Remote homology and the functions of metagenomic dark matter

Predicted open reading frames (ORFs) that lack detectable homology to known proteins are termed ORFans. Despite their prevalence in metagenomes, the extent to which ORFans encode real proteins, the degree to which they can be annotated, and their functional contributions, remain unclear. To gain insights into these questions, we applied sensitive remote-homology detection methods to functionally analyze ORFans from soil, marine, and human gut metagenome collections. ORFans were identified, clustered into sequence families, and annotated through profile-profile comparison to proteins of known structure. We found that a considerable number of metagenomic ORFans (73,896 of 484,121, 15.3%) exhibit significant remote homology to structurally characterized proteins, providing a means for ORFan functional profiling. The extent of detected remote homology far exceeds that obtained for artificial protein families (1.4%). As expected for real genes, the predicted functions of ORFans are significantly similar to the functions of their gene neighbors (p < 0.001). Compared to the functional profiles predicted through standard homology searches, ORFans show biologically intriguing differences. Many ORFan-enriched functions are virus-related and tend to reflect biological processes associated with extreme sequence diversity. Each environment also possesses a large number of unique ORFan families and functions, including some known to play important community roles such as gut microbial polysaccharide digestion. Lastly, ORFans are a valuable resource for finding novel enzymes of interest, as we demonstrate through the identification of hundreds of novel ORFan metalloproteases that all possess a signature catalytic motif despite a general lack of similarity to known proteins. Our ORFan functional predictions are a valuable resource for discovering novel protein families and exploring the boundaries of protein sequence space. All remote homology predictions are available at http://doxey.uwaterloo.ca/ORFans.

Census of solo LuxR genes in prokaryotic genomes

luxR genes encode transcriptional regulators that control acyl homoserine lactone-based quorum sensing (AHL QS) in Gram negative bacteria. On the bacterial chromosome, luxR genes are usually found next or near to a luxI gene encoding the AHL signal synthase. Recently, a number of luxR genes were described that have no luxI genes in their vicinity on the chromosome. These so-called solo luxR genes may either respond to internal AHL signals produced by a non-adjacent luxI in the chromosome, or can respond to exogenous signals. Here we present a survey of solo luxR genes found in complete and draft bacterial genomes in the NCBI databases using HMMs. We found that 2698 of the 3550 luxR genes found are solos, which is an unexpectedly high number even if some of the hits may be false positives. We also found that solo LuxR sequences form distinct clusters that are different from the clusters of LuxR sequences that are part of the known luxR-luxI topological arrangements. We also found a number of cases that we termed twin luxR topologies, in which two adjacent luxR genes were in tandem or divergent orientation. Many of the luxR solo clusters were devoid of the sequence motifs characteristic of AHL binding LuxR proteins so there is room to speculate that the solos may be involved in sensing hitherto unknown signals. It was noted that only some of the LuxR clades are rich in conserved cysteine residues. Molecular modeling suggests that some of the cysteines may be involved in disulfide formation, which makes us speculate that some LuxR proteins, including some of the solos may be involved in redox regulation.

The QQS orphan gene of Arabidopsis modulates carbon and nitrogen allocation in soybean

The genome of each species contains as high as 8% of genes that are uniquely present in that species. Little is known about the functional significance of these so-called species specific or orphan genes. The Arabidopsis thaliana gene Qua-Quine Starch (QQS) is species specific. Here, we show that altering QQS expression in Arabidopsis affects carbon partitioning to both starch and protein. We hypothesized QQS may be conserved in a feature other than primary sequence, and as such could function to impact composition in another species. To test the potential of QQS in affecting composition in an ectopic species, we introduced QQS into soybean. Soybean T1 lines expressing QQS have up to 80% decreased leaf starch and up to 60% increased leaf protein; T4 generation seeds from field-grown plants contain up to 13% less oil, while protein is increased by up to 18%. These data broaden the concept of QQS as a modulator of carbon and nitrogen allocation, and demonstrate that this species-specific gene can affect the seed composition of an agronomic species thought to have diverged from Arabidopsis 100 million years ago.

What makes orphans in Kigali, Rwanda, non-adherent to antiretroviral therapy? Perspectives of their caregivers

INTRODUCTION

Every year, approximately 260,000 children are infected with HIV in low- and middle-income countries. The timely initiation and high level of maintenance of antiretroviral therapy (ART) are crucial to reducing the suffering of HIV-positive children. We need to develop a better understanding of the background of children's ART non-adherence because it is not well understood. The purpose of this study is to explore the background related to ART non-adherence, specifically in relation to the orphan status of children in Kigali, Rwanda.

