996 resultados para Genome resources


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The extent to which low-frequency (minor allele frequency (MAF) between 1-5%) and rare (MAF genome sequencing (n = 2,882 from UK10K (ref. 10); a population-based genome sequencing consortium), whole-exome sequencing (n = 3,549), deep imputation of genotyped samples using a combined UK10K/1000 Genomes reference panel (n = 26,534), and de novo replication genotyping (n = 20,271). We identified a low-frequency non-coding variant near a novel locus, EN1, with an effect size fourfold larger than the mean of previously reported common variants for lumbar spine BMD (rs11692564(T), MAF = 1.6%, replication effect size = +0.20 s.d., Pmeta = 2 x 10(-14)), which was also associated with a decreased risk of fracture (odds ratio = 0.85; P = 2 x 10(-11); ncases = 98,742 and ncontrols = 409,511). Using an En1(cre/flox) mouse model, we observed that conditional loss of En1 results in low bone mass, probably as a consequence of high bone turnover. We also identified a novel low-frequency non-coding variant with large effects on BMD near WNT16 (rs148771817(T), MAF = 1.2%, replication effect size = +0.41 s.d., Pmeta = 1 x 10(-11)). In general, there was an excess of association signals arising from deleterious coding and conserved non-coding variants. These findings provide evidence that low-frequency non-coding variants have large effects on BMD and fracture, thereby providing rationale for whole-genome sequencing and improved imputation reference panels to study the genetic architecture of complex traits and disease in the general population.

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Medicinal and aromatic plants (MAPs) are an integral part of our biodiversity. In majority of MAP rich countries, wild collection practices are the livelihood options for a large number of rural peoples and MAPs play a significant role in socio-economic development of their communities. Recent concern over the alarming situation of the status of wild MAP resources, raw material quality, as well as social exploitation of rural communities, leads to the idea of certification for MAP resource conservation and management. On one hand, while MAP certification addresses environmental, social and economic perspectives of MAP resources, on the other hand, it ensures multi-stakeholder participation in improvement of the MAP sector. This paper presents an overview of MAP certification encompassing its different parameters, current scenario (Indian background), implementation strategies as well as stakeholders’ role in MAP conservation. It also highlights Indian initiatives in this direction.

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The current explosion of DNA sequence information has generated increasing evidence for the claim that noncoding repetitive DNA sequences present within and around different genes could play an important role in genetic control processes, although the precise role and mechanism by which these sequences function are poorly understood. Several of the simple repetitive sequences which occur in a large number of loci throughout the human and other eukaryotic genomes satisfy the sequence criteria for forming non-B DNA structures in vitro. We have summarized some of the features of three different types of simple repeats that highlight the importance of repetitive DNA in the control of gene expression and chromatin organization. (i) (TG/CA)n repeats are widespread and conserved in many loci. These sequences are associated with nucleosomes of varying linker length and may play a role in chromatin organization. These Z-potential sequences can help absorb superhelical stress during transcription and aid in recombination. (ii) Human telomeric repeat (TTAGGG)n adopts a novel quadruplex structure and exhibits unusual chromatin organization. This unusual structural motif could explain chromosome pairing and stability. (iii) Intragenic amplification of (CTG)n/(CAG)n trinucleotide repeat, which is now known to be associated with several genetic disorders, could down-regulate gene expression in vivo. The overall implications of these findings vis-à-vis repetitive sequences in the genome are summarized.

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BACKGROUND: Unnecessary intervention and overtreatment of indolent disease are common challenges in clinical management of prostate cancer. Improved tools to distinguish lethal from indolent disease are critical. METHODS: We performed a genome-wide survival analysis of cause-specific death in 24,023 prostate cancer patients (3,513 disease-specific deaths) from the PRACTICAL and BPC3 consortia. Top findings were assessed for replication in a Norwegian cohort (CONOR). RESULTS: We observed no significant association between genetic variants and prostate cancer survival. CONCLUSIONS: Common genetic variants with large impact on prostate cancer survival were not observed in this study. IMPACT: Future studies should be designed for identification of rare variants with large effect sizes or common variants with small effect sizes.

