125 research outputs found
Bioinformatics tools in predictive ecology: Applications to fisheries
This article is made available throught the Brunel Open Access Publishing Fund - Copygith @ 2012 Tucker et al.There has been a huge effort in the advancement of analytical techniques for molecular biological data over the past decade. This has led to many novel algorithms that are specialized to deal with data associated with biological phenomena, such as gene expression and protein interactions. In contrast, ecological data analysis has remained focused to some degree on off-the-shelf statistical techniques though this is starting to change with the adoption of state-of-the-art methods, where few assumptions can be made about the data and a more explorative approach is required, for example, through the use of Bayesian networks. In this paper, some novel bioinformatics tools for microarray data are discussed along with their ‘crossover potential’ with an application to fisheries data. In particular, a focus is made on the development of models that identify functionally equivalent species in different fish communities with the aim of predicting functional collapse
Stimulated emission and lasing in π-conjugated polymer films, microstructures and opal photonic crystals
SPIE's International Symposium on Optical Science, Engineering, and Instrumentation, 1999, Denver, CO, United StatesZ. Valy Vardeny, Sergey V. Frolov, Douglas Chinn, Maxim N. Shkunov, Werner Gellermann, Katsumi Yoshino, Akihiko Fujii, Richard V. Gregory, Ray H. Baughman, and Anvar A. Zakhidov "Stimulated emission and lasing in π-conjugated polymer films, microstructures, and opal photonic crystals", Proc. SPIE 3797, Organic Light-Emitting Materials and Devices III, (17 December 1999). DOI: https://doi.org/10.1117/12.37269
Genetic and epigenetic mutations affect the DNA binding capability of human ZFP57 in transient neonatal diabetes type 1
AbstractIn the mouse, ZFP57 contains three classical Cys2His2 zinc finger domains (ZF) and recognizes the methylated TGCmetCGC target sequence using the first and the second ZFs. In this study, we demonstrate that the human ZFP57 (hZFP57) containing six Cys2His2 ZFs, binds the same methylated sequence through the third and the fourth ZFs, and identify the aminoacids critical for DNA interaction. In addition, we present evidences indicating that hZFP57 mutations and hypomethylation of the TNDM1 ICR both associated with Transient Neonatal Diabetes Mellitus type 1 result in loss of hZFP57 binding to the TNDM1 locus, likely causing PLAGL1 activation
Ml proteins from Mesorhizobium loti and MucR from Brucella abortus: an AT-rich core DNA-target site and oligomerization ability
Mesorhizobium loti contains ten genes coding for proteins sharing high amino acid sequence identity with members of the Ros/MucR transcription factor family. Five of these Ros/MucR family members from Mesorhizobium loti (Ml proteins) have been recently structurally and functionally characterized demonstrating that Ml proteins are DNA-binding proteins. However, the DNA-binding studies were performed using the Ros DNA-binding site with the Ml proteins. Currently, there is no evidence as to when the Ml proteins are expressed during the Mesorhizobium loti life cycle as well as no information concerning their natural DNA-binding site. In this study, we examine the ml genes expression profile in Mesorhizobium loti and show that ml1, ml2, ml3 and ml5 are expressed during planktonic growth and
in biofilms. DNA-binding experiments show that the Ml proteins studied bind a conserved AT-rich site
in the promoter region of the exoY gene from Mesorhizobium loti and that the proteins make important contacts with the minor groove of DNA. Moreover, we demonstrate that the Ml proteins studied form higher-order oligomers through their N-terminal region and that the same AT-rich site is recognized by MucR from Brucella abortus using a similar mechanism involving contacts with the minor groove of DNA and oligomerization
A first search for coincident gravitational waves and high energy neutrinos using LIGO, Virgo and ANTARES data from 2007
We present the results of the first search for gravitational wave bursts associated with high energy neutrinos. Together, these messengers could reveal new, hidden sources that are not observed by conventional photon astronomy, particularly at high energy. Our search uses neutrinos detected by the underwater neutrino telescope ANTARES in its 5 line configuration during the period January - September 2007, which coincided with the fifth and first science runs of LIGO and Virgo, respectively. The LIGO-Virgo data were analysed for candidate gravitational-wave signals coincident in time and direction with the neutrino events. No significant coincident events were observed. We place limits on the density of joint high energy neutrino - gravitational wave emission events in the local universe, and compare them with densities of merger and core-collapse events. © 2013 IOP Publishing Ltd and Sissa Medialab srl
Status and Recent Results of the Acoustic Neutrino Detection Test System AMADEUS
The AMADEUS system is an integral part of the ANTARES neutrino telescope in
the Mediterranean Sea. The project aims at the investigation of techniques for
acoustic neutrino detection in the deep sea. Installed at a depth of more than
2000m, the acoustic sensors of AMADEUS are based on piezo-ceramics elements for
the broad-band recording of signals with frequencies ranging up to 125kHz.