METHODS

We conducted 19 focus group discussions with a total of 121 caregivers of HIV-positive children in Kigali. The primary data for analysis were verbatim transcripts and socio-demographic data. A content analysis was performed for qualitative data analysis and interpretation.

RESULTS

The study found several contextual factors that influenced non-adherence: among double orphans, there was psychological distance between the caregivers and children, whereas economic burden was the primary issue among paternal orphans. The factors promoting adherence also were unique to each orphan status, such as the positive attitude about disclosing serostatus to the child by double orphans' caregivers, and feelings of guilt about the child's condition among non-orphaned caregivers.

CONCLUSIONS

Knowledge of orphan status is essential to elucidate the factors influencing ART adherence among HIV-positive children. In this qualitative study, we identified the orphan-related contextual factors that influenced ART adherence. Understanding the social context is important in dealing with the challenges to ART adherence among HIV-positive children.

Prevalence of "HIV/AIDS related" parental death and its association with sexual behavior of secondary school youth in Addis Ababa, Ethiopia: a cross sectional study

BACKGROUND

Human immunodeficiency virus infection is a global crisis that represents a serious health threat, particularly among younger people. Various studies show that both orphan and non-orphan adolescents and youths experience vulnerability to HIV. Nevertheless, the findings hitherto are mixed and inconclusive. The aim of this study, therefore, was to assess the prevalence of parental death and its association with multiple sexual partners among secondary school students for evidence based interventions.

METHODS

A cross-sectional study was conducted among secondary school youth in Addis Ababa, Ethiopia. A multistage sampling technique was used to select a representative sample of 2,169 school youths. Sexual health behavior related data were collected using self-administered questionnaire. Binary logistic regression was employed to examine the relation between parental death and multiple sexual partners.

RESULTS

Among the 2,169 eligible study participants 1948 (90%) completed the self-administered questionnaires. Of those 1,182(60.7%) were females. The overall prevalence of parental death was 347(17.8%.) with 95% CI (16.2%, 19.6%). The HIV/AIDS proportionate mortality ratio was 28% (97/347).A multivariate logistic regression analysis showed that high HIV/AIDS related knowledge (AOR = 0.39; 95% CI, 0.18-0.84), positive attitude towards HIV prevention methods (AOR = 0.48; 95% CI, 0.23-0.97), being tested for HIV (AOR = 0.52; 95% CI, 0.31-0.87) and chewing Khat (AOR = 2.59; 95% CI,1.28-5.26)] were significantly associated with having multiple sexual partners among secondary school youths.

CONCLUSIONS

Significant proportion of secondary school youths had lost at least one parent due to various causes. High knowledge of HIV/AIDS, positive attitude towards 'ABC' rules for HIV prevention, being tested for HIV and chewing khat are more likely to be factors associated with multiple sexual partnership among secondary school students in Addis Ababa.Therefore, the school based interventions against the HIV/AIDS epidemic should be strengthened with particular emphasis on the effects of HIV/AIDS related knowledge, attitude towards preventive measures, mechanisms for improving HIV Counseling and Testing coverage and the associated prevailing risk factors.

Ataluren treatment of patients with nonsense mutation dystrophinopathy

INTRODUCTION

Dystrophinopathy is a rare, severe muscle disorder, and nonsense mutations are found in 13% of cases. Ataluren was developed to enable ribosomal readthrough of premature stop codons in nonsense mutation (nm) genetic disorders.

METHODS

Randomized, double-blind, placebo-controlled study; males ≥ 5 years with nm-dystrophinopathy received study drug orally 3 times daily, ataluren 10, 10, 20 mg/kg (N=57); ataluren 20, 20, 40 mg/kg (N=60); or placebo (N=57) for 48 weeks. The primary endpoint was change in 6-Minute Walk Distance (6MWD) at Week 48.

RESULTS

Ataluren was generally well tolerated. The primary endpoint favored ataluren 10, 10, 20 mg/kg versus placebo; the week 48 6MWD Δ=31.3 meters, post hoc P=0.056. Secondary endpoints (timed function tests) showed meaningful differences between ataluren 10, 10, 20 mg/kg, and placebo.

