Últimos itens adicionados do Acervo: Proceedings Nature

Nature é uma das mais prestigiosas e antigas revistas científicas do mundo: sua primeira edição é de 4 de novembro de 1869. Entre as inúmeras descobertas científicas publicadas na Nature estão a dos raios X, da estrutura em dupla hélice do ADN e o buraco na camada de ozônio.

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‣ Genetic incorporation of D-Lysine into diketoreductase in Escherichia coli cells

Zhi Zhi Liu; Xin Yang; Denghuan Yi; Shuzhen Wang; Yijun Chen
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
D-Lysine has been genetically introduced into diketoreductase in E. coli cells by utilization of an orthogonal Ph tRNA /Lysyl-tRNA synthetase pair. This is the first report on the genetic incoporation of D-amino acids into proteins, which may be generally applicable to a wide variety of applications.

‣ Incidence response to a suddenly increased cancer risk

Örjan Hallberg
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
Incidence rates of several cancers, including melanoma of the skin and breast cancer, have increased since the middle of the 20th century in Western countries. Here, we developed a model for cancer incidence over time, when considering a suddenly increased cancer risk from an environmental change. A two parameter exponential function was used to simulate cancer risk over calendar time since birth, taking into account the time lapse since the environmental change took place. The calculated incidence for all age cohorts over calendar time was used to calculate the age-standardized rates. The best fit between calculated and reported age-standardized rates was sought by parameter variation. The model was tested using reported rates for melanoma and breast cancer. The best fit was obtained when an increased cancer risk took place from 1955 and with the starting age being that of puberty. Age-standardized rates of melanoma and breast cancer were easily modeled and fit well with reported data. In addition, age-specific rates fit well with reported data without further parameter adjustments. The good fit with reported data when using this simple exponential model strongly supports the hypothesis that an environmental change in the mid-20th century was the main cause of the cancer epidemic noted after 1955. Other forms of cancer should be analyzed in a similar manner.

‣ Medicine beyond magic bullets: a formal case for multilevel interventions

Rodrick Wallace
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
Western medicine's paradigmatic search for 'magic bullet' interventions is facing increasing difficulty: Between 1950 and 2010 the inflation-adjusted cost per USFDA-approved drug has increased exponentially in time, a draconian inverse of the famous Moore's Law of computing. A sequence of empirically-oriented statistical models suggests that carefully designed synergistic multifactorial and multiscale strategies might evade this relationship.

‣ Comparative functional genomics approach for the annotation of proteins in Unclassified Halophilic archaeon DL31

N S. Sardeshmukh; S G. Sanmukh; E Nakkeeran
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
The structure, function and sub-cellular location prediction for the unknown proteins from Unclassified Halophilic archaeon DL31 were carried out for characterization of the proteins in their respective families. The 991 genes for hypothetical proteins in Halophilic archaeon DL31 chromosome were predicted by the application of computational methods and Bioinformatics web tools. The structure predictions for 206 unknown proteins were possible whereas functions were predicted in 825 protein sequences. The function prediction for the proteins were done by using Bioinformatics web tools like CDD-BLAST, INTERPROSCAN and PFAM by searching protein databases for the presence of conserved domains. The Sub-cellular location predictions were done for all the unknown proteins by using CELLO v 2.5 server. While tertiary structures were constructed using PS2 Server- Protein Structure Prediction server. This study revealed structural, functional and Sub-cellular localization of unknown proteins in Unclassified Halophilic archaeon DL31chromosome.