AMADEUS was completed in May 2008 and comprises six "acoustic clusters", each
one holding six acoustic sensors that are arranged at distances of roughly 1m
from each other. The clusters are installed with inter-spacings ranging from
15m to 340m. Acoustic data are continuously acquired and processed at a
computer cluster where online filter algorithms are applied to select a
high-purity sample of neutrino-like signals. 1.6 TB of data were recorded in
2008 and 3.2 TB in 2009. In order to assess the background of neutrino-like
signals in the deep sea, the characteristics of ambient noise and transient
signals have been investigated. In this article, the AMADEUS system will be
described and recent results will be presented.Comment: 7 pages, 8 figures. Proceedings of ARENA 2010, the 4th International
Workshop on Acoustic and Radio EeV Neutrino Detection Activitie
Measurement of Atmospheric Neutrino Oscillations with the ANTARES Neutrino Telescope
The data taken with the ANTARES neutrino telescope from 2007 to 2010, a total
live time of 863 days, are used to measure the oscillation parameters of
atmospheric neutrinos. Muon tracks are reconstructed with energies as low as 20
GeV. Neutrino oscillations will cause a suppression of vertical upgoing muon
neutrinos of such energies crossing the Earth. The parameters determining the
oscillation of atmospheric neutrinos are extracted by fitting the event rate as
a function of the ratio of the estimated neutrino energy and reconstructed
flight path through the Earth. Measurement contours of the oscillation
parameters in a two-flavour approximation are derived. Assuming maximum mixing,
a mass difference of eV is
obtained, in good agreement with the world average value.Comment: 9 pages, 5 figure
Enhancer Reprogramming Confers Dependence on Glycolysis and IGF Signaling in KMT2D Mutant Melanoma.
Histone methyltransferase KMT2D harbors frequent loss-of-function somatic point mutations in several tumor types, including melanoma. Here, we identify KMT2D as a potent tumor suppressor in melanoma through an in vivo epigenome-focused pooled RNAi screen and confirm the finding by using a genetically engineered mouse model (GEMM) based on conditional and melanocyte-specific deletion of KMT2D. KMT2D-deficient tumors show substantial reprogramming of key metabolic pathways, including glycolysis. KMT2D deficiency aberrantly upregulates glycolysis enzymes, intermediate metabolites, and glucose consumption rates. Mechanistically, KMT2D loss causes genome-wide reduction of H3K4me1-marked active enhancer chromatin states. Enhancer loss and subsequent repression of IGFBP5 activates IGF1R-AKT to increase glycolysis in KMT2D-deficient cells. Pharmacological inhibition of glycolysis and insulin growth factor (IGF) signaling reduce proliferation and tumorigenesis preferentially in KMT2D-deficient cells. We conclude that KMT2D loss promotes tumorigenesis by facilitating an increased use of the glycolysis pathway for enhanced biomass needs via enhancer reprogramming, thus presenting an opportunity for therapeutic intervention through glycolysis or IGF pathway inhibitors
A First Search for coincident Gravitational Waves and High Energy Neutrinos using LIGO, Virgo and ANTARES data from 2007
We present the results of the first search for gravitational wave bursts
associated with high energy neutrinos. Together, these messengers could reveal
new, hidden sources that are not observed by conventional photon astronomy,
particularly at high energy. Our search uses neutrinos detected by the
underwater neutrino telescope ANTARES in its 5 line configuration during the
period January - September 2007, which coincided with the fifth and first
science runs of LIGO and Virgo, respectively. The LIGO-Virgo data were analysed
for candidate gravitational-wave signals coincident in time and direction with
the neutrino events. No significant coincident events were observed. We place
limits on the density of joint high energy neutrino - gravitational wave
emission events in the local universe, and compare them with densities of
merger and core-collapse events.Comment: 19 pages, 8 figures, science summary page at
http://www.ligo.org/science/Publication-S5LV_ANTARES/index.php. Public access
area to figures, tables at
https://dcc.ligo.org/cgi-bin/DocDB/ShowDocument?docid=p120000
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