Publications by authors named "Miguel A García"

29 Publications

  • Page 1 of 1

Effects of Moderate Static Magnetic Field on Neural Systems Is a Non-invasive Mechanical Stimulation of the Brain Possible Theoretically?

Front Neurosci 2020 19;14:419. Epub 2020 May 19.

Functional Exploration and Neuromodulation of the Nervosus System Investigation Group, Hospital Nacional de Parapléjicos, Servicio de Salud de Castilla la Mancha, Toledo, Spain.

Static magnetic fields have been shown to induce effects on the human brain. Different experiments seem to support the idea that moderate static magnetic field can exert some influence on the gating processes of the membrane channels. In this article we visit the order of magnitude of the energy magnetic terms associated with moderate applied field (between 10 and 200 milliteslas). It is shown that gradients of the Zeeman energy associated with the inhomogeneous applied fields can induce pressures of the order of 10Pa. The surface tension generated by the magnetic pressure, on the surface delimiting the brain region subject to relevant field and gradients, is found to range between 10 and 1 mN⋅m. These pressures seem to be strong enough to interfere with the elastic and electrostatic energies involved in the channel activation-inactivation-deactivation mechanisms of biological membranes. It has been described that small mechanical force can activate voltage gated potassium channels. Moreover, stretch-activated ion channels are widely described in different biological tissues. Virtually, all these channels can modify their activity if stressed by a sufficient pressure delivered for enough time. We propose mechanical stimulation - possibly not exclusively - as a candidate mechanism how static magnetic field can produce effects in biological systems. It must be emphasized, that such field gradients were not previously proposed as a possible source of neural activity modification.
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http://dx.doi.org/10.3389/fnins.2020.00419DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7248270PMC
May 2020

Anchors Away: Glia-Neuron Adhesion Regulates Myelin Targeting and Growth.

Dev Cell 2019 12;51(6):659-661

Department of Neurosurgery, Stanford University, Stanford, CA, USA. Electronic address:

Myelination in the CNS requires oligodendrocytes to first select correct axonal targets and then extend their membranes around and along these axons. In this issue of Developmental Cell, Klingseisen et al. (2019) find that the adhesion protein Neurofascin is required in oligodendrocytes for both target selection and myelin growth.
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http://dx.doi.org/10.1016/j.devcel.2019.11.018DOI Listing
December 2019

MEMS device for applying shear and tension to an epithelium combined with fluorescent live cell imaging.

J Micromech Microeng 2020 15;30(12). Epub 2020 Oct 15.

Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106, United States of America.

Mechanical forces play important roles in the biological function of cells and tissues. While numerous studies have probed the force response of cells and measured cell-generated forces, they have primarily focused on tensile, but not shear forces. Here, we describe the design, fabrication, and application of a silicon micromachined device that is capable of independently applying and sensing both tensile and shear forces in an epithelial cell monolayer. We integrated the device with an upright microscope to enable live cell brightfield and fluorescent imaging of cells over many hours following mechanical perturbation. Using devices of increasing stiffness and the same displacement input, we demonstrate that epithelia exhibit concomitant higher maximum resistive tensile forces and quicker force relaxation. In addition, we characterized the force response of the epithelium to cyclic shear loading. While the maximum resistive forces of epithelia under cyclic shear perturbation remained unchanged between cycles, cyclic loading led to faster relaxation of the resistive forces. The device presented here can be applied to studying the force response of other monolayer-forming cell types and is compatible with pharmacological perturbation of cell structures and functions.
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http://dx.doi.org/10.1088/1361-6439/abb12cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8372846PMC
October 2020

Acute kidney injury in newborns with necrotizing enterocolitis: risk factors and mortality.

Bol Med Hosp Infant Mex 2019 ;76(5):210-214

Hospital del Niño de Saltillo Dr. Federico Gómez Santos, Saltillo, Coahuila, Mexico.

Background: Both necrotizing enterocolitis and acute kidney injury are tightly related conditions, which independently increase mortality in newborns. Necrotizing enterocolitis is an inflammatory disease with a systemic repercussion that leads to inflammatory kidney changes predisposing to renal damage.

Methods: This study assessed risk factors for the development of acute kidney injury in patients diagnosed with necrotizing enterocolitis and compared mortality between patients with or without acute kidney injury. Thirty-nine patients with the diagnosis of necrotizing enterocolitis were included, regardless of the gestational age.

Results: Of 39 patients, 38.5% developed acute kidney injury. Survival showed to be significantly lower in patients with acute kidney injury (54.4 days) when compared to newborns without acute kidney injury (76.22 days; p = 0.014). Mortality in patients with acute kidney injury was 46.7%, increasing up to 62.5% with severe kidney damage. The hazard ratio for mortality was 4.708 for acute kidney injury (p = 0.025). The severity of enterocolitis showed to be an independent risk factor in developing acute kidney injury and severe kidney injury (odds ratio [OR] = 1.841, p = 0.034 and OR = 1.917, p = 0.027, respectively).

Conclusions: Newborns with necrotizing enterocolitis should be evaluated for early recognition of acute kidney injury. Prospective studies with a higher number of patients are needed to identify modifiable risk factors to impact in the prevention of these conditions.
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http://dx.doi.org/10.24875/BMHIM.19000044DOI Listing
April 2020

Allopolyploid origin and genome differentiation of the parasitic species (Convolvulaceae) revealed by genomic in situ hybridization.

Genome 2019 Jul 9;62(7):467-475. Epub 2019 May 9.

a Laboratory of Plant Cytogenetics and Evolution - Federal University of Pernambuco, Department of Botany, Recife 50.372-970, PE, Brazil.

