Papers by Matias Rodriguez
American trypanosomiasis is a chronic and endemic disease which affects millions of people. Trypa... more American trypanosomiasis is a chronic and endemic disease which affects millions of people. Trypanosoma cruzi, its causative agent, has a life cycle that involves complex morphological and functional transitions, as well as a variety of environmental conditions. This requires a tight regulation of gene expression, which is achieved mainly by post-transcriptional regulation. In this work we conducted an RNAseq analysis of the three major life cycle stages of T. cruzi: amastigotes, epimastigotes and trypomastigotes. This analysis allowed us to delineate specific transcriptomic profiling for each stage, and also to identify those biological processes of major relevance in each state. Stage specific expression profiling evidenced the plasticity of T. cruzi to adapt quickly to different conditions, with particular focus on membrane remodeling and metabolic shifts along the life cycle. Epimastigotes, which replicate in the gut of insect vectors, showed higher expression of genes related t...
Transposable elements (TEs) are major genomic components in most eukaryotic genomes and play an i... more Transposable elements (TEs) are major genomic components in most eukaryotic genomes and play an important role in genome evolution. However, despite their relevance the identification of TEs is not an easy task and a number of tools were developed to tackle this problem. To better understand how they perform, we tested several widely used tools for de novo TE detection and compared their performance on both simulated data and well curated genomic sequences. As expected, tools that build TE-models performed better than k-mer counting ones, with RepeatModeler beating competitors in most datasets. However, there is a tendency for most tools to identify TE-regions in a fragmented manner and it is also frequent that small TEs or fragmented TEs are not detected. Consequently, the identification of TEs is still a challenging endeavor and it requires a significant manual curation by an experienced expert. The results will be helpful for identifying common issues associated with TE-annotatio...
Ion tracks are narrow cylindrical defects of displaced atoms, a few nanometres in diameter and up... more Ion tracks are narrow cylindrical defects of displaced atoms, a few nanometres in diameter and up to tens of micrometres in length. They result from the interaction of high-energy heavy ions with the electrons of a target material. We have performed a systematic investigation of the effects of the temperature during track formation in natural quartz samples, using synchrotron-based small angle x-ray scattering (SAXS). SAXS is a powerful and non-destructive technique well suited to measure ion track radii with high precision [1]. Natural quartz samples were irradiated at the UNILAC accelerator with 2.2-GeV Au ions and a fluence of 5 10 ions/cm. This leads to the formation of ion tracks of ~95 μm length, as estimated by SRIM2008 [2]. The irradiation was carried out at room-temperature (RT) as well as at elevated temperatures. The quartz was cut parallel to the c-axis, thus leading to a track alignment perpendicular to the crystal’s c-axis. Reference samples, irradiated at RT, underwen...
Modelación geotécnica tridimensional de la corta minera de cobre Las Cruces
Mobile elements and highly repetitive genomic regions are potent sources of lineage-specific geno... more Mobile elements and highly repetitive genomic regions are potent sources of lineage-specific genomic innovation and fingerprint individual genomes. Comprehensive analyses of large, composite or arrayed repeat elements and those found in more complex regions of the genome require a complete, linear genome assembly. Here we present the first de novo repeat discovery and annotation of a complete human reference genome, T2T-CHM13v1.0. We identified novel satellite arrays, expanded the catalog of variants and families for known repeats and mobile elements, characterized new classes of complex, composite repeats, and provided comprehensive annotations of retroelement transduction events. Utilizing PRO-seq to detect nascent transcription and nanopore sequencing to delineate CpG methylation profiles, we defined the structure of transcriptionally active retroelements in humans, including for the first time those found in centromeres. Together, these data provide expanded insight into the div...
Microbial genomics, Jan 30, 2018
Although the genome of Trypanosoma cruzi, the causative agent of Chagas disease, was first made a... more Although the genome of Trypanosoma cruzi, the causative agent of Chagas disease, was first made available in 2005, with additional strains reported later, the intrinsic genome complexity of this parasite (the abundance of repetitive sequences and genes organized in tandem) has traditionally hindered high-quality genome assembly and annotation. This also limits diverse types of analyses that require high degrees of precision. Long reads generated by third-generation sequencing technologies are particularly suitable to address the challenges associated with T. cruzi's genome since they permit direct determination of the full sequence of large clusters of repetitive sequences without collapsing them. This, in turn, not only allows accurate estimation of gene copy numbers but also circumvents assembly fragmentation. Here, we present the analysis of the genome sequences of two T. cruzi clones: the hybrid TCC (TcVI) and the non-hybrid Dm28c (TcI), determined by PacBio Single Molecular...
