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Search Results: 1 - 10 of 25852 matches for " Ricardo Ramirez-Gonzalez "
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Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments
Ricardo H Ramirez-Gonzalez, Raoul Bonnal, Mario Caccamo, Daniel MacLean
Source Code for Biology and Medicine , 2012, DOI: 10.1186/1751-0473-7-6
Abstract: The utility of SAMtools is encapsulated in 3 main classes, Bio::DB::Sam, representing the alignment files and providing access to the data in them, Bio::DB::Alignment, representing the individual read alignments inside the files and Bio::DB::Pileup, representing the summarised nucleotides of reads over a single point in the nucleotide sequence to which the reads are aligned.Bio-samtools is a flexible and easy to use interface that programmers of many levels of experience can use to access information in the popular and common SAM/BAM format.
PyroClean: Denoising Pyrosequences from Protein-Coding Amplicons for the Recovery of Interspecific and Intraspecific Genetic Variation
Ricardo Ramirez-Gonzalez, Douglas W. Yu, Catharine Bruce, Darren Heavens, Mario Caccamo, Brent C. Emerson
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0057615
Abstract: High-throughput parallel sequencing is a powerful tool for the quantification of microbial diversity through the amplification of nuclear ribosomal gene regions. Recent work has extended this approach to the quantification of diversity within otherwise difficult-to-study metazoan groups. However, nuclear ribosomal genes present both analytical challenges and practical limitations that are a consequence of the mutational properties of nuclear ribosomal genes. Here we exploit useful properties of protein-coding genes for cross-species amplification and denoising of 454 flowgrams. We first use experimental mixtures of species from the class Collembola to amplify and pyrosequence the 5′ region of the COI barcode, and we implement a new algorithm called PyroClean for the denoising of Roche GS FLX pyrosequences. Using parameter values from the analysis of experimental mixtures, we then analyse two communities sampled from field sites on the island of Tenerife. Cross-species amplification success of target mitochondrial sequences in experimental species mixtures is high; however, there is little relationship between template DNA concentrations and pyrosequencing read abundance. Homopolymer error correction and filtering against a consensus reference sequence reduced the volume of unique sequences to approximately 5% of the original unique raw reads. Filtering of remaining non-target sequences attributed to PCR error, sequencing error, or numts further reduced unique sequence volume to 0.8% of the original raw reads. PyroClean reduces or eliminates the need for an additional, time-consuming step to cluster reads into Operational Taxonomic Units, which facilitates the detection of intraspecific DNA sequence variation. PyroCleaned sequence data from field sites in Tenerife demonstrate the utility of our approach for quantifying evolutionary diversity and its spatial structure. Comparison of our sequence data to public databases reveals that we are able to successfully recover both interspecific and intraspecific sequence diversity.
Identifying and Classifying Trait Linked Polymorphisms in Non-Reference Species by Walking Coloured de Bruijn Graphs
Richard M. Leggett, Ricardo H. Ramirez-Gonzalez, Walter Verweij, Cintia G. Kawashima, Zamin Iqbal, Jonathan D. G. Jones, Mario Caccamo, Daniel MacLean
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0060058
Abstract: Single Nucleotide Polymorphisms are invaluable markers for tracing the genetic basis of inheritable traits and the ability to create marker libraries quickly is vital for timely identification of target genes. Next-generation sequencing makes it possible to sample a genome rapidly, but polymorphism detection relies on having a reference genome to which reads can be aligned and variants detected. We present Bubbleparse, a method for detecting variants directly from next-generation reads without a reference sequence. Bubbleparse uses the de Bruijn graph implementation in the Cortex framework as a basis and allows the user to identify bubbles in these graphs that represent polymorphisms, quickly, easily and sensitively. We show that the Bubbleparse algorithm is sensitive and can detect many polymorphisms quickly and that it performs well when compared with polymorphism detection methods based on alignment to a reference in Arabidopsis thaliana. We show that the heuristic can be used to maximise the number of true polymorphisms returned, and with a proof-of-principle experiment show that Bubbleparse is very effective on data from unsequenced wild relatives of potato and enabled us to identify disease resistance linked genes quickly and easily.