CONCLUSIONS

As the first investigational new drug targeting the underlying cause of nm-dystrophinopathy, ataluren offers promise as a treatment for this orphan genetic disorder with high unmet medical need.

Caregiver burden among adults caring for orphaned children in rural South Africa

The AIDS epidemic has created an unprecedented number of orphans. While largely absorbed by extended family, this additional responsibility can weigh heavily on their caregivers. The concept of caregiver burden captures multiple dimensions of well-being (e.g., physical, social and psychological). Measuring the extent and determinants of caregiving burden can inform the design of programmes to ease the negative consequences of caregiving. This study uses the baseline data from a study assessing interventions for orphans and vulnerable adolescents in the Eastern Cape, South Africa. Orphan caregivers (n = 726) completed an adapted version of the 12-item Zarit Burden Interview. In addition to basic caregiver and household demographics, the survey also collected information on AIDS-related illness and recent deaths. Descriptive data are presented, followed by multivariate Poisson regression models to explore factors associated with caregiver burden. Approximately 40% of caregivers reported high levels of orphan caregiving burden. Feelings of stress and inadequacy concerning their care responsibilities as well as anger towards the child were common. Household food insecurity was the most important predictor of orphan caregiving burden (marginal effect = 7.82; p < 0.001 for those reporting severe hunger); income was also a significant determinant. When other AIDS impacts were added to the model, only the AIDS-related illness of the caregiver was significantly associated with burden (marginal effect = 3.77; p < 0.001). This study suggests that caregivers with economic vulnerability and those struggling with their own AIDS-related illness feel most overburdened. These findings are particularly relevant to service providers who must identify caregivers in need of immediate assistance and allocate limited resources effectively. To alleviate caregiver burden, programmes must foster greater economic security (e.g., by facilitating access to social grants or directly providing cash transfers) and coordinate services with home-based care programmes serving the chronically ill.

[Oral health status of 4-17-year-old orphan children and adolescents of Chongqing]

OBJECTIVE

To examine the oral health status among the orphan children and adolescents of Chongqing and assist in planning of the oral health programs.

METHODS

According to the third national oral health investigation of epidemiology, the dental caries, gingival bleeding and calculus was examined among 317 orphan living in Chongqing, by cluster sampling. The statistical software SPSS 17.0 was used for the data analysis.

RESULTS

In primary and permanent teeth, the prevalence of dental caries and mean DMFT (dmft) were found to be 50.00%, 1.94 +/- 2.81 and 39.53%, 0.90 +/- 1.38. There were no significant difference between female and male (P>0.05). But there was significant difference of the prevalence of permanent tooth caries between the age group under 12 (include 12) and above 12 (P < 0.05). It was also found that 35.25% of the orphan children and adolescents had caries in the first permanent molar, and there was significant difference between female and male (P < 0.05). Neither of the caries teeth above was treated nor the healthy teeth were sealed. The prevalence rate of gingival bleeding was 78.22%, and the calculus rate was 67.66%.

CONCLUSION

The oral status of the orphan is poor, and this community has experienced a low utilization of preventive or therapeutic oral health services. In the future work, orphans should be considered as a priority group when make plans for oral health care.

The legal imperative for treating rare disorders

BACKGROUND

Life-saving orphan drugs are some of the most expensive medicines. European Union governments aim to accommodate their provision within stretched healthcare budgets but face pressure to reduce funding of such treatments. Patients struggle to retain or gain access to them as their special status is questioned, causing distress and in some cases, fears of premature death. In the UK and EU reimbursement and pricing model of drugs, and orphan drugs in particular, is being re-evaluated.

METHODS

Using the United Kingdom as a case study we present, for the first time, legal arguments which compel governments to provide orphan medicinal products. These include (i) disability legislation, (ii) national and organisational constitutions, (iii) judicial review, (iv) tort law and (v) human rights legislation. We then address directly potential objections to our analysis and counter arguments which aim to limit provision of orphan drugs to the intended patient recipients.

RESULTS

We demonstrate that a compelling case can be made that the law demands the treatment of orphan diseases.

CONCLUSIONS

Our legal framework will assist doctors and patients in ensuring the continued provision of treatments despite significant economic pressure to reduce funding. These legal avenues will empower stakeholders in drafting funding guidelines throughout the EU. The legal right to treatment extends beyond rare diseases and our analysis may therefore affect allocation of healthcare budgets throughout the EU.