EPJ Web of Conferences, 2012
We have studied the morphology and annealing kinetics of ion tracks in Durango apatite using sync... more We have studied the morphology and annealing kinetics of ion tracks in Durango apatite using synchrotron small angle X-ray scattering. The non-destructive, artefact-free technique enables us to determine the track radii with a resolution of fractions of a nanometre. The tracks were generated using different heavy ions with energies between 185 MeV and 2.6 GeV. The track morphology is consistent with the formation of long cylindrical amorphous tracks. The annealing kinetics, measured by SAXS in combination with ex situ and in situ annealing experiments, suggests structural relaxation followed by recrystallisation of the damaged material. The measurement methodology shown here provides a new means for in-depth studies of ion-track formation in minerals under a wide variety of geological conditions. This is an Open Access article distributed under the terms of the Creative Commons Attribution License 2 0 , which. permits unrestricted use, distributi and reproduction in any medium, provided the original work is properly cited. on,
Measurement of Fusion Excitation Functions using a Novel Superconducting Solenoid
AIP Conference Proceedings, 2006
This work presents the essential features of a highly efficient detector system developed to make... more This work presents the essential features of a highly efficient detector system developed to make precise measurements of evaporation residues produced following heavy ion fusion reactions. The details of the measurements of fusion excitation function performed with this device for the system 58Ni + 60Ni are presented, and the results are compared with an existing set of data.
PeerJ, 2017
American trypanosomiasis is a chronic and endemic disease which affects millions of people. Trypa... more American trypanosomiasis is a chronic and endemic disease which affects millions of people. Trypanosoma cruzi, its causative agent, has a life cycle that involves complex morphological and functional transitions, as well as a variety of environmental conditions. This requires a tight regulation of gene expression, which is achieved mainly by post-transcriptional regulation. In this work we conducted an RNAseq analysis of the three major life cycle stages of T. cruzi: amastigotes, epimastigotes and trypomastigotes. This analysis allowed us to delineate specific transcriptomic profiling for each stage, and also to identify those biological processes of major relevance in each state. Stage specific expression profiling evidenced the plasticity of T. cruzi to adapt quickly to different conditions, with particular focus on membrane remodeling and metabolic shifts along the life cycle. Epimastigotes, which replicate in the gut of insect vectors, showed higher expression of genes related t...
Fusion cross sections for the 6,7Li+27Al, 9Be+27Al systems
AIP Conference Proceedings, 2007
We present the results of total fusion cross sections measurements for the 6,7Li + 27Al, 9Be + 27... more We present the results of total fusion cross sections measurements for the 6,7Li + 27Al, 9Be + 27Al, systems at energies above and below the Coulomb barrier (0.8Vb <= E <= 2.0Vb). The experimental evidence at the measured energy regime show that the total fusion cross sections of 6Li and 9Be with a light mass target are not affected by the break-up process. The elastic break up cross sections for the 6Li + 27Al system were also measured and the results are being presented in this issue. The data for the 7Li + 27Al system are still being analyzed and therefore these results should be considered preliminary.
Shape manipulation of ion irradiated Ag nanoparticles embedded in lithium niobate
Nanotechnology, Jan 8, 2016
Spherical silver nanoparticles were prepared by means of ion beam synthesis in lithium niobate. T... more Spherical silver nanoparticles were prepared by means of ion beam synthesis in lithium niobate. The embedded nanoparticles were then irradiated with energetic (84)Kr and (197)Au ions, resulting in different electronic energy losses between 8.1 and 27.5 keV nm(-1) in the top layer of the samples. Due to the high electronic energy losses of the irradiating ions, molten ion tracks are formed inside the lithium niobate in which the elongated Ag nanoparticles are formed. This process is strongly dependent on the initial particle size and leads to a broad aspect ratio distribution. Extinction spectra of the samples feature the extinction maximum with shoulders on either side. While the maximum is caused by numerous remaining spherical nanoparticles, the shoulders can be attributed to elongated particles. The latter could be verified by COMSOL simulations. The extinction spectra are thus a superposition of the spectra of all individual particles.