‣ Hydrologic and climate trends for the Coldwater River watershed in south-central British Columbia, Canada

Sierra Rayne; Kaya Forest
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
Historical trends in streamflow and climate were investigated for the Coldwater River watershed in south-central British Columbia, Canada. Temporal increases in rainfall and total precipitation during the spring, summer, and autumn periods, as well as on an annual basis, at the city of Merritt near the mouth of the watershed, and year-round temperature increases at this site, compare with declining summertime and annual streamflows at the nearby Merritt hydrometric station on the Coldwater River. Declining summer flows at this site could reflect the dominance of temporally increasing evaporation that is offsetting increased precipitation over the same periods of the hydrologic year. Alternatively, increased water abstractions, altered regulation regimes, and/or land use changes in the watershed may also play significant/dominant roles. The relative absence of any coherent hydrological temporal patterns at the upstream Brookmere hydrometric station on the Coldwater River suggests that the net effects of warming temperatures, increasing precipitation, and any anthropogenic drivers over the past four decades are in approximate balance.

‣ Neural Coding of Green Flash in Retinal Bipolar Pathways

Caiping Hu
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
What visual information do the graded potentials among retinal bipolar pathways actually transmit from photoreceptors to ganglion cells? The answer does not exist. Even the graded electric signals have not been understood completely. Here, this paper tries to analyze the encoding mechanisms of graded signals among the parallel bipolar pathways in response to brief green flash. The typical ON, OFF and ON-OFF bipolar cells simultaneously abstracted vectors from green flash stimulus with sine-like functions on their dendritic plane. Atypical bipolar cell had the synchronously monopolar response in contrast to the bipolar responses of typical bipolar cells, they also annotated green flash with facilitated stochastic (asynchronous and rate-coded) responses. Some complex ON-OFF bipolar cells with large voltage-gated Na+ current could generate high-frequent asynchronous responses, others had synchronous ON-OFF responses to green flash. The green flash was synchronously and asynchronously represented by the multiple-dimension signaling space among the parallel bipolar pathways. These results unraveled the multiple-dimension neural codes for brief green flash, demonstrated the superior encoding capability of parallel bipolar pathways, and suggested the electrophysiological mechanisms of vision such as color space.

‣ Changes in enzyme activities and in the functional diversity of actinomycetes due to long term agricultural management

Jessica L. M. Gutknecht; Elke Schulz; Venukumar Vemula; Jana Schmidt; Gabi Henning; Jackie Rose; Yvonne Eckstein; Mika Tarkka
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Poster
Português
Long-term agricultural management alters soil organic matter, nutrient status, and potentially the decomposer community. We measured the abundance and activity of cellulose, chitin, and protease degrading bacteria, and total soil extra-cellular enzyme activity for cellulose (β-glucosidase), chitinase (N-acetyl-glucosaminidase), xylosidase, and phosphatase activity. By combining these methods, we could determine how bacterial decomposer abundance and function were altered by long-term management, and how the bacterial decomposer community relates to overall soil enzyme activity. We also measured microbial total fungal and bacterial biomass, soil organic carbon pools, and extractable nitrogen for supplementary comparisons. Soil samples were taken in June of 2010 from the Bad Lauchstädt field station’s Static Fertilization Experiment, under treatment for 108 years. Treatments include mineral (NPK) fertilizer (none or added at 140, 60, and 230 kg ha-1 yr-1) and manure addition (none, 20 T ha-1 2yr-1, and 30 T ha-1 2yr-1) in a full factorial experiment. We found that total cellulase activity and the abundance of cellulase degrading bacteria were higher in plots with manure addition. We observed the same pattern for total phosphatase activity...

‣ SED-ML: Nested Simulation Proposal

Frank T. Bergmann
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
This document describes a second version of the proposal for nested simulation experiments for SED-ML (http://sed-ml.org). The proposal has been updated to include the feedback received in the meantime and has been enhanced by examples. A full implementation is available with libSedML (http://libsedml.sf.net) and the SED-ML Web Tools (http://sysbioapps.dyndns.org/SED-ML_Web_Tools/)

‣ USP4 is regulated by Akt phosphorylation and deubiquitylates TGF-beta type I receptor