Interspecific hybridization and genome duplication to form allopolyploids are major evolutionary events in angiosperms. In the parasitic genus (Convolvulaceae), molecular data suggested the existence of species of hybrid origin. One of them, , has been proposed as a hybrid between and , both included in sect. . To test this hypothesis, a cytogenetic analysis was performed with CMA/DAPI staining and fluorescent in situ hybridization using 5S and 35S rDNA and genomic probes. Chromosomes of were small with a well-defined centromeric region, whereas had larger, densely stained chromosomes, and less CMA heterochromatic bands. had 2 = 60 chromosomes, about 30 of them similar to those of and the remaining to . GISH analysis confirmed the presence of both subgenomes in the allotetraploid . However, the number of rDNA sites and the haploid karyotype length in were not additive. The diploid parentals had already diverged in their chromosomes structure, whereas the reduction in the number of rDNA sites more probably occurred after hybridization. As phylogenetic data suggested a recent divergence of the progenitors, these species should have a high rate of karyotype evolution.
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http://dx.doi.org/10.1139/gen-2018-0184DOI Listing
July 2019

Shear-induced damped oscillations in an epithelium depend on actomyosin contraction and E-cadherin cell adhesion.

Elife 2018 11 14;7. Epub 2018 Nov 14.

Department of Bioengineering, Stanford University, Stanford, United States.

Shear forces between cells occur during global changes in multicellular organization during morphogenesis and tissue growth, yet how cells sense shear forces and propagate a response across a tissue is unknown. We found that applying exogenous shear at the midline of an epithelium induced a local, short-term deformation near the shear plane, and a long-term collective oscillatory movement across the epithelium that spread from the shear-plane and gradually dampened. Inhibiting actomyosin contraction or E-cadherin -cell adhesion blocked oscillations, whereas stabilizing actin filaments prolonged oscillations. Combining these data with a model of epithelium mechanics supports a mechanism involving the generation of a shear-induced mechanical event at the shear plane which is then relayed across the epithelium by actomyosin contraction linked through E-cadherin. This causes an imbalance of forces in the epithelium, which is gradually dissipated through oscillatory cell movements and actin filament turnover to restore the force balance across the epithelium.
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http://dx.doi.org/10.7554/eLife.39640DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6235569PMC
November 2018

Hybrid nanoparticles for magnetic and plasmonic hyperthermia.

Phys Chem Chem Phys 2018 Sep;20(37):24065-24073

Instituto de Magnetismo Aplicado, 'Salvador Velayos', UCM-CSIC-ADIF, Las Rozas, PO Box 155, Madrid 28230, Spain.

The present manuscript reports the use of hybrid magneto-plasmonic nanoparticles (HMPNPs) based on iron oxide nanoparticles and Au nanorods as colloidal nanoheaters. The individual synthesis of the magnetic and plasmonic components allowed optimizing their features for heating performance separately, before they were hybridized. Besides, a detailed characterization and finite element simulations were carried out to explain the interaction effects observed between the phases of the HMPNPs. The study also analyzed the heating power of these nanostructures when they were excited with infrared light and AC magnetic fields, and compared this with the heating power of their plasmonic and magnetic components. In the latter case, the AC magnetization curves revealed that the magnetic dipolar interactions increase the amount of heat released by the hybrid nanostructures.
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http://dx.doi.org/10.1039/c8cp02513dDOI Listing
September 2018

Synthesis of hybrid magneto-plasmonic nanoparticles with potential use in photoacoustic detection of circulating tumor cells.

Mikrochim Acta 2018 01 25;185(2):130. Epub 2018 Jan 25.

Instituto de Magnetismo Aplicado, 'Salvador Velayos', UCM-CSIC-ADIF, Las Rozas, PO Box 155, 28230, Madrid, Spain.

This article describes a novel synthetic route to obtain hybrid nanostructures that combine the plasmonic properties of gold nanorods with the magnetic properties of iron oxide nanoparticles in a robust silica nanostructure. The silica matrix enhances the physico-chemical stability of the nanostructure and preserves its magneto-plasmonic properties by avoiding the interface between gold and iron oxide. In addition, the magneto-plasmonic features of the nanohybrids can be tuned due to the independent synthesis of each component. The magnetic and plasmonic properties of these nanostructures can potentially enhance the photoacoustic detection of circulating tumor cells. Graphical abstract Schematic presentation of a hybrid magneto-plasmonic nanoparticle with an [email protected]@SiO core-satellite-shell arrangement. The magnetic and plasmonic responses of this kind of nanostructure enable magnetic trapping and photoacoustic detection of circulating tumor cells.
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http://dx.doi.org/10.1007/s00604-017-2637-xDOI Listing
January 2018

Cladogenesis and reticulation in sect. (Convolvulaceae).

Org Divers Evol 2018 28;18(4):383-398. Epub 2018 Oct 28.

3Department of Biology, Wilfrid Laurier University, Waterloo, ON N2L3C5 Canada.

