107 research outputs found
Genetic Structure Among 50 Species of the Northeastern Pacific Rocky Intertidal Community
Comparing many species' population genetic patterns across the same seascape can identify species with different levels of structure, and suggest hypotheses about the processes that cause such variation for species in the same ecosystem. This comparative approach helps focus on geographic barriers and selective or demographic processes that define genetic connectivity on an ecosystem scale, the understanding of which is particularly important for large-scale management efforts. Moreover, a multispecies dataset has great statistical advantages over single-species studies, lending explanatory power in an effort to uncover the mechanisms driving population structure. Here, we analyze a 50-species dataset of Pacific nearshore invertebrates with the aim of discovering the most influential structuring factors along the Pacific coast of North America. We collected cytochrome c oxidase I (COI) mtDNA data from populations of 34 species of marine invertebrates sampled coarsely at four coastal locations in California, Oregon, and Alaska, and added published data from 16 additional species. All nine species with non-pelagic development have strong genetic structure. For the 41 species with pelagic development, 13 show significant genetic differentiation, nine of which show striking FST levels of 0.1–0.6. Finer scale geographic investigations show unexpected regional patterns of genetic change near Cape Mendocino in northern California for five of the six species tested. The region between Oregon and Alaska is a second focus of intraspecific genetic change, showing differentiation in half the species tested. Across regions, strong genetic subdivision occurs more often than expected in mid-to-high intertidal species, a result that may reflect reduced gene flow due to natural selection along coastal environmental gradients. Finally, the results highlight the importance of making primary research accessible to policymakers, as unexpected barriers to marine dispersal break the coast into separate demographic zones that may require their own management plans
A novel extracellular role for tissue transglutaminase in matrix-bound VEGF-mediated angiogenesis
The importance of tissue transglutaminase (TG2) in angiogenesis is unclear and contradictory. Here we show that inhibition of extracellular TG2 protein crosslinking or downregulation of TG2 expression leads to inhibition of angiogenesis in cell culture, the aorta ring assay and in vivo models. In a human umbilical vein endothelial cell (HUVEC) co-culture model, inhibition of extracellular TG2 activity can halt the progression of angiogenesis, even when introduced after tubule formation has commenced and after addition of excess vascular endothelial growth factor (VEGF). In both cases, this leads to a significant reduction in tubule branching. Knockdown of TG2 by short hairpin (shRNA) results in inhibition of HUVEC migration and tubule formation, which can be restored by add back of wt TG2, but not by the transamidation-defective but GTP-binding mutant W241A. TG2 inhibition results in inhibition of fibronectin deposition in HUVEC monocultures with a parallel reduction in matrix-bound VEGFA, leading to a reduction in phosphorylated VEGF receptor 2 (VEGFR2) at Tyr1214 and its downstream effectors Akt and ERK1/2, and importantly its association with b1 integrin. We propose a mechanism for the involvement of matrix-bound VEGFA in angiogenesis that is dependent on extracellular TG2-related activity
The Hubbard model within the equations of motion approach
The Hubbard model has a special role in Condensed Matter Theory as it is
considered as the simplest Hamiltonian model one can write in order to describe
anomalous physical properties of some class of real materials. Unfortunately,
this model is not exactly solved except for some limits and therefore one
should resort to analytical methods, like the Equations of Motion Approach, or
to numerical techniques in order to attain a description of its relevant
features in the whole range of physical parameters (interaction, filling and
temperature). In this manuscript, the Composite Operator Method, which exploits
the above mentioned analytical technique, is presented and systematically
applied in order to get information about the behavior of all relevant
properties of the model (local, thermodynamic, single- and two- particle ones)
in comparison with many other analytical techniques, the above cited known
limits and numerical simulations. Within this approach, the Hubbard model is
shown to be also capable to describe some anomalous behaviors of the cuprate
superconductors.Comment: 232 pages, more than 300 figures, more than 500 reference
Out of Their Depth? Isolated Deep Populations of the Cosmopolitan Coral Desmophyllum dianthus May Be Highly Vulnerable to Environmental Change