Long Zhang; Fangfang Zhou; Yvette Drabsch; Ewa Snaar-Jagalska; Craig Mickanin; Huizhe Huang; Kelly-Ann Sheppard; Chris Lu; Peter ten Dijke
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
Stability and membrane localization of Transforming growth factor-β (TGF-β) type I receptor (TβRI) is essential for controlling TGF-β signaling. TβRI is targeted for ubiquitination-mediated degradation by Smad7/Smurf2 complex. However, it is unclear whether polyubiquitin modified TβRI can be reversed. Here we performed a genome-wide gain of function screen and identified ubiquitin-specific protease (USP) 4 as a strong inducer of TGF-β signaling. Putative oncogenic USP4 was found to interact with TβRI as deubiquitinating enzyme thus maintains TβR1 levels at the plasma membrane. Depletion of USP4 mitigates TGF-β-induced breast cancer cell migration, epithelial to mesenchymal transition and metastasis. Importantly, Akt/Protein kinase B (PKB), which has been associated with poor prognosis in breast cancer, associates with and phosphorylates USP4. Akt mediated phosphorylation relocates USP4 to cytoplasm and membrane and is required for maintaining its protein stability. Moreover, Akt-induced breast cancer cell migration was inhibited by USP4 depletion and TβRI kinase inhibition. Our results identified USP4 as an important determinant for crosstalk between TGF-β and Akt...

‣ A subset of co-expressed genes in Slug-based cancer mesenchymal transition signature remains coexpressed in normal samples in a tissue-specific manner

Weiyi Cheng; Dimitris Anastassiou
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
A recently identified gene expression signature of EMT markers containing the transcription factor Slug was found present in samples from many publicly available cancer gene expression datasets of multiple cancer types except leukemia. We also found many of these genes co-expressed in human cancer xenografted cells, but not in mouse stroma cells, suggesting that the signature is largely produced by cancer cells undergoing some type of EMT. Here we report that a partial signature consisting of a subset of the co-expressed genes of the full signature, including at least Slug (SNAI2), collagens COL1A1, COL1A2, COL3A1, COL6A3 and genes DCN and LUM, is also present in leukemia, in which case it is also strongly associated with the chemokine CXCL12 (aka SDF1). The same subset of co-expressed genes is also strongly present even in normal samples in a tissue-specific manner, with lowest expression in brain tissues and highest expression in reproductive system tissues. The full signature, with prominent presence of COL11A1, THBS2 and INHBA appears to be triggered in solid cancers particularly when cancer cells encounter adipocytes.

‣ Aluminium - Magnesium Silicate enhances antibacterial activity of Ampicillin trihydrate, against Salmonella gallinarum

Madike Ezeibe; George Anosa; Okechi Okorie; Nnenna Elendu-Eleke; Obianuju Okoroafor; Augustine Ngene; Ogechukwu Chikelu
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
Solutions of different concentrations, of Ampicillin trihydrate (AT) and of a formulation of AT in Aluminium Magnesium Silicate (AMS), were used for sensitivity test on Salmonella gallinarum cultures. Also, S. gallinarum-infected chicks were treated with; 10 mg / Kg (AT), 10 mg / Kg (AT in AMS), 7.5 mg / Kg ( AT), 7.5 mg /Kg (AT in AMS). Mean inhibition area, 28.39 mm produced by AT did not vary significantly (P ) from 26.36 mm produced by AT in AMS. However, 17.5 105 Salmonella gallinarum culture forming units per ml of bile of the untreated chicks and 3.4 105 (80.58 % reduction), 2.5 105 (85.7 % reduction) , 5.4 105 (69.2 % reduction ) and 0.38 105 (97.8 % reduction ) of the respective treated groups, showed AMS significantly (P 0.01) improved AT`s ability to clear the infection, in vivo.

‣ Plasmodium falciparum has rare correlation properties

Kushal Shah
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
A plot of the correlation function of a given DNA sequence has certain characteristic features common to almost all organisms. One common feature is that the correlation values at distances that are multiples of three is higher than correlation values at other distances. Because of this such a correlation plot can be divided into two or three curves with different scalings. P. falciparum has a rare correlation property which is probably unique. I have analyzed genomes of many bacteria, fungi and protozoa and found that P. falciparum is the only organism whose DNA sequence correlation plot can be divided into four curves with different scalings. This property is neither shared by other species of the Plasmodium genus nor by other AT rich genomes. This could be a hint that the DNA sequence of P. falciparum has undergone certain rare mutational events.