As traditionally circumscribed, sect. is a group of three parasitic plant species native to the deserts of Western USA (, ) and the central region of Baja California, Mexico (). Molecular phylogenetic studies confirmed the monophyly of this group and suggested that the disjunct is a hybrid between the other two species. However, the limited sampling left the possibility of alternative biological and methodological explanations. We expanded our sampling to multiple individuals of all the species collected from across their entire geographical ranges. Sequence data from the nuclear and plastid regions were used to reconstruct the phylogeny and find out if the topological conflict was maintained. We obtained karyotype information from multiple individuals, investigated the morphological variation of the group thorough morphometric analyses, and compiled data on ecology, host range, and geographical distribution. Our results confirmed that is an allotetraploid. Furthermore, we found previously unknown autotetraploid population of , and we describe a new hybrid species, . We suggest that this newly discovered natural hybrid is resulting from an independent (and probably more recent) hybridization event between the same diploid parental species as those of . All the polyploids showed host shift associated with hybridization and/or polyploidy and are found growing on hosts that are rarely or never frequented by their diploid progenitors. The great potential of this group as a model to study host shift in parasitic plants associated with recurrent allopolyploidy is discussed.
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http://dx.doi.org/10.1007/s13127-018-0383-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6405177PMC
October 2018

The Henry's constant of monochloramine.

Chemosphere 2018 Feb 30;192:244-249. Epub 2017 Oct 30.

Department of Environmental Sciences, University of California Riverside, USA. Electronic address:

Monochloramine is a secondary disinfectant used in drinking water and is also formed in chlorinated wastewater. While known to hydrolyze over time and react with dissolved organic matter, its partitioning between the aqueous and gas phase has not been extensively studied. Preliminary experiments demonstrated that monochloramine concentrations in solutions open to the atmosphere or actively aerated decreased more rapidly than in sealed solutions, indicating significant losses to the atmosphere. For example, a monochloramine solution open to the atmosphere yielded a loss rate constant of 0.08 d, a value twice that for sealed samples without headspace (0.04 d) where loss occurs exclusively as a result of hydrolysis. A solution aerated at 10 mL s had a loss rate constant nearly 10× greater than that for hydrolysis alone (0.35 d). To better understand partitioning of monochloramine to the gas phase and potential for volatilization, the dimensionless Henry's law constants of monochloramine (K) were determined using an equilibrium headspace technique at five different temperatures (11, 16, 21, 27, and 32 °C). The resulting values ranged from 8 × 10 to 4 × 10, indicating a semi-volatile compound, and were found to be consistent with quantitative structure activity relationship predictions. At 20 °C, monochloramine exhibits a dimensionless Henry's constant of about 1.7 × 10 which is 35 times greater than ammonia but comparable to the Henry's constant of inorganic semi-volatile compounds such sulfur dioxide. The Henry's constant values for monochloramine suggests that volatilization could be a relevant loss process in open systems such as rivers receiving chlorinated wastewater effluent, swimming pools and cooling towers.
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http://dx.doi.org/10.1016/j.chemosphere.2017.10.157DOI Listing
February 2018

Cell-Cell Junctions Organize Structural and Signaling Networks.

Cold Spring Harb Perspect Biol 2018 04 2;10(4). Epub 2018 Apr 2.

Department of Biology, Stanford University, Stanford, California 94305.

Cell-cell junctions link cells to each other in tissues, and regulate tissue homeostasis in critical cell processes that include tissue barrier function, cell proliferation, and migration. Defects in cell-cell junctions give rise to a wide range of tissue abnormalities that disrupt homeostasis and are common in genetic abnormalities and cancers. Here, we discuss the organization and function of cell-cell junctions primarily involved in adhesion (tight junction, adherens junction, and desmosomes) in two different epithelial tissues: a simple epithelium (intestine) and a stratified epithelium (epidermis). Studies in these tissues reveal similarities and differences in the organization and functions of different cell-cell junctions that meet the requirements for the specialized functions of each tissue. We discuss cell-cell junction responses to genetic and environmental perturbations that provide further insights into their roles in maintaining tissue homeostasis.
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http://dx.doi.org/10.1101/cshperspect.a029181DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5773398PMC
April 2018

More than one fungus in the pepper pot: Integrative taxonomy unmasks hidden species within Myriostoma coliforme (Geastraceae, Basidiomycota).

PLoS One 2017 7;12(6):e0177873. Epub 2017 Jun 7.

Departamento de Micología, Real Jardín Botánico-CSIC, Plaza de Murillo 2, Madrid, Spain.

Since the nineteenth century, Myriostoma has been regarded as a monotypic genus with a widespread distribution in north temperate and subtropical regions. However, on the basis of morphological characters and phylogenetic evidence of DNA sequences of the internal transcribed spacer (ITS) regions and the large subunit nuclear ribosomal RNA gene (LSU), four species are now delimited: M. areolatum comb. & stat. nov., M. calongei sp. nov., M. capillisporum comb. & stat. nov., and M. coliforme. Myriostoma coliforme is typified by selecting a lectotype (iconotype) and a modern sequenced collection as an epitype. The four species can be discriminated by a combination of morphological characters, such as stomatal form, endoperidial surface texture, and basidiospore size and ornamentation.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0177873PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5462367PMC
September 2017

Waterfowl endozoochory: An overlooked long-distance dispersal mode for Cuscuta (dodder).

Am J Bot 2016 05 27;103(5):957-62. Epub 2016 Apr 27.

Wetland Ecology Department, Estación Biológica de Doñana (EBD-CSIC), Sevilla 41092 Spain.

Premise Of The Study: Dispersal of parasitic Cuscuta species (dodders) worldwide has been assumed to be largely anthropomorphic because their seeds do not match any previously known dispersal syndrome and no natural dispersal vectors have been reliably documented. However, the genus has a subcosmopolitan distribution and recent phylogeographic results have indicated that at least18 historical cases of long-distance dispersal (LDD) have occurred during its evolution. The objective of this study is to report the first LDD biological vector for Cuscuta seeds.