Deep sea scleractinian corals will be particularly vulnerable to the effects of
climate change, facing loss of up to 70% of their habitat as the
Aragonite Saturation Horizon (below which corals are unable to form calcium
carbonate skeletons) rises. Persistence of deep sea scleractinian corals will
therefore rely on the ability of larvae to disperse to, and colonise, suitable
shallow-water habitat. We used DNA sequence data of the internal transcribed
spacer (ITS), the mitochondrial ribosomal subunit (16S) and mitochondrial
control region (MtC) to determine levels of gene flow both within and among
populations of the deep sea coral Desmophyllum dianthus in SE
Australia, New Zealand and Chile to assess the ability of corals to disperse
into different regions and habitats. We found significant genetic subdivision
among the three widely separated geographic regions consistent with isolation
and limited contemporary gene flow. Furthermore, corals from different depth
strata (shallow <600 m, mid 1000–1500 m, deep >1500 m) even on the
same or nearby seamounts were strongly differentiated, indicating limited
vertical larval dispersal. Genetic differentiation with depth is consistent with
the stratification of the Subantarctic Mode Water, Antarctic Intermediate Water,
the Circumpolar Deep and North Pacific Deep Waters in the Southern Ocean, and we
propose that coral larvae will be retained within, and rarely migrate among,
these water masses. The apparent absence of vertical larval dispersal suggests
deep populations of D. dianthus are unlikely to colonise
shallow water as the aragonite saturation horizon rises and deep waters become
uninhabitable. Similarly, assumptions that deep populations will act as refuges
for shallow populations that are impacted by activities such as fishing or
mining are also unlikely to hold true. Clearly future environmental management
strategies must consider both regional and depth-related isolation of deep-sea
coral populations
Molecular Approach to the Identification of Fish in the South China Sea
BACKGROUND: DNA barcoding is one means of establishing a rapid, accurate, and cost-effective system for the identification of species. It involves the use of short, standard gene targets to create sequence profiles of known species against sequences of unknowns that can be matched and subsequently identified. The Fish Barcode of Life (FISH-BOL) campaign has the primary goal of gathering DNA barcode records for all the world's fish species. As a contribution to FISH-BOL, we examined the degree to which DNA barcoding can discriminate marine fishes from the South China Sea. METHODOLOGY/PRINCIPAL FINDINGS: DNA barcodes of cytochrome oxidase subunit I (COI) were characterized using 1336 specimens that belong to 242 species fishes from the South China Sea. All specimen provenance data (including digital specimen images and geospatial coordinates of collection localities) and collateral sequence information were assembled using Barcode of Life Data System (BOLD; www.barcodinglife.org). Small intraspecific and large interspecific differences create distinct genetic boundaries among most species. In addition, the efficiency of two mitochondrial genes, 16S rRNA (16S) and cytochrome b (cytb), and one nuclear ribosomal gene, 18S rRNA (18S), was also evaluated for a few select groups of species. CONCLUSIONS/SIGNIFICANCE: The present study provides evidence for the effectiveness of DNA barcoding as a tool for monitoring marine biodiversity. Open access data of fishes from the South China Sea can benefit relative applications in ecology and taxonomy
X-Ray Phase-Contrast Tomography of Renal Ischemia-Reperfusion Damage
Purpose: The aim of the study was to investigate microstructural changes occurring in unilateral renal ischemia-reperfusion injury in a murine animal model using synchrotron radiation. Material and Methods: The effects of renal ischemia-reperfusion were investigated in a murine animal model of unilateral ischemia. Kidney samples were harvested on day 18. Grating-Based Phase-Contrast Imaging (GB-PCI) of the paraffin-embedded kidney samples was performed at a Synchrotron Radiation Facility (beam energy of 19 keV). To obtain phase information, a two-grating Talbot interferometer was used applying the phase stepping technique. The imaging system provided an effective pixel size of 7.5 mu m. The resulting attenuation and differential phase projections were tomographically reconstructed using filtered back-projection. Semi-automated segmentation and volumetry and correlation to histopathology were performed. Results: GB-PCI provided good discrimination of the cortex, outer and inner medulla in non-ischemic control kidneys. Post-ischemic kidneys showed a reduced compartmental differentiation, particularly of the outer stripe of the outer medulla, which could not be differentiated from the inner stripe. Compared to the contralateral kidney, after ischemia a volume loss was detected, while the inner medulla mainly retained its volume (ratio 0.94). Post-ischemic kidneys exhibited severe tissue damage as evidenced by tubular atrophy and dilatation, moderate inflammatory infiltration, loss of brush borders and tubular protein cylinders. Conclusion: In conclusion GB-PCI with synchrotron radiation allows for non-destructive microstructural assessment of parenchymal kidney disease and vessel architecture. If translation to lab-based approaches generates sufficient density resolution, and with a time-optimized image analysis protocol, GB-PCI may ultimately serve as a non-invasive, non-enhanced alternative for imaging of pathological changes of the kidney