Evolution of an Eurasian Avian-like Influenza Virus in Na?ve and Vaccinated Pigs
Pablo R. Murcia,Joseph Hughes,Patrizia Battista,Lucy Lloyd,Gregory J. Baillie,Ricardo H. Ramirez-Gonzalez,Doug Ormond,Karen Oliver,Debra Elton,Jennifer A. Mumford,Mario Caccamo,Paul Kellam,Bryan T. Grenfell,Edward C. Holmes,James L. N. Wood
PLOS Pathogens , 2012, DOI: 10.1371/journal.ppat.1002730
Abstract: Influenza viruses are characterized by an ability to cross species boundaries and evade host immunity, sometimes with devastating consequences. The 2009 pandemic of H1N1 influenza A virus highlights the importance of pigs in influenza emergence, particularly as intermediate hosts by which avian viruses adapt to mammals before emerging in humans. Although segment reassortment has commonly been associated with influenza emergence, an expanded host-range is also likely to be associated with the accumulation of specific beneficial point mutations. To better understand the mechanisms that shape the genetic diversity of avian-like viruses in pigs, we studied the evolutionary dynamics of an Eurasian Avian-like swine influenza virus (EA-SIV) in na?ve and vaccinated pigs linked by natural transmission. We analyzed multiple clones of the hemagglutinin 1 (HA1) gene derived from consecutive daily viral populations. Strikingly, we observed both transient and fixed changes in the consensus sequence along the transmission chain. Hence, the mutational spectrum of intra-host EA-SIV populations is highly dynamic and allele fixation can occur with extreme rapidity. In addition, mutations that could potentially alter host-range and antigenicity were transmitted between animals and mixed infections were commonplace, even in vaccinated pigs. Finally, we repeatedly detected distinct stop codons in virus samples from co-housed pigs, suggesting that they persisted within hosts and were transmitted among them. This implies that mutations that reduce viral fitness in one host, but which could lead to fitness benefits in a novel host, can circulate at low frequencies.
Equilibration and aging of dense soft-sphere glass-forming liquids
Luis Enrique Sanchez-Diaz,Pedro Ramirez-Gonzalez,Magdaleno Medina-Noyola
Physics , 2012, DOI: 10.1103/PhysRevE.87.052306
Abstract: The recently-developed non-equilibrium extension of the self-consistent generalized Langevin equation theory of irreversible relaxation [Phys. Rev. E (2010) 82, 061503; ibid. 061504] is applied to the description of the irreversible process of equilibration and aging of a glass-forming soft-sphere liquid that follows a sudden temperature quench, within the constraint that the local mean particle density remains uniform and constant. For these particular conditions, this theory describes the non-equilibrium evolution of the static structure factor S(k;t) and of the dynamic properties, such as the self-intermediate scattering function F_S(k,\tau;t), where tau is the correlation delay time and t is the evolution or waiting time after the quench. Specific predictions are presented, for the deepest quench (to zero temperature). The predicted evolution of the alpha-relaxation time \tau_\alpha(t) as a function of t allows us to define the equilibration time t^{eq}, as the time after which \tau_\alpha has attained its equilibrium value \tau_\alpha^{eq}. It is predicted that both, t^{eq}(\phi) and \tau_{\alpha}^{eq}, diverge as \phi \to \phi^{(a)}, where \phi^{(a)} is the hard-sphere dynamic-arrest volume fraction \phi^{(a)}\ (\approx 0.582), thus suggesting that the measurement of equilibrium properties at and above \phi^{(a)} is experimentally impossible.
Role of Free Fatty Acids in Physiological Conditions and Mitochondrial Dysfunction  [PDF]
Zbigniew K. Binienda, Sumit Sarkar, Sonia Silva-Ramirez, Carmen Gonzalez
Food and Nutrition Sciences (FNS) , 2013, DOI: 10.4236/fns.2013.49A1002
Abstract:

The role of free fatty acids (FFAs) as a source of energy and their functions in energy transport within the body are well established. Equally important is a role that FFAs play in oxidative stress following cell membrane depolarization. FFAs are physiologically active, not only as nutritional components, but also as molecules involved in cell signaling and stabilization of membranes via palmitoylation and myristoylation. Protein palmitoylation is involved in numerous cellular processes, including apoptosis, and neuronal transmission. Besides nuclear peroxisome proliferator-activated receptors that mediate the biological effects of FFAs, G protein-coupled receptors (GPCRs) that are activated by FFA, have been recently identified. Those multiple FFA receptors (FFARs), which function on the cell surface as activated FFAs, play significant roles in the regulation of energy metabolism and mediate a wide range of important metabolic processes. FFARs have been targeted in drug development for the treatment of type 2 diabetes and metabolic syndrome. FFAs upregulate transcription of uncoupling proteins, increasing their expression in brain, cardiac, and skeletal muscle that may be protective or cytotoxic, depending on the cellular energy state. Recently, FFA effects on the endothelial function and dysfunction are being recognized. FFAs play a key role in endothelium-dependent nitric oxide production. A disturbance of endothelial function, due to an imbalance in production and release of relaxing and constricting factors, has implications in the development of cardiovascular problems, such as hypertension, as well as neurotoxicity following loss of blood-brain barrier integrity. This review presents information on broad range of FFAs actions of prime importance for physiological processes. Understanding of FFA functions in the body is crucial for developing new therapeutic strategies against several metabolic disorders.