‣ The Diet of the Rhinolophidae in the “Kabylia of the Babors” Region, Northern Algeria

Ahmim Mourad; Moali Aissa
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
Many bats of the Rhinolophidae family are currently threatened all over the world. In Algeria they are represented by six species listed in the IUCN red list and whose hunting habits and diet are, at best, poorly known. This paper describes the diet composition of four of these species (Rhinolophus ferrumequinum, R. hipposideros, R. euryale and R. blasii) in the Bejaia and Jijel districts, and in Kabylia of the Babors region, in northern Algeria. Between March 2007 and January 2008 guano was sampled every fortnight in the different sites used by the species and preys remains identified under microscope. Results show that these Algerian Rhinolophidae prey on three groups of Arthropodes (Insects, Chilopodes and Spiders) whose frequencies vary from one species to another.

‣ Mobile Image Ratiometry: A New Method for Instantaneous Analysis of Rapid Test Strips

Donald C. Cooper; Bryan Callahan; Phil Callahan; Lee Burnett
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
Here we describe Mobile Image Ratiometry (MIR), a new method for the automated quantification of standardized rapid immunoassay strips using consumer-based mobile smartphone and tablet cameras. To demonstrate MIR we developed a standardized method using rapid immunotest strips directed against cocaine (COC) and its major metabolite, benzoylecgonine (BE). We performed image analysis of three brands of commercially available dye-conjugated anti-COC/BE antibody test strips in response to three different series of cocaine concentrations ranging from 0.1 to 300 ng/ml and BE concentrations ranging from 0.003 to 0.1 ng/ml. These data were then used to create standard curves to allow quantification of COC/BE in biological samples. MIR quantification of COC and BE proved to be a sensitive, economical, and faster alternative to more costly methods, such as gas chromatography-mass spectrometry, tandem mass spectrometry, or high pressure liquid chromatography. MIR is a valuable tool that provides instant data acquisition, tracking and analysis for the emerging field of mobile platform informatics (MPI).

‣ A New Method for Characterization of Natural Zeolites and Organic Nanostructure using Atomic Force Microscopy

Domenico P. R. O. F. Fuoco
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
In order to study and develop an economic solution to environmental pollution in water, a wide variety of materials were investigated. Natural zeolites emerge from that research as the best in class of this category. Zeolites are natural materials relatively abundant and non biodegradable, economic and good to perform processes of environmental remediation. This paper contains a full description of a new method to characterize superficial properties of natural zeolites of exotic provenience (Caribbean Islets) with atomic force microscopy (AFM). AFM works with the optical microscope simplicity and the high resolution typical of a transmission electron microscope (TEM). Structural information of mesoporous material is obtained using scanning and transmission electron microscopy (SEM and TEM), only if the sample is conductive, otherwise the sample has to be processed through the grafitation technique, but this procedure induces errors of topography. Therefore, the existing AFM method, to observe zeolite powders, is made in a liquid cell-head scanner, but this work puts in evidence and confirms that it is possible to use an ambient air-head scanner to obtain a new kind of microtopography. Once optimized, this new method allows investigating of organic micelles...