Methods: Twelve northern pintails (Anas acuta) were collected from Suisun Marsh, California and the contents of their lowest part of the large intestine (rectum) were extracted and analyzed. Seed identification was done both morphologically and using a molecular approach. Extracted seeds were tested for germination and compared to seeds not subjected to gut passage to determine the extent of structural changes caused to the seed coat by passing through the digestive tract.

Key Results: Four hundred and twenty dodder seeds were found in the rectum of four northern pintails. From these, 411 seeds were identified as Cuscuta campestris and nine as most likely C. pacifica. The germination rate of C. campestris seeds after gut passage was 55%. Structural changes caused by the gut passage in both species were similar to those caused by an acid scarification.

Conclusions: Endozoochory by waterbirds may explain the historical LDD cases in the evolution of Cuscuta. This also suggests that current border quarantine measures may be insufficient to stopping spreading of dodder pests along migratory flyways.
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http://dx.doi.org/10.3732/ajb.1500507DOI Listing
May 2016

Virus-Templated Near-Amorphous Iron Oxide Nanotubes.

Langmuir 2016 06 27;32(23):5899-908. Epub 2016 May 27.

CIC nanoGUNE Consolider, E-20018, Donostia-San Sebastián, Spain.

We present a simple synthesis of iron oxide nanotubes, grown under very mild conditions from a solution containing Fe(II) and Fe(III), on rod-shaped tobacco mosaic virus templates. Their well-defined shape and surface chemistry suggest that these robust bionanoparticles are a versatile platform for synthesis of small, thin mineral tubes, which was achieved efficiently. Various characterization tools were used to explore the iron oxide in detail: Electron microscopy (SEM, TEM), magnetometry (SQUID-VSM), diffraction (XRD, TEM-SAED), electron spectroscopies (EELS, EDX, XPS), and X-ray absorption (XANES with EXAFS analysis). They allowed determination of the structure, crystallinity, magnetic properties, and composition of the tubes. The protein surface of the viral templates was crucial to nucleate iron oxide, exhibiting analogies to biomineralization in natural compartments such as ferritin cages.
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http://dx.doi.org/10.1021/acs.langmuir.5b04491DOI Listing
June 2016

Molecular and morphological analyses confirm Rhizopogon verii as a widely distributed ectomycorrhizal false truffle in Europe, and its presence in South America.

Mycorrhiza 2016 Jul 14;26(5):377-88. Epub 2016 Jan 14.

Departamento de Micología, Real Jardín Botánico, RJB-CSIC, Plaza Murillo 2, Madrid, 28014, Spain.

The genus Rhizopogon includes species with hypogeous or subepigeus habit, forming ectomycorrhizae with naturally occurring or planted pines (Pinaceae). Species of the genus Rhizopogon can be distinguished easily from the other hypogeous basidiomycetes by their lacunose gleba without columella and their smooth elliptical spores; however, the limit between species is not always easy to establish. Rhizopogon luteolus, the type species of the genus, has been considered one of the species that are more abundant in Europe, as well as it has been cited in pine plantation of North and South America, different parts of Africa, Australia, and New Zealand. However, in this study, based on molecular analyses of the ITS nuclear ribosomal DNA (nrDNA) sequences (19 new sequences; 37 sequences from GenBank/UNITE, including those from type specimens), we prove that many GenBank sequences under R. luteolus were misidentified and correspond to Rhizopogon verii, a species described from Tunisia. Also, we confirm that basidiomes and ectomycorrhizae recently collected in Germany under Pinus sylvestris, as well as specimens from South of Brazil under Pinus taeda belong to R. verii. Thanks to the numerous ectomycorrhizal tips collected in Germany, a complete description of R. verii/P. sylvestris ectomycorrhiza is provided. Moreover, since in this paper the presence of R. verii in South America is here reported for the first time, a short description of basidiomes collected in Brazil, compared with collections located in different European herbaria, is included.
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http://dx.doi.org/10.1007/s00572-015-0678-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4909799PMC
July 2016

Genetic divergence and diversity in the Mona and Virgin Islands Boas, Chilabothrus monensis (Epicrates monensis) (Serpentes: Boidae), West Indian snakes of special conservation concern.

Mol Phylogenet Evol 2015 Jul 30;88:144-53. Epub 2015 Mar 30.

Bureau of Fisheries and Wildlife, Department of Natural and Environmental Resources, P.O. Box 366147, San Juan, PR 00936-6147, USA; Center for Applied Tropical Ecology and Conservation, University of Puerto Rico, P.O. Box 23341, Río Piedras, PR 00931-3341, USA. Electronic address:

Habitat fragmentation reduces the extent and connectivity of suitable habitats, and can lead to changes in population genetic structure. Limited gene flow among isolated demes can result in increased genetic divergence among populations, and decreased genetic diversity within demes. We assessed patterns of genetic variation in the Caribbean boa Chilabothrus monensis (Epicrates monensis) using two mitochondrial and seven nuclear markers, and relying on the largest number of specimens of these snakes examined to date. Two disjunct subspecies of C. monensis are recognized: the threatened C. m. monensis, endemic to Mona Island, and the rare and endangered C. m. granti, which occurs on various islands of the Puerto Rican Bank. Mitochondrial and nuclear markers revealed unambiguous genetic differences between the taxa, and coalescent species delimitation methods indicated that these snakes likely are different evolutionary lineages, which we recognize at the species level, C. monensis and C. granti. All examined loci in C. monensis (sensu stricto) are monomorphic, which may indicate a recent bottleneck event. Each population of C. granti exclusively contains private mtDNA haplotypes, but five of the seven nuclear genes assayed are monomorphic, and nucleotide diversity is low in the two remaining markers. The faster pace of evolution of mtDNA possibly reflects the present-day isolation of populations of C. granti, whereas the slower substitution rate of nuDNA may instead mirror the relatively recent episodes of connectivity among the populations facilitated by the lower sea level during the Pleistocene. The small degree of overall genetic variation in C. granti suggests that demes of this snake could be managed as a single unit, a practice that would significantly increase their effective population size.
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http://dx.doi.org/10.1016/j.ympev.2015.03.019DOI Listing
July 2015

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi.