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Background Multiple sclerosis (MS) is thought to be a T cell-mediated autoimmune disorder. MS pathogenesis is likely due to a genetic predisposition triggered by a variety of environmental factors. Epigenetics, particularly DNA methylation, provide a logical interface for environmental factors to influence the genome. In this study we aim to identify DNA methylation changes associated with MS in CD8+ T cells in 30 relapsing remitting MS patients and 28 healthy blood donors using Illumina 450K methylation arrays. Findings Seventy-nine differentially methylated CpGs were associated with MS. The methylation profile of CD8+ T cells was distinctive from our previously published data on CD4+ T cells in the same cohort. Most notably, there was no major CpG effect at the MS risk gene HLA-DRB1 locus in the CD8+ T cells. Conclusion CD8+ T cells and CD4+ T cells have distinct DNA methylation profiles. This case–control study highlights the importance of distinctive cell subtypes when investigating epigenetic changes in MS and other complex diseases.

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The complete genome of an Australian isolate of zantedeschia mild mosaic virus (ZaMMV) causing mosaic symptoms on Alocasia sp. (designated ZaMMVAU) was cloned and sequenced. The genome comprises 9942 nucleotides (excluding the poly-A tail) and encodes a polyprotein of 3167 amino acids. The sequence is most closely related to a previously reported ZaMMV isolate from Taiwan (ZaMMV-TW), with 82 and 86 % identity at the nucleotide and amino acid level, respectively. Unlike the amino acid sequence of ZaMMV-TW, however, ZaMMV-AU does not contain a polyglutamine stretch at the N-terminus of the coat-protein-coding region upstream of the DAG motif. This is the first report of ZaMMV from Australia and from Alocasia sp.

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We report the first genome sequence of a Colocasia bobone disease-associated virus (CBDaV) derived from bobone-affected taro [Colocasia esculenta L. Schott] from Solomon Islands. The negative-strand RNA genome is 12,193 nt long, with six major open reading frames (ORFs) with the arrangement 3′-N-P-P3-M-G-L-5′. Typical of all rhabdoviruses, the 3′ leader and 5′ trailer sequences show complementarity to each other. Phylogenetic analysis indicated that CBDaV is a member of the genus Cytorhabdovirus, supporting previous reports of virus particles within the cytoplasm of bobone-infected taro cells. The availability of the CBDaV genome sequence now makes it possible to assess the role of this virus in bobone, and possibly alomae disease of taro and confirm that this sequence is that of Colocasia bobone disease virus (CBDV).

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Optimal allocation of water resources for various stakeholders often involves considerable complexity with several conflicting goals, which often leads to multi-objective optimization. In aid of effective decision-making to the water managers, apart from developing effective multi-objective mathematical models, there is a greater necessity of providing efficient Pareto optimal solutions to the real world problems. This study proposes a swarm-intelligence-based multi-objective technique, namely the elitist-mutated multi-objective particle swarm optimization technique (EM-MOPSO), for arriving at efficient Pareto optimal solutions to the multi-objective water resource management problems. The EM-MOPSO technique is applied to a case study of the multi-objective reservoir operation problem. The model performance is evaluated by comparing with results of a non-dominated sorting genetic algorithm (NSGA-II) model, and it is found that the EM-MOPSO method results in better performance. The developed method can be used as an effective aid for multi-objective decision-making in integrated water resource management.

