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*100 Semi-supercentenarians and older as a proposed sample set for the Archon Genomics X PRIZE Validation Protocol* Nature Precedings
Thomas Perls; Nir Barzilai.
The "Archon Genomics X PRIZE Validation Protocol":http://precedings.nature.com/documents/5731/version/1 has been posted in part to solicit comments from the scientific community. Here, we suggest 100 subjects age >=105 years as the source of DNAs for the competition.

Tipo: Manuscript Palavras-chave: Biotechnology; Genetics & Genomics; Bioinformatics; Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/5756/version/1
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11-amino-5-N-methyl-7-fluorine- quindoline derivatives: The Potential Anti-angiogenic Agents Targeting G-quadruplex Structure in Vascular Endothelial Cell Growth Factor Nature Precedings
Tian-miao Ou; Yu-jing Lu; Xiao-dong Wang; Zeng-yun An; Yan-ping Li; Zhi-shu Huang; Lian-quan Gu.
Vascular endothelial growth factor (VEGF), a pluripotent cytokine and angiogenic growth factor, plays crucial roles in embryonic development and tumour progression, and is over-expressed in many types of cancer and generally associated with tumour progression and survival rate. The polypurine/polypyrimide sequence located upstream (-89 to -43) of the promoter region of the human VEGF gene that can form specific G-quadruplex structures and raise the possibility for transcriptional control of the VEGF gene by G-quadruplex ligands. In the present study, we investigated the interaction between the 5-N-methyl-7-fluorine-quindoline derivatives (11-amino-5-N-methyl-7-fluorine- quindoline derivatives) and the G-rich sequence in VEGF's promoter and the...
Tipo: Manuscript Palavras-chave: Cancer.
Ano: 2008 URL: http://precedings.nature.com/documents/1946/version/1
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11[beta]-hydroxysteroid dehydrogenase-type 2 evolved from an ancestral 17[beta]-hydroxysteroid dehydrogenase-type 2 Nature Precedings
Michael E. Baker.
11[beta]-hydroxysteroid dehydrogenase type-2 (11[beta]-HSD2) regulates the local concentration of cortisol that can activate the glucocorticoid receptor and mineralocorticoid receptor, as well as the concentration of 11-keto-testosterone, the active androgen in fish. Similarly, 17[beta]-HSD2 regulates the levels of testosterone and estradiol that activate the androgen receptor and estrogen receptor, respectively. Interestingly, although human 11[beta]-HSD2 and 17[beta]-HSD2 act at different positions on different steroids, these enzymes are paralogs. Despite the physiological importance of 11[beta]-HSD2 and 17[beta]-HSD2, details of their origins and divergence from a common ancestor are not known. An opportunity to understand their evolution is...
Tipo: Manuscript Palavras-chave: Cancer; Developmental Biology; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4649/version/1
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14-3-3ζ is Amplified, Overexpressed and Possesses Oncogenic Activities in Head and Neck Squamous Cell Carcinoma Nature Precedings
Mauting Lin; Carl D. Morrison; Susie Jones; Nehad Mohamed; Jason Bacher; Christoph Plass.
Gene amplification, a common mechanism for oncogene activation in cancers, has been used in the discovery of novel oncogenes. DNA amplification is frequently observed in head and neck squamous cell carcinomas (HNSCCs) where numerous amplification events and potential oncogenes have already been reported. Recently, we applied restriction landmark genome scanning (RLGS) to study gene amplifications in HNSCC and located novel amplified and uncharacterized regions in primary tumor samples. DNA amplification on 8q22.3, the location of 14-3-3[zeta] (YWHAZ, KCIP-1) is found in 30-40% HNSCC cases. Data obtained from fluorescent in-situ hybridization (FISH) and immunohistochemistry on HNSCC tissue microarrays confirmed frequent low-level 14-3-3[zeta] copy number...
Tipo: Manuscript Palavras-chave: Cancer.