Database (Oxford) 2014 30;2014. Epub 2014 Jun 30.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA, CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands, Department of Pharmaceutical Sciences - Microbiology, Università degli Studi di Perugia, Perugia, Italy, Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School-Westmead Hospital, The University of Sydney, Westmead Millennium Institute, Westmead, Australia, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden, Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37920, USA, Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA, Mycology Section, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK, Natural History Museum, University of Tartu, 46 Vanemuise, 51014 Tartu, Estonia, Purdue University, Department of Botany and Plant Pathology, 915 W. State Street, West Lafayette, IN 47907, USA, Institute of Excellence in Fungal Research, and School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand, Imperial College London, Royal Botanic Gardens, Kew TW9 3DS, England, UK, Muséum National d'Histoire Naturelle, Dépt. Systématique et Evolution CP39, UMR7205, 12 Rue Buffon, F-75005 Paris, France, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, P. R. China, Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid 28040, Spain, Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806 Görlitz, Germany, Department of Microbiology and Plant Pathology, Forestry Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0001, South Africa, Real Jardín Botánico, RJB-CSIC,

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi. Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353.
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http://dx.doi.org/10.1093/database/bau061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4075928PMC
February 2015

Phylogeny, character evolution, and biogeography of Cuscuta (dodders; Convolvulaceae) inferred from coding plastid and nuclear sequences.

Am J Bot 2014 Apr 31;101(4):670-90. Epub 2014 Mar 31.

Department of Biology, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.

Premise Of The Study: The parasitic genus Cuscuta, containing some 200 species circumscribed traditionally in three subgenera, is nearly cosmopolitan, occurring in a wide range of habitats and hosts. Previous molecular studies, on subgenera Grammica and Cuscuta, delimited major clades within these groups. However, the sequences used were unalignable among subgenera, preventing the phylogenetic comparison across the genus.

Methods: We conducted a broad phylogenetic study using rbcL and nrLSU sequences covering the morphological, physiological, and geographical diversity of Cuscuta. We used parsimony methods to reconstruct ancestral states for taxonomically important characters. Biogeographical inferences were obtained using statistical and Bayesian approaches.

Key Results: Four well-supported major clades are resolved. Two of them correspond to subgenera Monogynella and Grammica. Subgenus Cuscuta is paraphyletic, with section Pachystigma sister to subgenus Grammica. Previously described cases of strongly supported discordance between plastid and nuclear phylogenies, interpreted as reticulation events, are confirmed here and three new cases are detected. Dehiscent fruits and globose stigmas are inferred as ancestral character states, whereas the ancestral style number is ambiguous. Biogeographical reconstructions suggest an Old World origin for the genus and subsequent spread to the Americas as a consequence of one long-distance dispersal.

Conclusions: Hybridization may play an important yet underestimated role in the evolution of Cuscuta. Our results disagree with scenarios of evolution (polarity) previously proposed for several taxonomically important morphological characters, and with their usage and significance. While several cases of long-distance dispersal are inferred, vicariance or dispersal to adjacent areas emerges as the dominant biogeographical pattern.
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http://dx.doi.org/10.3732/ajb.1300449DOI Listing
April 2014

Subnanometer local temperature probing and remotely controlled drug release based on azo-functionalized iron oxide nanoparticles.

Nano Lett 2013 Jun 9;13(6):2399-406. Epub 2013 May 9.

Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy.

Local heating can be produced by iron oxide nanoparticles (IONPs) when exposed to an alternating magnetic field (AMF). To measure the temperature profile at the nanoparticle surface with a subnanometer resolution, here we present a molecular temperature probe based on the thermal decomposition of a thermo-sensitive molecule, namely, azobis[N-(2-carboxyethyl)-2-methylpropionamidine]. Fluoresceineamine (FA) was bound to the azo molecule at the IONP surface functionalized with poly(ethylene glycol) (PEG) spacers of different molecular weights. Significant local heating, with a temperature increase up to 45 °C, was found at distances below 0.5 nm from the surface of the nanoparticle, which decays exponentially with increasing distance. Furthermore, the temperature increase was found to scale linearly with the applied field at all distances. We implemented these findings in an AMF-triggered drug release system in which doxorubicin was covalently linked at different distances from the IONP surface bearing the same thermo-labile azo molecule. We demonstrated the AMF triggered distance-dependent release of the drug in a cytotoxicity assay on KB cancer cells.
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http://dx.doi.org/10.1021/nl400188qDOI Listing
June 2013

Variational optical flow estimation based on stick tensor voting.

IEEE Trans Image Process 2013 Jul 20;22(7):2589-99. Epub 2013 Mar 20.

Department of Computer Science and Mathematics, Rovira i Virgili University, Tarragona 43007, Spain.

