes compared with the control group.

The effect of treatment on radiological progression in rheumatoid arthritis: a systematic review of randomized placebo-controlled trials

OBJECTIVE

To undertake a systematic review of randomized placebo-controlled trials to assess and rank the efficacy of pharmacological interventions in preventing radiological progression of rheumatoid arthritis.

METHODS

The two outcome measures were the weighted standardized mean difference and the odds of progression of X-ray scores pooled as close to 12 months as possible to minimize heterogeneity.

RESULTS

A total of 38 trials were identified. Of these, 13 were excluded, leaving data on 3907 subjects. Infliximab, cyclosporin, sulphasalazine, leflunomide, methotrexate, parenteral gold, corticosteroids, auranofin and interleukin 1 receptor antagonist were statistically better than placebo in terms of change in erosion scores. All agents were equivalent statistically, with the exception of infliximab (which was superior to the last five agents). There were similar findings for the odds of progression, with the exception of auranofin (P=0.06) and the infliximab-methotrexate comparison (P=0.07). Other agents did not reach statistical significance in either outcome measure. With the exception of the antimalarials, the magnitude of the effect was consistent with the effect seen in short-term disease activity trials.

CONCLUSION

There is published evidence which supports the efficacy of nine agents in decreasing radiological progression in rheumatoid arthritis.

Primary care-based physical activity programs: effectiveness in sedentary older patients with osteoarthritis symptoms

OBJECTIVE

This study examined, in a group of older patients, (a) the effectiveness of an invitation to participate in a program providing individualized physical activity advice in a primary care setting and (b) the changes in self-reported physical activity and symptoms in patients with osteoarthritis (OA).

METHODS

Healthy, sedentary community-dwelling men and women aged 60 years or more were invited to participate. Following random allocation, the intervention group received individualized physical activity advice at baseline and at 3, 6, and 12 months followup.

RESULTS

Of the 299 people who satisfied the study's inclusion criteria, a subgroup of 69 people reported pain and stiffness of the hip or knee at baseline. These patients reported increases in frequency and time of walking and vigorous exercise (all P < 0.001), with no change to OA symptom scores (pain and stiffness), and a small decline in physical functioning was reported at 12 months followup in the control group only (P = 0.027). At the 12-month followup more intervention participants than control participants (P = 0.013) reported a greater intention to exercise.

CONCLUSIONS

An offer of primary care-based physical activity advice, with an emphasis on the benefits for general health (rather than "treatment" for OA), will attract individuals with OA symptoms. Although the present study was unable to demonstrate intervention-control group differences for the majority of outcomes, intention to exercise did appear to be positively influenced.

Purification and properties of gammagamma-enolase from pig brain

Isoelectric focusing revealed three enolase isoforms in pig brain, which were designated as alphaalpha-(pI = 6.5), alphagamma- (pI = 5.6), and gammagamma-enolase (pI = 5.2). The pI of purified gammagamma-enolase was also 5.2. The gammagamma-enolase isoform of enolase was purified from pig brain by a purification protocol involving heating to 55 degrees C for 3 min, acetone precipitation, ammonium sulfate precipitation (40%-80%), DEAE Sephadex ion-exchange chromatography (pH 6.2), and Sephadex G200 gel filtration. The final specific activity was 82 units/mg protein. As with other vertebrate enolases, gammagamma-enolase from pig proved to be a dimer with a native mass of 85 kDa and a subunit mass of 45 kDa. The pH optimum for the reaction in the glycolytic direction is 7.2. The Km values for 2-PGA, PEP, and Mg2+ were determined to be 0.05, 0.25, and 0.50 mM, respectively, similar to Km values of other vertebrate enolases. The amino acid composition of pig gammagamma-enolase, as determined by amino acid analysis, shows strong similarity to the compositions of gammagamma-enolases from rat, human, and mouse, as determined from their amino acid sequences. Despite the differences seen with some residues, and considering the ways that the compositions were obtained, it is assumed that pig gammagamma-enolase is more similar than the composition data would indicate. Moreover, it is likely that the sequences of pig gammagamma-enolase and the other gammagamma-enolases are almost identical. Li+ proved to be a noncompetitive inhibitor with either 2-PGA or Mg2+ as the variable substrate. This enolase crystallized in the monoclinic space group P2, or P2(1). An Rsymm <5% was obtained for data between 50 and 3.65 A, but was a disappointing 30% for data between 3.65 and 3.10 A, indicating crystal disorder.