Ano: 2008 URL: http://precedings.nature.com/documents/1953/version/1
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16S rRNA based identification of _Aeromonas sp. kumar_ by constructing phylogenetic tree and identification of regulatory elements from the harmful Red Tide bloom, Gulf of Mannar Nature Precedings
P. Kumar; C. M. Ramakritinan; A. K. Kumaraguru.
A bacterial strain, designated _Aeromonas sp. kumar_, was isolated from a water sample collected from Red tide Bloom occurred in the region of Gulf of Mannar region, Puthumadam Coast, India and the strain was identified using 16S rRNA based identification. During the sample collection, microbiology analysis was done to study the morphology of the bacteria. Pure culture of strain was maintained through out the study. DNA was isolated and sequenced using 16S rRNA primers. A length of 1452 nucleotide was sequenced and was put in public data base for obtaining accession number. The sequence was studied using MEGA 4, to estimate the evolutionary distances and to construct the Phylogenetic tree. Along with that Regulatory elements and Transcription factors were...
Tipo: Manuscript Palavras-chave: Ecology; Microbiology; Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3898/version/1
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1st INCF Workshop on Genetic Animal Models for Brain Diseases Nature Precedings
Olaf Riess; Holm Graessner.
The INCF Secretariat organized a workshop to focus on the “role of neuroinformatics in the processes of building, evaluating, and using genetic animal models for brain diseases” in Stockholm, December 13–14, 2009. Eight scientists specialized in the fields of neuroinformatics, database, ontologies, and brain disease participated together with two representatives of the National Institutes of Health and the European Union, as well as three observers of the national INCF nodes of Norway, Poland, and the United Kingdom.
Tipo: Manuscript Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2011 URL: http://precedings.nature.com/documents/5909/version/1
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1st INCF Workshop on Global Portal Services for Neuroscience Nature Precedings
Jaap van Pelt; Gordon Shepherd.
The goal of this meeting was to map out existing portal services for neuroscience, identify their features and future plans, and outline opportunities for synergistic developments. The workshop discussed alternative formats of future global and integrated portal services.
Tipo: Manuscript Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2008 URL: http://precedings.nature.com/documents/1779/version/1
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1st INCF Workshop on Needs for Training in Neuroinformatics Nature Precedings
David Willshaw.
The INCF workshop on Needs for Training in Neuroinformatics was organized by the INCF National Node of the UK. The scope of the workshop was to provide as overview of the current state of neuroinformatics training and recommendations for future provision of training. The report presents a summary of the workshop discussions and recommendations to the INCF.
Tipo: Manuscript Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2008 URL: http://precedings.nature.com/documents/2563/version/1
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1st INCF Workshop on Neuroanatomical Nomenclature and Taxonomy Nature Precedings
Mihail Bota; Larry Swanson.
The goal of this workshop was to agree on a general strategy for developing a systematic, useful, and scientifically appropriate framework for neuroanatomical nomenclature. The workshop focused on general principles that will serve as a basis for future decisions on implementation strategies. The report discusses the problems arising from the use of different parcellation schemes and use of different terminologies and highlights the need of a universal vocabulary for describing the structural organization of the nervous system. Workshop participants encourage the creation of an International Coordinating Committee for Neuroanatomical Nomenclature and propose short- and long-term goals for such a committee.
Tipo: Manuscript Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2008 URL: http://precedings.nature.com/documents/1780/version/1
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1st INCF Workshop on NeuroImaging Database Integration Nature Precedings
Lars Forsberg; Per Roland.
The goal of this meeting was to map existing neuroimaging databases, particularly databases containing primary data, and to identify mechanisms that could facilitate integrated use of such databases, including possible fusion of databases. The report provides an overview of existing neuroimaging databases that were discussed during the workshop and examines the feasibility of database federations. The report includes several recommendations for future developments.
Tipo: Manuscript Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2008 URL: http://precedings.nature.com/documents/1781/version/1
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1st INCF Workshop on Sustainability of Neuroscience Databases Nature Precedings
Jack Van Horn; Jaap van Pelt.
The goal of the workshop was to discuss issues related to the sustainability of neuroscience databases, identify problems and propose solutions, and formulate recommendations to the INCF. The report summarizes the discussions of invited participants from the neuroinformatics community as well as from other disciplines where sustainability issues have already been approached. The recommendations for the INCF involve rating, ranking, and supporting database sustainability.