Child abuse and neglect among orphaned children and youth living in extended families in sub-Saharan Africa: What have we learned from qualitative inquiry?

Researchers and aid organizations have reported that orphans in sub-Saharan Africa (SSA) are particularly vulnerable to abuse and neglect. This article is a review of qualitative studies that address experiences of maltreatment among orphaned children and youth living in extended families in SSA. It aims to inform policy and programming by providing a better understanding of the types of maltreatment encountered and the perceived risk factors. A literature search was carried out using Google, PubMed, Scholars Portal Search and Scopus. Searches of relevant bibliographies and publications of authors were also undertaken. Studies from peer-reviewed journals and the grey literature were reviewed for relevance and quality. Eligible studies had to include orphans living with extended family in SSA as participants, explore their maltreatment experiences and employ a sound qualitative methodology. Findings were coded, extracted, compared and synthesized. Twenty articles, representing 15 studies, were selected. These studies, from diverse SSAn countries, reported similar forms of maltreatment among orphaned children and youth: experiences of intra-household discrimination; material and educational neglect; excessive child labour; exploitation by family members and psychological, sexual and physical abuse. The perceived risk factors were poverty, living with a non-biological caregiver, stigma and alcohol abuse. The findings of the included studies suggest that awareness, prevention and intervention initiatives aimed to curb child abuse and neglect within communities in SSA are needed and should be coupled with efforts to promote education and reduce poverty and stigma.

Synaptic localization of growth-associated protein 43 in cultured hippocampal neurons during synaptogenesis

Growth-associated protein 43 (GAP-43), a novel axonal phosphoprotein, is originally identified as a growth-cone-specific protein of developing neurons in vitro. The expression of GAP-43 is also shown to be up-regulated concomitant with increased synaptic plasticity in the brains in vivo, but how GAP-43 is concerned with synaptic plasticity is not well understood. In the present study, therefore, we aimed to elucidate subcellular localization of GAP-43 as culture development of rat hippocampal neurons. Western blotting showed that the expression of GAP-43 in the cerebral and hippocampal tissues was prominently high at postnatal days 14 and 21 or the active period of synaptogenesis. Double-labelling immunohistochemistry with an axonal marker Tau revealed that the immunoreactivity of GAP-43 was seen throughout axons of cultured hippocampal neurons but stronger at axonal puncta of developing neurons than axonal processes. Double-labelling immunohistochemistry with presynaptic terminal markers of synapsin and synaptotagmin revealed that the immunoreactivity of GAP-43 was observed mostly at weak synapsin- and synaptotagmin-positive puncta rather than strong ones. The quantitative analysis of immunofluorescent intensity showed a clear inverse correlation between GAP-43 and either synapsin or synaptotagmin expression. These data indicate that GAP-43 is highly expressed at immature growing axonal terminals and its expression is decreased along with the maturation of synaptogenesis.

[Epidermal Tuberculosis in an orphan living with HIV in the Pediatric Unit of Bangui (Central African Republic)]

We report the case of ulceration of the anterior chest region in a non BCG vaccinated adolescent. Tuberculosis confirmations has been made by the isolation of M. tuberculosis from the pus culture in Löwenstein-Jensen medium. Topography and chronology of the clinical manifestations argue in favour of scrofuloderma. For technical reasons, we were not able to distinguish scrofuloderma from the gum. The use of the single standard regime of tuberculosis treatment according to the immunological status has provided a healing of skin injury in children living with HIV. In addition, this observation emphasises the medical interest to implement systematic vaccination against tuberculosis and to ensure effective control of the disease, particularly in orphans.

Depression among carers of AIDS-orphaned and other-orphaned children in Umlazi Township, South Africa

South Africa faces the challenge of supporting the well-being of adults caring for growing numbers of AIDS-orphaned children. These adults play a critical role in responses to the epidemic, but little information exists in regard to their mental health needs. This paper reports on findings from n=1599 adults, recruited through representative household sampling, who serve as primary carers for children in Umlazi Township, an HIV-endemic community. Overall, 22% of participants were carers of AIDS-orphaned children, 11% were carers of other-orphaned children and 67% were carers of non-orphaned children. Prevalence of depression was 30.3%. Orphan carers, regardless of whether they cared for AIDS-orphaned or other-orphaned children, were significantly more likely than carers of non-orphaned children to meet the clinical threshold for depression (35.2% vs. 27.9%, p < 0.01). In multivariate logistic regressions, food insecurity and being a female carer were identified as additional risk factors for greater depression. In contrast, households with access to running water and households dependent on salaries as the main source of income were identified as protective factors for disparities in depression. Mental health interventions are urgently needed to address an increased risk for depression among all orphan carers, not just those caring for AIDS-orphaned children.