Temporal trends in HIV risk behaviors of out-of-treatment injection drug users and injection drug users who smoke crack

This study compared the baseline sociodemographic characteristics and HIV risk behaviors of two groups of out-of-treatment injection drug users (IDUs): 366 who concurrently smoked crack (smoking IDUs) and 212 who did not smoke crack (IDUs) in the past 30 days. Temporal trends in recent risk behaviors were also assessed for each drug user group over an 18-month period, January 1992 through June 1994. Baseline data were collected in South Philadelphia before the implementation of a multisite HIV intervention research project funded by the National Institute on Drug Abuse. For the temporal trend analysis, the sample was grouped into four intake periods based on the date of the baseline interview. The results indicated that although both groups were economically disadvantaged and at high risk of HIV infection and transmission, smoking injectors had fewer economic resources and were at a moderately greater risk because of higher levels of sexual risk behaviors. Analysis of temporal trends revealed few reductions in drug risk behaviors and none in sexual risk behaviors. This study points to the need for examining differences between types of drug users, developing appropriate multidrug treatment programs and assessing the characteristics of communities so that theory-based interventions can be tailored for maximum effectiveness.

Correlates of HIV seropositivity and HIV testing among out-of-treatment drug users

This study: 1) examined the rate and correlates of human immunodeficiency virus (HIV) seropositivity; and 2) assessed whether self-selection in HIV testing influenced the rate and correlates of HIV seropositivity in a group of out-of-treatment drug users. Data were collected from 856 out-of-treatment drug users in Philadelphia between January 1993 and August 1994. Seventy-four percent of the sample elected to take an HIV test that was included in the project in which the drug users were enrolled, and of these, 11% were HIV positive. Multivariate analyses indicated that those who were younger, those who had an injection-drug-using sex partner, and those who reported no recent sexual activity were more likely to be HIV positive. An examination of the multivariate correlates of HIV testing indicated that subjects who took an HIV test had higher rates of participation in some risk behaviors than did subjects who did not take an HIV test, but lower rates for other risk behaviors. None of the correlates of HIV seropositivity were correlates of HIV testing. Although the generalizability of the HIV seroprevalence rate is unclear, it is probable that the correlates of HIV seropositivity are generalizable to the total sample. The results of this study indicate the importance of interventions that target sexual risk behavior among out-of-treatment drug users, and of assessing the impact of self-selection bias whenever the rate and correlates of HIV seropositivity are examined.

Effectiveness of an HIV risk reduction counseling intervention for out-of-treatment drug users

This study examined and compared the effectiveness of two counseling interventions designed to reduce the HIV drug and sexual risk behaviors of 684 out-of-treatment drug users recruited from South Philadelphia, PA. All study participants received a standard intervention and one half were randomly assigned to also receive the enhanced intervention. The standard intervention provided HIV risk reduction education, HIV testing with pretest and posttest counseling, and training in condom use and needle cleaning. The enhanced intervention provided additional information on STD risk reduction. Both interventions were effective in influencing behavior change between baseline and 6-month follow-up. A higher proportion of persons reduced their drug risk behaviors compared to their sexual risk behaviors. As sexual risk behaviors are more resistant to change, there is a need for tailored interventions that target out-of-treatment drug users.

Neighborhood variations in the use of city-supported primary health care services by an elderly population

The purpose of this paper is to examine the elderly's use of city-supported primary health care services. The provision of free or low cost health care to the elderly population is a major health policy issue, especially as the size of the elderly population increases and there is a concomitant increase in the need for health services and increases in the out-of-pocket cost of health care. The data analyzed here are based on client records for approximately 6,000 persons 65 and older who utilized the City of Philadelphia's Family Medical Care Program in 1982. Demographic and socioeconomic characteristics, diagnoses and types of services used are examined for all clients citywide and by neighborhood. Elderly clients of the city primary care system tended to be 65-74, female and black. Most clients had low incomes, with about 75-87% having incomes below $6,000. The problems for which care is sought involve long-term, ongoing care. The data show that the elderly are underrepresented in the city-supported primary care system relative to their numbers in the general population. Our findings on diagnosis and services utilization characteristics of those elderly who do use city-supported primary health care services indicate that the elderly are likely to place demands on the existing system for a substantial amount of resources. The demands for such services are likely to increase especially as the size of the elderly population increases.