Tipo: Manuscript Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2008 URL: http://precedings.nature.com/documents/1983/version/1
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2011 German Escherichia coli O104:H4 outbreak: Alignment-free whole-genome phylogeny by feature frequency profiles Nature Precedings
Man Kit Cheung; Lei Li; Wenyan Nong; Hoi Shan Kwan.
Accuracy of SNP-based whole-genome phylogeny reconstruction relies heavily on quality of sequence alignment which is particularly hindered by poorly assembled genomes. Alignment-free methods might provide additional insights. Here, we constructed a whole-genome phylogeny of 10 isolates from the current German E. coli outbreak against 30 existing E. coli genomes as well as that of a historical EHEC isolate using the alignment-free feature frequency profile method. Our results revealed a high similarity among E. coli isolates from the current outbreak and the historical EHEC being the most closely related isolate sequenced thus far.
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6109/version/2
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2011 German Escherichia coli outbreak: Alignment-free whole-genome phylogeny by feature frequency profiles Nature Precedings
Man Kit Cheung; Lei LI; Wenyan Nong; Hoi Shan Kwan.
Accuracy of SNP-based whole-genome phylogeny reconstruction relies heavily on quality of sequence alignment which is particularly hindered by poorly assembled genomes. Alignment-free methods might provide additional insights. Here, we constructed a whole-genome phylogeny of 9 E.coli isolates from the 2011 German outbreak against existing E. coli genomes using the alignment-free feature frequency profile method. In addition, we looked for gene elements that distinguish the outbreak group from the other E. coli strains and possibly accounted for the emergence of the outbreak isolates using the distinguishing feature analysis.
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6109/version/1
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2011 German Escherichia coli outbreak: Prophage analysis of close-assembled TY2482 against 55989 using PHAST Nature Precedings
Man Kit Cheung; Lei LI; Wenyan Nong; Hoi Shan Kwan.
Using the Hiseq data of the German E. coli outbreak isolate TY2482, preliminary prophage analyses have been performed by some researchers previously. With the closed assembly of the same isolate being available, another round of analysis might help in resolving questions that remain unclear due to the incompleteness of the dataset.
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics.
Ano: 2011 URL: http://precedings.nature.com/documents/6110/version/1
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26Al/10Be Age of Peking Man Nature Precedings
Guanjun Shen; Xing Gao; Bin Gao; Darryl Granger.
The chronological position of Peking Man, or Homo erectus pekinensis, has long been pursued, but has remained problematic due to lack of a suitable dating method^1-7^. Here we report cosmogenic ^26^Al/ ^10^Be burial dating of quartz sediments and artifacts from the lower strata of Zhoukoudian Locality 1 where the remains of early members of the Peking Man family were discovered. This study marks the first radioisotopic dating of any early hominin site in China beyond the range of mass spectrometric U-series dating. The weighted mean of six meaningful measurements, 0.75 +/-; 0.09 (0.11) Ma (million years), provides the best age estimate for lower cultural Layers ^7-10^. Together with previously reported U-series^3^ and paleomagnetic^4^ data, as well as...
Tipo: Manuscript Palavras-chave: Earth & Environment.
Ano: 2008 URL: http://precedings.nature.com/documents/2275/version/1
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3D computer modeling in micropalaeontology – Late Paleozoic conodonts and foraminifers as example Nature Precedings
Andrey V. Zhuravlev; Yadviga A. Vevel.
Three-dimension modeling of fossils is one of the branches of computer using in palaeontology. The branch has wide perspectives but it is hardly developed, especially in micropalaeontology. Proposed method of 3D modelling of microfossils demands no unique and expansive equipment and can be realized practically in any palaeontological laboratory. Lower accuracy of the models developed is not critical for most the fields of their utilization: for teaching purposes, construction of illustrated databases and virtual atlases, and for the display of microfossils to a general audience.
Tipo: Manuscript Palavras-chave: Earth & Environment.
Ano: 2008 URL: http://precedings.nature.com/documents/1632/version/1
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3D model of amphioxus steroid receptor complexed with estradiol Nature Precedings
Michael E. Baker; David J. Chang.