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FRDC project 2008/306 Building economic capability to improve the management of marine resources in Australia was developed and approved in response to the widespread recognition and acknowledgement of the importance of incorporating economic considerations into marine management in Australia and of the persistent undersupply of suitably trained and qualified individuals capable of providing this input. The need to address this shortfall received broad based support and following widespread stakeholder consultation and building on previous unsuccessful State-based initiatives, a collaborative, cross-jurisdictional cross-institutional capability building model was developed. The resulting project sits within the People Development Program as part of FRDC’s ‘investment in RD&E to develop the capabilities of the people to whom the industry entrusts its future’, and has addressed its objectives largely through three core activities: 1. The Fisheries Economics Graduate Research Training Program which provides research training in fisheries/marine economics through enrolment in postgraduate higher degree studies at the three participating Universities; 2. The Fisheries Economics Professional Training Program which aims to improve the economic literacy of non-economist marine sector stakeholders and was implemented in collaboration with the Seafood Cooperative Research Centre through the Future Harvest Masterclass in Fisheries Economics; and, 3. The Australian Fisheries Economics Network (FishEcon) which aims to strengthen research in the area of fisheries economics by creating a forum in which fisheries economists, fisheries managers and Ph.D. students can share research ideas and results, as well as news of upcoming research opportunities and events. These activities were undertaken by a core Project team, comprising economic researchers and teachers from each of the four participating institutions (namely the University of Tasmania, the University of Adelaide, Queensland University of Technology and the Commonwealth Scientific and Industrial Research Organisation), spanning three States and the Commonwealth. The Project team reported to and was guided by a project Steering Committee. Commensurate with the long term nature of the project objectives and some of its activities the project was extended (without additional resources) in 2012 to 30th June 2015.

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We present the complete mitochondrial genome (accession number: LK995454) of an iconic Australian species, the eastern grey kangaroo (Macropus giganteus). The mitogenomic organization is consistent with other marsupials, encoding 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, an origin of light strand replication and a control region or Dloop. No repetitive sequences were detected in the control region. The M. giganteus mitogenome exemplifies a combination of tRNA gene order and structural peculiarities that appear to be unique to marsupials. We present a maximum likelihood phylogeny based on complete mitochondrial protein and RNA coding sequences that confirms the phylogenetic position of the grey kangaroo among macropodids.

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Jarvis et al. (Research Articles, 12 December 2014, p. 1320) presented molecular clock analyses that suggested that most modern bird orders diverged just after the mass extinction event at the Cretaceous-Paleogene boundary (about 66 million years ago). We demonstrate that this conclusion results from the use of a single inappropriate maximum bound, which effectively precludes the Cretaceous diversification overwhelmingly supported by previous molecular studies.

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The phosphoprotein P of paramyxoviruses is known to play more than one role in genome transcription and replication. Phosphorylation of P at the NH2 terminus by cellular casein kinase II has been shown to be necessary for transcription of the genome in some of the viruses, while it is dispensable for replication. The phosphorylation null mutant of rinderpest virus P protein, in which three serine residues have been mutated, has been shown earlier to be non-functional in an in vivo minigenome replication/transcription system. In this work, we have shown that the phosphorylation of P protein is essential for transcription, whereas the null mutant is active in replication of the genome in vivo. The null mutant P acts as a transdominant repressor of transcriptional activity of wild-type P and as an activator of replication carried out by wild-type P protein. These results suggest the phosphorylation status of P may act as a replication switch during virus replication. We also show that the phosphorylation null mutant P is capable of interacting with L and N proteins and is able to form a tripartite complex of L-(N-P) when expressed in insect cells, similar to wild-type P protein.

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Potable water resources are being depleted at an alarming rate worldwide. Storm water is a hugely under-utilized resource that could help as extreme weather events become more frequent...

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The complete mitochondrial genome of the tarnished plant bug, Lygus lineolaris, comprised 17,027 bp. The genome contained 13 protein coding regions, 22 tRNA genes and 2 ribosomal RNA genes. The gene arrangement corresponded to the common order found among insect mtDNAs which was considered to be the ancestral arrangement. The protein coding genes started with ATN and stopped with TAA or TAG. The nucleotide distribution was 76.0% A + T. The control region contained two repeat regions, one was 24 bp and the other was 161 bp. The Genbank accession for the complete L. lineolaris mt genome is EU401991.