Variational optical flow techniques allow the estimation of flow fields from spatio-temporal derivatives. They are based on minimizing a functional that contains a data term and a regularization term. Recently, numerous approaches have been presented for improving the accuracy of the estimated flow fields. Among them, tensor voting has been shown to be particularly effective in the preservation of flow discontinuities. This paper presents an adaptation of the data term by using anisotropic stick tensor voting in order to gain robustness against noise and outliers with significantly lower computational cost than (full) tensor voting. In addition, an anisotropic complementary smoothness term depending on directional information estimated through stick tensor voting is utilized in order to preserve discontinuity capabilities of the estimated flow fields. Finally, a weighted non-local term that depends on both the estimated directional information and the occlusion state of pixels is integrated during the optimization process in order to denoise the final flow field. The proposed approach yields state-of-the-art results on the Middlebury benchmark.
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http://dx.doi.org/10.1109/TIP.2013.2253481DOI Listing
July 2013

Elevated IL-1β and IL-6 levels in lumbar herniated discs in patients with sciatic pain.

Eur Spine J 2013 Apr 27;22(4):714-20. Epub 2012 Sep 27.

Department of Neurosurgery, Maastricht University Medical Center, Maastricht, The Netherlands.

Purpose: Previous experimental models have shown that proinflammatory cytokines modulate peripheral and central nociception. However, the direct correlation between inflammation and pain in patients remains unclear. Our aim is to correlate the levels of inflammation in the spine with pre- and postoperative pain scores after discectomy.

Methods: Paravertebral muscle, annulus fibrosus (AF) and nucleus pulposus (NP) biopsies were intraoperatively collected from ten lumbar disc hernia (LDH) patients suffering from chronic sciatic pain and, as painless controls, five scoliosis patients. IL-1β and IL-6 expressions in these biopsies were assessed by qPCR and western blot. The amount of pain, indicated on a 0-10 point visual analogue scale (VAS), was assessed 1 day before surgery and 6 weeks and 1 year after surgery. For analysis purposes, LDH patients were grouped into painful (VAS ≥ 3.5) and non-painful (VAS < 3.5). LDH painful patient group showed a onefold increased mRNA expression of IL-1β in the NP, and IL-6 in the AF and NP (p < 0.05 vs. controls).

Results: By western blot analysis, both cytokines were clearly visible in all LDH biopsies, but not in controls. However, cytokine expression of the painful patient group did not differ from those of the non-painful patient group. In addition, there was no correlation between VAS scores and either marker.

Conclusions: These findings support the idea that LDH is accompanied by a local inflammatory process. Yet, the lack of correlation between IL-1β or IL-6 expression and the severity pain suggests that these cytokines may not play a leading role in maintaining a pain generating network.
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http://dx.doi.org/10.1007/s00586-012-2502-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631043PMC
April 2013

On the brink of holoparasitism: plastome evolution in dwarf mistletoes (Arceuthobium, Viscaceae).

J Mol Evol 2009 Jun 29;68(6):603-15. Epub 2009 May 29.

Department of Plant Biology, Southern Illinois University, Carbondale, IL 62901-6509, USA.

Chloroplast sequences spanning rps7 to 23S rDNA in Arceuthobium campylopodum and A. pendens were generated and compared to Arabidopsis and seven other parasitic plants. Pseudogenes for trnV, trnI (GAU), and trnA (UGC) were seen in both Arceuthobium species, paralleling the situation in the holoparasite Epifagus (Orobanchaceae). These tRNA genes were intact, however, in two other members of Santalales (Ximenia and Phoradendron). The 16S-23S rDNA intergenic spacer was sequenced for 13 additional species of Arceuthobium representing both Old and New World taxa. All species examined had pseudogenes for trnI and trnA, however, deletions in these tRNAs have occurred in different regions among various lineages of the genus. The aligned 16S-23S rDNA intergenic spacer was analyzed using maximum parsimony and compared with nuclear ITS rDNA using a similar suite of species. Overall species relationships were generally congruent, although two cases of potential lineage sorting or chloroplast capture were detected. Arceuthobium is a valuable genetic model to contrast with holoparasites because, despite significant alteration and truncation of its plastome, it still maintains photosynthetic function.
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http://dx.doi.org/10.1007/s00239-009-9224-7DOI Listing
June 2009

Phylogenetic relationships among plant and animal parasites, and saprotrophs in Aphanomyces (Oomycetes).

Fungal Genet Biol 2009 May 21;46(5):365-76. Epub 2009 Feb 21.

Real Jardín Botánico CSIC, Madrid, Spain.

Molecular phylogenetic relationships among 12 species of Aphanomyces de Bary (Oomycetes) were analyzed based on 108 ITS sequences of nuclear rDNA. Sequences used in the analyses belonged to the major species currently available in pure culture and GenBank. Bayesian, maximum likelihood, and maximum parsimony analyses support that Aphanomyces constitutes a monophyletic group. Three independent lineages were found: (i) plant parasitic, (ii) animal parasitic, and (iii) saprotrophic or opportunistic parasitic. Sexual reproduction appeared to be critical in plant parasites for survival in soil environments while asexual reproduction seemed to be advantageous for exploiting specialization in animal parasitism. Repeated zoospore emergence seems to be an advantageous property for both plant and animal parasitic modes of life. Growth in unspecific media was generally faster in saprotrophs compared with parasitic species. A number of strains and GenBank sequences were found to be misidentified. It was confirmed molecularly that Aphanomyces piscicida and Aphanomyces invadans appear to be conspecific, and found that Aphanomyces iridis and Aphanomyces euteiches are closely related, if not the same, species. This study has shown a clear evolutionary separation between Aphanomyces species that are plant parasites and those that parasitize animals. Saprotrophic or opportunistic species formed a separate evolutionary lineage except Aphanomyces stellatus whose evolutionary position has not yet been resolved.
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http://dx.doi.org/10.1016/j.fgb.2009.02.004DOI Listing
May 2009

Changes in myocardial electrical impedance in human heart graft rejection.