Desmophyllum dianthus (Esper, 1794) in the scleractinian phylogeny and its intraspecific diversity
© The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 7 (2012): e50215, doi:10.1371/journal.pone.0050215.The cosmopolitan solitary deep-water scleractinian coral Desmophyllum dianthus (Esper, 1794) was selected as a representative model species of the polyphyletic Caryophylliidae family to (1) examine phylogenetic relationships with respect to the principal Scleractinia taxa, (2) check population structure, (3) test the widespread connectivity hypothesis and (4) assess the utility of different nuclear and mitochondrial markers currently in use. To carry out these goals, DNA sequence data from nuclear (ITS and 28S) and mitochondrial (16S and COI) markers were analyzed for several coral species and for Mediterranean populations of D. dianthus. Three phylogenetic methodologies (ML, MP and BI), based on data from the four molecular markers, all supported D. dianthus as clearly belonging to the “robust” clade, in which the species Lophelia pertusa and D. dianthus not only grouped together, but also shared haplotypes for some DNA markers. Molecular results also showed shared haplotypes among D. dianthus populations distributed in regions separated by several thousands of kilometers and by clear geographic barriers. These results could reflect limited molecular and morphological taxonomic resolution rather than real widespread connectivity. Additional studies are needed in order to find molecular markers and morphological features able to disentangle the complex phylogenetic relationship in the Order Scleractinia and to differentiate isolated populations, thus avoiding the homoplasy found in some morphological characters that are still considered in the literature.This study was funded by CTM2009-00496 and CGL2011-23306 projects of the “Ministerio de Ciencia e Innovación” (Spain). Research at sea was partly supported by the European Commission F. P.VI Project HERMES Contract No. GOCE-CT-2005-511234-1) and the EU F.P. VII Project HERMIONE(contract number no. 226354)
Population genomics of marine zooplankton
Author Posting. © The Author(s), 2017. This is the author's version of the work. It is posted here for personal use, not for redistribution. The definitive version was published in Bucklin, Ann et al. "Population Genomics of Marine Zooplankton." Population Genomics: Marine Organisms. Ed. Om P. Rajora and Marjorie Oleksiak. Springer, 2018. doi:10.1007/13836_2017_9.The exceptionally large population size and cosmopolitan biogeographic distribution that
distinguish many – but not all – marine zooplankton species generate similarly exceptional patterns of
population genetic and genomic diversity and structure. The phylogenetic diversity of zooplankton has
slowed the application of population genomic approaches, due to lack of genomic resources for closelyrelated
species and diversity of genomic architecture, including highly-replicated genomes of many
crustaceans. Use of numerous genomic markers, especially single nucleotide polymorphisms (SNPs), is
transforming our ability to analyze population genetics and connectivity of marine zooplankton, and
providing new understanding and different answers than earlier analyses, which typically used
mitochondrial DNA and microsatellite markers. Population genomic approaches have confirmed that,
despite high dispersal potential, many zooplankton species exhibit genetic structuring among geographic
populations, especially at large ocean-basin scales, and have revealed patterns and pathways of population
connectivity that do not always track ocean circulation. Genomic and transcriptomic resources are
critically needed to allow further examination of micro-evolution and local adaptation, including
identification of genes that show evidence of selection. These new tools will also enable further
examination of the significance of small-scale genetic heterogeneity of marine zooplankton, to
discriminate genetic “noise” in large and patchy populations from local adaptation to environmental
conditions and change.Support was provided by the
US National Science Foundation to AB and RJO (PLR-1044982) and to RJO (MCB-1613856); support to
IS and MC was provided by Nord University (Norway)
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