‣ Phylogenetic Codivergence Supports Coevolution of Mimetic Heliconius Butterflies

Jennifer Hoyal Cuthill; Michael Charleston
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
The unpalatable and warning-patterned butterflies _Heliconius erato_ and _Heliconius melpomene_ provide the best studied example of mutualistic Müllerian mimicry, thought – but rarely demonstrated – to promote coevolution. Some of the strongest available evidence for coevolution comes from phylogenetic codivergence, the parallel divergence of ecologically associated lineages. Early evolutionary reconstructions suggested codivergence between mimetic populations of _H. erato_ and _H. melpomene_, and this was initially hailed as the most striking known case of coevolution. However, subsequent molecular phylogenetic analyses found discrepancies in phylogenetic branching patterns and timing (topological and temporal incongruence) that argued against codivergence. We present the first explicit cophylogenetic test of codivergence between mimetic populations of _H. erato_ and _H. melpomene_, and re-examine the timing of these radiations. We find statistically significant topological congruence between multilocus coalescent population phylogenies of _H. erato_ and _H. melpomene_, supporting repeated codivergence of mimetic populations. Divergence time estimates, based on a Bayesian coalescent model, suggest that the evolutionary radiations of _H. erato_ and _H. melpomene_ occurred over the same time period...

‣ SBGN PD: Current status, future changes and unresolved issues.

Stuart L. Moodie
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Conferência ou Objeto de Conferência
Português
The presentations reports and the current status of the SBGN-PD specification and highlights issues for further discussion.

‣ A Database for TSSs of Human MicroRNAs

Malay Bhattacharyya; Sanghamitra Bandyopadhyay
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
MicroRNAs (miRNAs) are small endogeneous non-coding RNAs of about 22nt length. These short RNAs regulate the expression of mRNAs by hybridizing with their 3'-UTRs or by translational repression. They have been shown to take crucial roles in many biological processes. Many of the current studies are focused over how mature miRNAs regulate mRNAs, even though there is very limited knowledge about their transcriptional loci. Primary miRNAs (pri-miRs) are first transcribed from the DNA, followed by the formation of precursor miRNA (pre-miR) by endonucleases activity, which finally produces mature miRNAs. Unfortunately, the identification of the loci of pri-miRs, and the associated information about transcription start sites (TSSs) and promoters is still in progress. This information, even though limited, may be useful for further study on the regulation of miRNAs. In this paper, we provide a novel database of miRNA TSSs (miRT) that might be a valuable resource for advanced research on miRNA regulation.

‣ Structural and functional validation of Microsystin synthetases

Swapnil G. Sanmukh; Waman N. Paunikar
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
The structure and function prediction for the Microsystin synthetases from Microsystis aerogenosa (LNSAMB) were carried out for verifying the authenticity of the sequenced genes. The genes for Microsystin synthetases (mcyA, mcyB, mcyD and mcyE,), were predicted by the application of computational methods and Bioinformatics web tools. The probable function prediction for the proteins was done by using Bioinformatics web tools like CDD-BLAST, INTERPROSCAN, PFAM and COGs by searching protein databases for the presence of conserved domains. While tertiary structures were constructed using PS2 Server- Protein Structure Prediction server. This study revealed structural and functional validation of sequenced genes.

‣ Unique features of Plasmids among different Citrobacter species

Swapnil G. Sanmukh; Waman N. Paunikar
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
The _Citrobacter_ plasmids are supposed to represent the host genetic association within the living bacterial cell. The plasmids impart various beneficial characteristics to the host, helping it to retain suitable characteristics for adaptation as well as evolution. The study aims at understanding the role of prophage in influencing host functional characteristics by horizontal gene transfer or as whole plasmids. The _Citrobacter_ plasmid can be understood by analyzing many hypothetical protein sequences within its genome. Our study included 82 hypothetical proteins in 5 _Citrobacter_ plasmids genomes. The function predictions in 31 hypothetical proteins and 3-D structures were predicted for 11 protein sequences using PS2 server. The probable function prediction was done by using Bioinformatics web tools like CDD-BLAST, INTERPROSCAN, PFAM and COGs by searching sequence databases for the presence of orthologous enzymatic conserved domains in the hypothetical sequences. This study identified many uncharacterized proteins, whose roles are yet to be discovered in _Citrobacter_ plasmids. These results for unknown proteins within plasmids can be used in linking the genetic interactions of _Citrobacter_ species and their functions in different environmental conditions.