Taq1B CETP Polymorphism and Cardiovascular Risk in an Endogamous Pop-ulation of Diabetic Men: A Study in Santa Rosa Del Conlara, San Luis, Argentina  [PDF]
Susana Siewert, Irma Gonzalez, Sergio Filipuzzi, Dario C. Ramirez, Marta S. Ojeda
Journal of Diabetes Mellitus (JDM) , 2015, DOI: 10.4236/jdm.2015.52015
Abstract: Objectives: Type 2 diabetes mellitus (T2DM) patients are at increased risk of cardiovascular diseases (CVDs). Several polymorphisms in the cholesterol ester transfer protein (CETP) gene have been reported. The aim of this study was to determine the distribution and effect of the Taq1B polymorphism in the CETP gene on clinical and biochemical indicators of CVD risk in a population of endogamous-T2DM men. Methods: 102 men (57.5 ± 9.3 years old) inhabitants of Santa Rosa del Conlara, San Luis, Argentina, were recruited and assigned into two groups (22 control and 80 T2DM). Further, these two groups were subdivided according to their Taq1B CETP gene genotypes (i.e., B1B1, B1B2 and B2B2). Clinical and fasting-plasma biochemical indicators of CVD risk were measured and their association with the B1 allele was determined. Results: Compared to control, T2DM men had more central obesity, hypertension, atherogenic index, insulin resistance and poorly controlled diabetes. Compared to T2DM men having the B2 allele, those T2DM men having the B1 allele have increased risk of CVD as assessed by systolic blood pressure (156 ± 16.0 vs 135.8 ± 19.2, p = 0.015), atherogenic index (6.15 ± 1.3 vs 4.4 ± 0.7, p = 0.0008), HDL-c levels (38.9 ± 5.3 vs 64.4 ± 8.2, p < 0.0001) and insulin resistance (HOMA-IR, 5.78 ± 3.0 vs 2.4 ± 0.78, p = 0.004). Interestingly, only body mass index (r = 0.559, p = 0.01) and HDL-c concentration (r = 0.492, p = 0.02) negatively correlated with CVD risk in the endogamous population of B1B1 and B1B2 T2DM men. Conclusion: The B1 allele of the CETP gene predicts cardiovascular complications in an endogamous population of T2DM men.
Scaling of the Structure Factor in Fractal Aggregation of Colloids: Computer Simulations
Agustin E. Gonzalez,Guillermo Ramirez-Santiago
Physics , 1996,
Abstract: In the volume fraction range (0.005,0.08), we have obtained the temporal evolution of the structure factor $S(q)$, in extensive numerical simulations of both diffusion-limited and reaction-limited colloid aggregation in three dimensions. We report the observation of scaling of this structure function in the diffusion-limited case, analogous to a spinodal decomposition type of scaling. By comparing $S(q)$ with the pair correlation function between particles, we were able to identify the peak in the structure factor as arising from the correlations between particles belonging to nearest-neighbor clusters. The exponents $a\prime$ and $a\prime \prime$ that relate the position and the height of the maximum in $S(q)$ vs. time, respectively, were also obtained and shown to differ somewhat from the spinodal decomposition exponents. We also found a terminal shape for $S(q)$ that corresponds to a close packing of the clusters after gelation. Moreover, this picture was shown to be valid in a concentration range larger than the one suggested in recent experiments. Although the $S(q)$ for reaction-limited colloid aggregation does not show a pronounced peak for the earlier times, eventually the peak stretches and becomes higher than in the diffusion-limited case. The $S(q)$ curves, however, do not present the scaling shown for diffusion-limited aggregation.
Internal transitions in the confined biexciton
Ricardo Perez,Augusto Gonzalez
Physics , 2001,
Abstract: Optical internal transitions relevant to ODR experiments are computed for the biexciton in a quantum dot in the strong confinement regime. Valence sub-band mixing effects are taken into account in second order pertubation theory. The transition probability from the ground state is concentrated in a few states with relatively high excitation energies. Level collissions with oscillator strength transfer are observed as the magnetic field is raised.
Few-anyon systems in a parabolic dot
Ricardo Perez,Augusto Gonzalez
Physics , 1997, DOI: 10.1103/PhysRevB.58.7412
Abstract: The energy levels of two and three anyons in a two-dimensional parabolic quantum dot and a perpendicular magnetic field are computed as power series in 1/|J|, where J is the angular momentum. The particles interact repulsively through a coulombic (1/r) potential. In the two-anyon problem, the reached accuracy is better than one part in 10^5. For three anyons, we study the combined effects of anyon statistics and coulomb repulsion in the ``linear'' anyonic states.
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