| 1. |
- Richards, Stephen, et al.
(författare)
-
Genome Sequence of the Pea Aphid Acyrthosiphon pisum
- 2010
-
Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 8:2, s. e1000313-
-
Tidskriftsartikel (refereegranskat)abstract
- Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.
|
|
| 2. |
- Beecham, Ashley H, et al.
(författare)
-
Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis.
- 2013
-
Ingår i: Nature genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 45:11, s. 1353-60
-
Tidskriftsartikel (refereegranskat)abstract
- Using the ImmunoChip custom genotyping array, we analyzed 14,498 subjects with multiple sclerosis and 24,091 healthy controls for 161,311 autosomal variants and identified 135 potentially associated regions (P < 1.0 × 10(-4)). In a replication phase, we combined these data with previous genome-wide association study (GWAS) data from an independent 14,802 subjects with multiple sclerosis and 26,703 healthy controls. In these 80,094 individuals of European ancestry, we identified 48 new susceptibility variants (P < 5.0 × 10(-8)), 3 of which we found after conditioning on previously identified variants. Thus, there are now 110 established multiple sclerosis risk variants at 103 discrete loci outside of the major histocompatibility complex. With high-resolution Bayesian fine mapping, we identified five regions where one variant accounted for more than 50% of the posterior probability of association. This study enhances the catalog of multiple sclerosis risk variants and illustrates the value of fine mapping in the resolution of GWAS signals.
|
|
| 3. |
|
|
| 4. |
- Minja, Daniel T. R., et al.
(författare)
-
Plasmodium falciparum Mutant Haplotype Infection during Pregnancy Associated with Reduced Birthweight, Tanzania
- 2013
-
Ingår i: Emerging Infectious Diseases. - : Centers for Disease Control and Prevention (CDC). - 1080-6040 .- 1080-6059. ; 19:9, s. 1446-1454
-
Tidskriftsartikel (refereegranskat)abstract
- Intermittent preventive treatment during pregnancy with sulfadoxine pyrimethamine (IPTp-SP) is a key strategy in the control of pregnancy-associated malaria. However, this strategy is compromised by widespread drug resistance from single-nucleotide polymorphisms in the Plasmodium falciparum dihydrofolate reductase and dihydropteroate synthetase genes. During September 2008 October 2010, we monitored a cohort of 924 pregnant women in an area of Tanzania with declining malaria transmission. P falciparum parasites were genotyped, and the effect of infecting haplotypes on birthweight was assessed. Of the genotyped parasites, 9.3%, 46.3%, and 44.4% had quadruple or less, quintuple, and sextuple mutated haplotypes, respectively. Mutant haplotypes were unrelated to SP doses. Compared with infections with the less-mutated haplotypes, infections with the sextuple haplotype mutation were associated with lower (359 g) birth-weights. Continued use of the suboptimal IPTp-SP regimen should be reevaluated, and alternative strategies (e.g., intermittent screening and treatment or intermittent treatment with safe and effective alternative drugs) should be evaluated.
|
|
| 5. |
- Minja, Daniel T. R., et al.