Eur J Heart Fail 2008 Jun 23;10(6):594-600. Epub 2008 May 23.

Department of Cardiology, Hospital de la Santa Creu i Sant Pau, Autonomous University of Barcelona, Barcelona, Spain.

Background: Monitoring of post-transplant heart rejection is currently based on endomyocardial biopsy analysis. This study aimed to assess the effects of heart graft rejection on myocardial electrical impedance.

Methods And Results: Twenty-nine cardiac transplant patients and 9 controls underwent measurement of myocardial electrical impedance using a specifically designed amplifying system. The module and phase angle of myocardial impedance were measured. Histopathological rejection grading was performed according to ISHLT classification. Fifty impedance tests were performed in transplanted patients. Myocardial impedance (Z) was higher in controls than in transplanted patients (p<0.001) and followed a progressive decline at increasing current frequencies (p<0.001). Likewise, the phase angle of impedance in controls ranged from positive values at low frequencies to negative values at higher frequencies (from 2.5+/-0.9 degrees at 10 kHz to -3.8+/-2.1 degrees at 300 kHz, p<0.001). Rejection was associated with a significant decrease in myocardial impedance (Z) (15+/-6.6 Omega in grade 0, 13+/-6.0 Omega in grade 1A, and 3.3+/-0.9 Omega in grade 3A at 10 kHz, p<0.003).

Conclusions: Mild degrees of cardiac graft rejection are associated with significant changes in myocardial electrical impedance in transplant patients. Further clinical investigation is warranted to assess the potential of cardiac impedance to detect heart graft rejection.
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http://dx.doi.org/10.1016/j.ejheart.2008.04.013DOI Listing
June 2008

Orthodontic tooth movement after different coxib therapies.

Eur J Orthod 2007 Dec 18;29(6):596-9. Epub 2007 Sep 18.

Departamento de Cirugia y Especialidades Medico-Quirurgicas, Servicio de Ortodoncia, Universidad de Oviedo, C/Catedrático José Serrano, 33006 Oviedo, Spain.

Anti-inflammatory substances used for treatment of pain and discomfort related to orthodontic treatment (OT) could slow down tooth movement. Selective cyclooxygenase-2 inhibitors are an alternative to conventional non-steroidal anti-inflammatory drugs. The aim of this study was to compare different coxibs on dental movement in the rat. Twenty-eight Wistar male rats (3 months old) divided into four experimental groups were studied: (1) Five rats underwent a 50 g coil spring implantation and received three injections of 0.5 mg/kg body weight (bw) of Rofecoxib in the maxillary gingiva, close to the first molar, on the day of implantation and after 3 and 5 days. Similar procedures were carried out (2) on six animals receiving 8 mg/kg bw of Celecoxib and (3) on five animals receiving 25 mg/kg bw of Parecoxib. (4) For the controls, 12 rats received the same OT but only equivolumetric 0.9 per cent saline solution injections. Tooth movement was measured on lateral cranial teleradiographs after 10 days of treatment. Non-parametric standard techniques (Wilcoxon, H, and Mann-Whitney, U) were used for statistical analysis. Mesial tooth displacement in the control animals was 0.33 +/- 0.07 mm. While no movement was found in rats treated with Rofecoxib, the Celecoxib- and Parecoxib-treated rats showed tooth movement of 0.42 +/- 0.09 mm and 0.22 +/- 0.04 mm, respectively. The differences were statistically significant (H = 13.07; P < 0.004). Celecoxib and Parecoxib, but not Rofecoxib, seem appropriate for discomfort and pain relief while avoiding interference during tooth movement.
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http://dx.doi.org/10.1093/ejo/cjm072DOI Listing
December 2007

Heterochromatin and rDNA sites distribution in the holocentric chromosomes of Cuscuta approximata Bab. (Convolvulaceae).

Genome 2004 Feb;47(1):134-40

Department of Botany, Federal University of Pernambuco, Pernambuco, Brazil.

Cuscuta is a widely distributed genus of holoparasitic plants. Holocentric chromosomes have been reported only in species of one of its subgenera (Cuscuta subg. Cuscuta). In this work, a representative of this subgenus, Cuscuta approximata, was investigated looking for its mitotic and meiotic chromosome behaviour and the heterochromatin distribution. The mitotic chromosomes showed neither primary constriction nor Rabl orientation whereas the meiotic ones exhibited the typical quadripartite structure characteristic of holocentrics, supporting the assumption of holocentric chromosomes as a synapomorphy of Cuscuta subg. Cuscuta. Chromosomes and interphase nuclei displayed many heterochromatic blocks that stained deeply with hematoxylin, 4',6-diamidino-2-phenylindole (DAPI), or after C banding. The banded karyotype showed terminal or subterminal bands in all chromosomes and central bands in some of them. The single pair of 45S rDNA sites was observed at the end of the largest chromosome pair, close to a DAPI band and a 5S rDNA site. Two other 5S rDNA site pairs were found, both closely associated with DAPI bands. The noteworthy giant nuclei of glandular cells of petals and ovary wall exhibited large chromocentres typical of polytenic nuclei. The chromosomal location of heterochromatin and rDNA sites and the structure of the endoreplicated nuclei of C. approximata seemed to be similar to those known in monocentric nuclei, suggesting that centromeric organization has little or no effect on chromatin organization.
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http://dx.doi.org/10.1139/g03-098DOI Listing
February 2004

Extensive intraindividual variation in plastid rDNA sequences from the holoparasite Cynomorium coccineum (Cynomoriaceae).