Caring for AIDS-orphaned children: an exploratory study of challenges faced by carers in KwaZulu-Natal, South Africa

Fifteen million children have been orphaned because of AIDS and these numbers are expected to grow in the coming decade. Individuals providing noninstitutional care for AIDS-orphaned children play a critical role in the capacity of communities to respond to the epidemic. However, a limited body of evidence exists on these carers. Studies are urgently needed to build the evidence base on this population, particularly in South Africa which has the largest population of people living with HIV globally. An exploratory qualitative study with carers of AIDS-orphaned children and informants from nongovernmental organizations in KwaZulu-Natal (KZN) province, South Africa, was conducted to (1) explore challenges associated with caring for AIDS-orphaned children and (2) identify areas for more detailed quantitative studies. Findings from this study contribute to a better understanding of AIDS-related impacts on the family by specifically identifying challenges associated with care for AIDS-orphaned children in South Africa.

Gender and the effects of an economic empowerment program on attitudes toward sexual risk-taking among AIDS-orphaned adolescent youth in Uganda

PURPOSE

This article examines gender differences in attitudes toward sexual risk-taking behaviors of acquired immune deficiency syndrome (AIDS)-orphaned youth participating in a randomized control trial testing an economic empowerment intervention in rural Uganda.

METHODS

Adolescents (average age 13.7 years) who had lost one or both parents to AIDS from 15 comparable schools were randomly assigned to either an experimental (n=135) or a control condition (n=142). Adolescents in the experimental condition, in addition to usual care, also received support and incentives to save money toward secondary education.

RESULTS

Findings indicate that although adolescent boys and girls within the experimental condition saved comparable amounts, the intervention appears to have benefited girls, in regard to the attitudes toward sexual risk-taking behavior, in a different way and to a lesser extent than boys.

CONCLUSIONS

Future research should investigate the possibility that adolescent girls might be able to develop equally large improvements in protective attitudes toward sexual risk taking through additional components that address gendered social norms.

Grandmother Co-Residence and School Enrollment in sub-Saharan Africa

The HIV/AIDS pandemic in sub-Saharan Africa has brought renewed attention to the role of grandmothers as caregivers of children. Using 2004 DHS data, we examine the relationship between co-residence with a grandmother and child schooling in Lesotho, a country with one of the highest rates of HIV infection. Results confirm the critical role grandmothers play in the event of maternal death. Maternal orphans who live with a grandmother are just as likely to be in school as children living with a mother. The protective effect of living with a grandmother is also important for children whose mothers are alive but not affiliated with their households. The results of the analysis underscore the importance of attending to the simultaneous presence of mothers and grandmothers, as well as the circumstances associated with mother absence, when assessing the relationship between grandmother co-residence and child outcomes.

Orphan G-protein-coupled receptors: the next generation of drug targets?

The pharmaceutical industry has readily embraced genomics to provide it with new targets for drug discovery. Large scale DNA sequencing has allowed the identification of a plethora of DNA sequences distantly related to known G protein-coupled receptors (GPCRs), a superfamily of receptors that have a proven history of being excellent therapeutic targets. In most cases the extent of sequence homology is insufficient to assign these 'orphan' receptors to a particular receptor subfamily. Consequently, reverse molecular pharmacological and functional genomic strategies are being employed to identify the activating ligands of the cloned receptors. Briefly, the reverse molecular pharmacological methodology includes cloning and expression of orphan GPCRs in mammalian cells and screening these cells for a functional response to cognate or surrogate agonists present in biological extract preparations, peptide libraries, and complex compound collections. The functional genomics approach involves the use of 'humanized yeast cells, where the yeast GPCR transduction system is engineered to permit functional expression and coupling of human GPCRs to the endogenous signalling machinery. Both systems provide an excellent platform for identifying novel receptor ligands. Once activating ligands are identified they can be used as pharmacological tools to explore receptor function and relationship to disease.