The origins of signaling by vertebrate steroids are not fully understood. An important advance was the report that an estrogen-binding steroid receptor [SR] is present in amphioxus, a basal chordate with a similar body plan as vertebrates. To investigate the evolution of estrogen binding to steroid receptors, we constructed a 3D model of amphioxus SR complexed with estradiol. This 3D model indicates that although the SR is activated by estradiol, some interactions between estradiol and human ER[alpha] are not conserved in the SR, which can explain the low affinity of estradiol for the SR. These differences between the SR and ER[alpha] in the steroid-binding domain are sufficient to suggest that another steroid is the physiological regulator of the SR....
Tipo: Manuscript Palavras-chave: Cancer; Developmental Biology; Bioinformatics; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/3316/version/1
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3D model of lamprey estrogen receptor with estradiol and 15[alpha]-hydroxy-estradiol Nature Precedings
Michael E. Baker; David J. Chang; Charlie Chandsawangbhuwana.
Lamprey, a basal vertebrate, contains orthologs of the estrogen receptor (ER), progesterone receptor and corticoid receptor. A perplexing property of lamprey is that 15[alpha]-hydroxy-steroids are active steroids. For example, 15[alpha]-hydroxy-estradiol [15[alpha]-OH-E2] is the estrogen, instead of estradiol (E2). To investigate how 15[alpha]-OH-E2 binds lamprey ER, we constructed a 3D model of the lamprey ER with E2 and 15[alpha]-OH-E2. Our 3D model shows that S[delta] on Met-409 can form a hydrogen bond with the 15[alpha]-hydroxyl on 15[alpha]-OH-E2. In human ER[alpha], the corresponding residue Ile-424 has a van der Waals contact with 15[alpha]-OH-E2. BLAST analysis of GenBank indicates that among vertebrate ERs, only lamprey ER contains a...
Tipo: Manuscript Palavras-chave: Developmental Biology; Ecology; Earth & Environment.
Ano: 2009 URL: http://precedings.nature.com/documents/2768/version/1
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3D models of lamprey corticoid receptor complexed with 11-deoxycortisol and deoxycorticosterone Nature Precedings
Michael E. Baker; Kayla Y. Uh; Paiyuam Asnaashari.
The serum of Atlantic sea lamprey, a basal vertebrate, contains two corticosteroids, 11-deoxycortisol and deoxycorticosterone. Only 11-deoxycortisol has high affinity [Kd~3 nM] for the corticoid receptor [CR] in lamprey gill cytosol. To investigate the binding of 11-deoxycortisol to the CR, we constructed 3D models of lamprey CR complexed with 11-deoxycortisol and deoxycorticosterone. These 3D models reveal that Leu-220 and Met-299 in lamprey CR have contacts with the 17[alpha]-hydroxyl on 11-deoxycortisol. Lamprey CR is the ancestor of the mineralocorticoid receptor [MR] and glucocorticoid receptor [GR]. Unlike human MR and human GR, the 3D model of lamprey CR finds a van der Waals contact between Cys-227 in helix 3 and Met-264 in helix 5. Mutant...
Tipo: Manuscript Palavras-chave: Cancer; Developmental Biology; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6216/version/1
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3D Structure Development of Chikungunya Virus and its Structural Characterization – an In silico approach Nature Precedings
Anuraj Nayarisseri; Mukesh Yadav; Dowlathabad Muralidhara Rao; Sonam Kukreja; Sheaza Ahmed; Pooja Singh.
The 3 Dimensional structure of a protein is an expedient for structure based drug design and identifying the conformational epitopes that are foremost for designing the vaccines. Chikungunya (CHIKV) is a heat sensitive RNA virus which causes a viral disease which is transmitted in humans by human-mosquito-human transmission. Disease mostly found in the tropic and subtropical countries mainly in South India and in few other Asian countries. The primary transmission agents of Chikungunya Virus are yellow fever mosquito (_Aedes aegypti_) and forest day mosquito (_Aedes albopictus_). The forest day mosquito bites during day time and hence day time mosquito bite is the main reason for transmission. The main distinctive of the disease is a fever along with an...
Tipo: Manuscript Palavras-chave: Bioinformatics.
Ano: 2010 URL: http://precedings.nature.com/documents/5143/version/1
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