J Mol Evol 2004 Mar;58(3):322-32

Real Jardín Botánico, CSIC, Plaza de Murillo 2, 28014-Madrid, Spain.

Ribosomal genes are considered to have a high degree of sequence conservation between species and also at higher taxonomic levels. In this paper we document a case where a single individual of Cynomorium coccineum (Cynomoriaceae), a nonphotosynthetic holoparasitic plant, contains highly divergent plastid ribosomal genes. PCR amplification a nearly complete ribosomal DNA cistron was performed using genomic DNA, the products cloned, and the 23S rDNA genes were sequenced from 19 colonies. Of these, five distinct types were identified. Fifteen of the sequences were nearly identical (11 or fewer differences) and these were designated Type I. The remaining types (II-V) were each represented by a single clone and differed from Type I by 93 to 255 changes. Compared with green vascular plants, we found that there are more substitutional differences in the 23S rDNA sequences within a single individual of Cynomorium than among all sequenced photosynthetic vascular plants. Several trends of molecular evolution observed in 16S rDNA from other holoparasitic angiosperms and heterotrophic green algae have been also observed in Cynomorium 23S rDNA. Higher-order structures were constructed for representatives of the five clone types, and in all cases these possessed complete complements of the major structural elements present in functional plastid 23S rRNAs. These data indicate that such molecules may be subject to purifying selection, thus providing indirect evidence that they have retained some degree of functionality. This intraindividual polymorphism is probably a case of plastid heteroplasmy but translocation of ribosomal cistrons to the nucleus or mitochondria has not been tested and therefore cannot be ruled out.
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http://dx.doi.org/10.1007/s00239-003-2554-yDOI Listing
March 2004

A phylogeny of all species of Arceuthobium (Viscaceae) using nuclear and chloroplast DNA sequences.

Am J Bot 2004 Jan;91(1):125-38

Department of Plant Biology and Center for Systematic Biology, Southern Illinois University, Carbondale, Illinois 62901-6509 USA;

The genus Arceuthobium (dwarf mistletoes, Viscaceae) comprises 42 species that parasitize hosts in Pinaceae and Cupressaceae in the Old and New Worlds. Maximum parsimony analyses were conducted on two data partitions (separately and combined): nuclear ribosomal internal transcribed spacer (ITS) sequences for all 42 currently recognized species and chloroplast trnT-L-F sequences for 34 New World species. The Old and New World species were phylogenetically distinct using ITS, thus making subgenus Arceuthobium paraphyletic. Arceuthobium pendens and A. guatemalense comprise the basalmost clade of subgenus Vaginata, characterized by the presence of flabellate secondary branching. The trnT-L-F sequences, which vary widely in length depending upon taxon, contain three times less phylogenetic signal than ITS, although homoplasy for this partition is lower. Several of the clades obtained from analysis of nuclear ITS sequences are also recovered using trnT-L-F sequences such as A. guatemalense and A. pendens, the A. rubrum group, the A. vaginatum group, and the A. campylopodum group. The ITS + trnT-L-F tree is well resolved except for four internal nodes. A revised classification of the genus is discussed that recognizes only monophyletic species that are well differentiated by molecular data.
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http://dx.doi.org/10.3732/ajb.91.1.125DOI Listing
January 2004

Phylogeography of New World isolates of Anaplasma marginale based on major surface protein sequences.

Vet Microbiol 2002 Sep;88(3):275-85

Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, 250 McElroy Hall, Stillwater, OK 74078, USA.

Gene and protein sequences of major surface proteins (MSP) 1a and 4 of Anaplasma marginale (Rickettsiales: Anaplasmataceae) were used to infer phylogenetic relationships between New World isolates from Argentina, Brazil, Mexico and the United States. Seventeen isolates of A. marginale plus two outgroup taxa (A. centrale and A. ovis) were used for maximum-parsimony analysis of MSP4, while 20 isolates were used for phylogenetic analysis of MSP1a. msp4 analysis provided strong bootstrap support for a Latin American clade and, within this clade, support was detected for Mexican and South American clades. Isolates of A. marginale from the United States also grouped into two clades from the southern (isolates from Florida, Mississippi, and Virginia) and west-central (isolates from California, Idaho, Illinois, Oklahoma, and Texas) states. Although little phylogeographic resolution was detected within these higher clades, msp4 sequences appear to be a good genetic marker for inferring phylogeographic patterns of A. marginale isolates. In contrast to the phylogeographic resolution provided by msp4, MSP1a DNA and protein sequence were quite variable and did not provide phylogeographic resolution. Most variation in MSP1a sequences appeared unique to a given isolate and similar DNA sequence variation in msp1alpha was detected within isolates from Idaho and Florida and from Idaho and Argentina. The results of these studies demonstrated that msp4 provided phylogenetic information on the evolution of A. marginale isolates. In contrast MSP1a sequences appeared to be rapidly evolving and these sequences may provide phylogeographic information only when numerous isolate MSP1a sequences are analyzed from a geographic area.
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http://dx.doi.org/10.1016/s0378-1135(02)00122-0DOI Listing
September 2002
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