(författare)
-
Reliability of rapid diagnostic tests in diagnosing pregnancy associated malaria in North Eastern Tanzania
- 2012
-
Ingår i: Malaria Journal. - : Springer Science and Business Media LLC. - 1475-2875 .- 1475-2875. ; 11, s. 211-
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Accurate diagnosis and prompt treatment of pregnancy-associated malaria (PAM) are key aspects in averting adverse pregnancy outcomes. Microscopy is the gold standard in malaria diagnosis, but it has limited detection and availability. When used appropriately, rapid diagnostic tests (RDTs) could be an ideal diagnostic complement to microscopy, due to their ease of use and adequate sensitivity in detecting even sub-microscopic infections. Polymerase chain reaction (PCR) is even more sensitive, but it is mainly used for research purposes. The accuracy and reliability of RDTs in diagnosing PAM was evaluated using microscopy and PCR. Methods: A cohort of pregnant women in north-eastern Tanzania was followed throughout pregnancy for detection of plasmodial infection using venous and placental blood samples evaluated by histidine rich protein 2 (HRP-2) and parasite lactate dehydrogenase (pLDH) based RDTs (Parascreen (TM)) or HRP-2 only (Paracheck Pf (R) and ParaHIT (R) f), microscopy and nested Plasmodium species diagnostic PCR. Results: From a cohort of 924 pregnant women who completed the follow up, complete RDT and microscopy data was available for 5,555 blood samples and of these 442 samples were analysed by PCR. Of the 5,555 blood samples, 49 ((proportion and 95% confidence interval) 0.9% [0.7 - 1.1]) samples were positive by microscopy and 91 (1.6% [1.3-2.0]) by RDT. Forty-six (50.5% [40.5 - 60.6]) and 45 (49.5% [39.4 - 59.5]) of the RDT positive samples were positive and negative by microscopy, respectively, whereas nineteen (42.2% [29.0 - 56.7]) of the microscopy negative, but RDT positive, samples were positive by PCR. Three (0.05% [0.02 - 0.2]) samples were positive by microscopy but negative by RDT. 351 of the 5,461 samples negative by both RDT and microscopy were tested by PCR and found negative. There was no statistically significant difference between the performances of the different RDTs. Conclusions: Microscopy underestimated the real burden of malaria during pregnancy and RDTs performed better than microscopy in diagnosing PAM. In areas where intermittent preventive treatment during pregnancy may be abandoned due to low and decreasing malaria risk and instead replaced with active case management, screening with RDT is likely to identify most infections in pregnant women and out-performs microscopy as a diagnostic tool.
|
|
| 6. |
- Olesen, Pernille J, et al.
(författare)
-
Reducing Global Warming and Adapting to Climate Change: The Potential of Organic Agriculture
- 2012
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Climate change mitigation is urgent, and adaptation to climate change is crucial, particularly in agriculture, where food security is at stake. Agriculture, currently responsible for 20-30% of global greenhouse gas emissions (counting direct and indirect agricultural emissions), can however contribute to both climate change mitigation and adaptation. The main mitigation po-tential lies in the capacity of agricultural soils to sequester CO2 through building organic matter. This potential can be realized by employing sustainable agricultural practices, such as those com-monly found within organic farming systems. Examples of these practices are the use of organic fertilizers and crop rotations including legume leys and cover crops. Mitigation is also achieved in organic agriculture through the avoidance of open biomass burning, and the avoidance of synthetic fertilizers, the production of which causes emissions from fossil fuel use. Common organic practices also contribute to adaptation. Building soil organic matter increases water retention capacity, and creates more stabile, fertile soils, thus reducing vulnerability to drought, extreme precipitation events, floods and water logging. Adaptation is further supported by increased agro-ecosystem diversity of organic farms, based on management decisions, reduced ni-trogen inputs and the absence of chemical pesticides. The high diversity together with the lower input costs of organic agriculture is key to reducing production risks associated with extreme weather events. All these advantageous practices are not exclusive to organic agriculture. However, they are core parts of the organic production system, in contrast to most non-organic agriculture, where they play a minor role only. Mitigation in agriculture is however not restricted to the agricultural sector alone. Consumer pref-erences for products from conventional or organic farms, seasonal and local production, pest and disease resistant varieties, etc. strongly influence agricultural production systems, and thus the overall mitigation potential of agriculture. Even more influential are meat consumption and food wastage. Any discussion on mitigation of climate change in agriculture thus needs to address the entire food chain, and to be linked to general sustainable development strategies. The main challenges to dealing appropriately with the climate change mitigation and adaptation potential of organic agriculture, and agriculture in general, stem from a) insufficient understanding of some of the basic processes, such as the interaction of N2O emissions and soil carbon sequestra-tion, contributions of roots to soil carbon sequestration, and the life-cycle emissions of organic fer-tilizers, such as compost; b) lack of procedures for emissions accounting which adequately repre-sent agricultural production systems with multiple and diverse outputs, which also encompass eco-system services; c) the problem to identify and design adequate policy frameworks for supporting mitigation and adaptation in agriculture, i.e. such that do not put systemic approaches at a disad-vantage due to difficulties in the quantification of emissions, and in their allocation to single prod-ucts; d) the necessity to assure that the current focus on mitigation does not lead to neglect of other factors influencing the sustainability of agriculture, such as pesticide loads, eutrophication, acidifi-cation or soil erosion; and e) the open questions, how to address consumer behaviour and how to further changes in consumption patterns, in order to utilize their mitigation potential.