Physical Review B, 2014
The thermal response of nanoscale cylindrical inclusions of amorphous SiO 2 embedded in crystalli... more The thermal response of nanoscale cylindrical inclusions of amorphous SiO 2 embedded in crystalline quartz (c-SiO 2) is investigated by means of small-angle x-ray scattering. The inclusions are generated by swift heavy-ion irradiation that leads to the formation of amorphous ion tracks along the ion trajectories. During in situ annealing between room temperature and 620°C, we observe an irreversible expansion of the track cylinders followed by a reversible contraction. The reversible "elastic" response of the tracks can be modeled using the temperature-dependent elastic properties of bulk amorphous and crystalline SiO 2 for the inclusions and the matrix, respectively. A high initial interface pressure of the nanocylinders is apparent from the calculations.
Physics Letters B, 2006
Complete and incomplete fusion cross sections for the 9 Be + 144 Sm reaction have been measured a... more Complete and incomplete fusion cross sections for the 9 Be + 144 Sm reaction have been measured at near-barrier energies, using the delayed X-ray detection technique. At above-barrier energies these show a suppression of complete fusion for this weakly bound projectile on an intermediate mass target. The suppression factor, attributed to 9 Be break-up, was deduced from a comparison of complete fusion yields with coupled-channels calculations, and appears consistent with measured incomplete fusion product yields. At ∼ 10%, it is considerably smaller than the value of ∼ 30% previously found for a 208 Pb target. Simultaneous measurements of elastic and inelastic scattering permit a clearer picture of the reaction mechanisms.
Physics Letters B, 1997
We present a new measurement of the spin-dependent structure function gf of the deuteron from dee... more We present a new measurement of the spin-dependent structure function gf of the deuteron from deep inelastic scattering of 190 GeV polarized muons on polarized deuterons. The results are combined with our previous measurements of gf. A perturbative QCD evolution in next-to-leading order is used to compute g;'(x) at a constant Q2. At Q* = 10 GeV*, we obtain a first moment rt = so1 gidx = 0.041 f 0.008, a flavour-singlet axial charge of the nucleon uo = 0.30 f 0.08, and an axial charge of the strange quark as =-0.09 f 0.03. Using our earlier determination of ry, we obtain ry-r; = 0.183 f 0.035 at Q2 = IOGeV2. This result is in agreement with the Bjorken sum rule which predicts ry-r; = 0.186 f 0.002 at the same Q2.
Physical Review D, 1998
We present a next-to-leading order QCD analysis of the presently available data on the spin struc... more We present a next-to-leading order QCD analysis of the presently available data on the spin structure function g 1 including the final data from the Spin Muon Collaboration. We present results for the first moments of the proton, deuteron, and neutron structure functions, and determine singlet and nonsinglet parton distributions in two factorization schemes. We also test the Bjorken sum rule and find agreement with the theoretical prediction at the level of 10%. ͓S0556-2821͑98͒07117-3͔ PACS number͑s͒: 13.60.Hb, 13.88.ϩe I. INTRODUCTION We present a perturbative QCD ͑PQCD͒ analysis in nextto-leading order ͑NLO͒ of the world data on polarized lepton-nucleon deep inelastic scattering ͑DIS͒. The data used in this analysis include the final results ͓1͔ presented by the Spin Muon Collaboration ͑SMC͒. From the world data we determine the first moments of the polarized structure functions. The accuracy of the experimental data on the polarized
Physical Review C, 2007
Elastic scattering of identical nuclei results in oscillatory Mott scattering. The separation of ... more Elastic scattering of identical nuclei results in oscillatory Mott scattering. The separation of the peaks is perturbed by the presence of the nuclear potential. Near-barrier measurements of Mott scattering of 58 Ni from 58 Ni have been made to obtain information on the diffuseness of the nuclear potential, giving a diffuseness parameter of 0.62±0.04 fm.
Physical Review C, 2005
The total fusion cross section for the 9 Be + 27 Al system has been measured at energies close an... more The total fusion cross section for the 9 Be + 27 Al system has been measured at energies close and above the Coulomb barrier. Reaction cross sections for this system were derived from elastic scattering data, and the breakup-plus-transfer-channel cross sections were estimated from the difference between these data and measured cross-section fusion.
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Papers by Matias Rodriguez