|
|
| 7. |
|
|
| 8. |
- Roy, Sushmita, et al.
(författare)
-
Identification of functional elements and regulatory circuits by Drosophila modENCODE.
- 2010
-
Ingår i: Science (New York, N.Y.). - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 330:6012, s. 1787-1797
-
Tidskriftsartikel (refereegranskat)abstract
- To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation.
|
|
| 9. |
- Sawcer, Stephen, et al.
(författare)
-
Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis
- 2011
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 476:7359, s. 214-219
-
Tidskriftsartikel (refereegranskat)abstract
- Multiple sclerosis is a common disease of the central nervous system in which the interplay between inflammatory and neurodegenerative processes typically results in intermittent neurological disturbance followed by progressive accumulation of disability. Epidemiological studies have shown that genetic factors are primarily responsible for the substantially increased frequency of the disease seen in the relatives of affected individuals, and systematic attempts to identify linkage in multiplex families have confirmed that variation within the major histocompatibility complex (MHC) exerts the greatest individual effect on risk. Modestly powered genome-wide association studies (GWAS) have enabled more than 20 additional risk loci to be identified and have shown that multiple variants exerting modest individual effects have a key role in disease susceptibility. Most of the genetic architecture underlying susceptibility to the disease remains to be defined and is anticipated to require the analysis of sample sizes that are beyond the numbers currently available to individual research groups. In a collaborative GWAS involving 9,772 cases of European descent collected by 23 research groups working in 15 different countries, we have replicated almost all of the previously suggested associations and identified at least a further 29 novel susceptibility loci. Within the MHC we have refined the identity of the HLA-DRB1 risk alleles and confirmed that variation in the HLA-A gene underlies the independent protective effect attributable to the class I region. Immunologically relevant genes are significantly overrepresented among those mapping close to the identified loci and particularly implicate T-helper-cell differentiation in the pathogenesis of multiple sclerosis.
|
|
| 10. |
- Thodi, Chryssola, et al.
(författare)
-
Adult Hearing Screening : Follow-Up and Outcomes
- 2013
-
Ingår i: American Journal of Audiology. - : American Speech-Language-Hearing Association. - 1059-0889 .- 1558-9137. ; 22, s. 183-185
-
Tidskriftsartikel (refereegranskat)abstract
- PURPOSE:To screen hearing and evaluate outcomes in community-dwelling older adults.METHOD:Three thousand and twenty-five adults responded to an invitation to be screened by questionnaire, otoscopy, and pure-tone audiometry. Pure-tone average (PTA) >35 dB HL in the worse ear, unilateral hearing loss, or otoscopic findings were the criteria for referral for services. A questionnaire related to compliance with referral recommendations was completed by telephone interview for 160 randomly selected participants after 1-2 years from referral.RESULTS:The referral rate for audiologic/hearing aid evaluation was 46%, and referral for cerumen removal/medical evaluation was 17%. Of the people referred for audiologic/hearing aid evaluation, 18% tried a hearing aid; 2 years later, 11% were using a hearing aid. Screening recommendations affected participants' decision to seek help. Study participants stated that the screening was helpful, it should be offered to everybody, and they would participate in future screenings.CONCLUSION:Although adult hearing screening offered timely identification of hearing loss for adults seeking help, follow-up with hearing aid treatment was low.
|
|
