Interactive Local Super-Resolution Reconstruction of Whole-Body MRI Mouse Data: A Pilot Study with Applications to Bone and Kidney Metastases

In small animal imaging studies, when the locations of the micro-structures of interest are unknown a priori, there is a simultaneous need for full-body coverage and high resolution. In MRI, additional requirements to image contrast and acquisition time will often make it impossible to acquire such images directly. Recently, a resolution enhancing post-processing technique called super-resolution reconstruction (SRR) has been demonstrated to improve visualization and localization of micro-structures in small animal MRI by combining multiple low-resolution acquisitions. However, when the field-of-view is large relative to the desired voxel size, solving the SRR problem becomes very expensive, in terms of both memory requirements and computation time. In this paper we introduce a novel local approach to SRR that aims to overcome the computational problems and allow researchers to efficiently explore both global and local characteristics in whole-body small animal MRI. The method integrates state-of-the-art image processing techniques from the areas of articulated atlas-based segmentation, planar reformation, and SRR. A proof-of-concept is provided with two case studies involving CT, BLI, and MRI data of bone and kidney tumors in a mouse model. We show that local SRR-MRI is a computationally efficient complementary imaging modality for the precise characterization of tumor metastases, and that the method provides a feasible high-resolution alternative to conventional MRI.     

One-pot, mix-and-read peptide-MHC tetramers

Background

Cytotoxic T Lymphocytes (CTL) recognize complexes of peptide ligands and Major Histocompatibility Complex (MHC) class I molecules presented at the surface of Antigen Presenting Cells (APC). Detection and isolation of CTL''s are of importance for research on CTL immunity, and development of vaccines and adoptive immune therapy. Peptide-MHC tetramers have become important reagents for detection and enumeration of specific CTL''s. Conventional peptide-MHC-tetramer production involves recombinant MHC production, in vitro refolding, biotinylation and tetramerization; each step followed by various biochemical steps such as chromatographic purification, concentration etc. Such cumbersome production protocols have limited dissemination and restricted availability of peptide-MHC tetramers effectively precluding large-scale screening strategies involving many different peptide-MHC tetramers.

Methodology/Principal Findings

We have developed an approach whereby any given tetramer specificity can be produced within 2 days with very limited effort and hands-on time. The strategy is based on the isolation of correctly oxidized, in vivo biotinylated recombinant MHC I heavy chain (HC). Such biotinylated MHC I HC molecules can be refolded in vitro, tetramerized with streptavidin, and used for specific T cell staining-all in a one-pot reaction without any intervening purification steps.

Conclusions/Significance

We have developed an efficient “one-pot, mix-and-read” strategy for peptide-MHC tetramer generation, and demonstrated specific T cell straining comparable to a commercially available MHC-tetramer. Here, seven peptide-MHC tetramers representing four different human MHC (HLA) class I proteins have been generated. The technique should be readily extendable to any binding peptide and pre-biotinylated MHC (at this time we have over 40 different pre-biotinylated HLA proteins). It is simple, robust, and versatile technique with a very broad application potential as it can be adapted both to small- and large-scale production of one or many different peptide-MHC tetramers for T cell isolation, or epitope screening.     

Microbial biomass C,N and P in two arctic soils and responses to addition of NPK fertilizer and sugar: implications for plant nutrient uptake

The soil microbial carbon (C), nitrogen (N) and phosphorus (P) pools were quantified in the organic horizon of soils from an arctic/alpine low-altitude heath and a high-altitude fellfield by the fumigation-extraction method before and after factorial addition of sugar, NPK fertilizer and benomyl, a fungicide. In unamended soil, microbial C, N and P made up 3.3–3.6%, 6.1–7.3% and 34.7% of the total soil C, N and P content, respectively. The inorganic extractable N pool was below 0.1% and the inorganic extractable P content slightly less than 1% of the total soil pool sizes. Benomyl addition in spring and summer did not affect microbial C or nutrient content analysed in the autumn. Sugar amendments increased microbial C by 15 and 37% in the two soils, respectively, but did not affect the microbial nutrient content, whereas inorganic N and P either declined significantly or tended to decline. The increased microbial C indicates that the microbial biomass also increased but without a proportional enhancement of N and P uptake. NPK addition did not affect the amount of microbial C but almost doubled the microbial N pool and more than doubled the P pool. A separate study has shown that CO₂ evolution increased by more than 50% after sugar amendment and by about 30% after NPK and NK additions to one of the soils. Hence, the microbial biomass did not increase in response to NPK addition, but the microbes immobilized large amounts of the added nutrients and, judging by the increased CO₂ evolution, their activity increased. We conclude: (1) that microbial biomass production in these soils is stimulated by labile carbon and that the microbial activity is stimulated by both labile C and by nutrients (N); (2) that the microbial biomass is a strong sink for nutrients and that the microbial community probably can withdraw substantial amounts of nutrients from the inorganic, plant-available pool, at least periodically; (3) that temporary declines in microbial populations are likely to release a flush of inorganic nutrients to the soil, particularly P of which the microbial biomass contained more than one third of the total soil pool; and (4) that the mobilization-immobilization cycles of nutrients coupled to the population dynamics of soil organisms can be a significant regulating factor for the nutrient supply to the primary producers, which are usually strongly nutrient-limited in arctic ecosystems.     

Eight decades of sampling reveal a contemporary novel fish assemblage in coastal nursery habitats

In order to adequately monitor biodiversity trends through time and their responses to natural or anthropogenic impacts, researchers require long time series that are often unavailable. This general lack of datasets that are several decades or longer makes establishing a background or baseline of diversity metrics difficult – especially when attempting to understand species composition changes against a backdrop of climate and ecological variability. Here, we present an analysis of a community of juvenile nearshore fishes based on nearly 8 decades of highly standardized Norwegian survey records. Using multivariate statistical techniques, we: (i) characterize the change in taxonomic community composition through time, (ii) determine whether there has been an increase in warm‐water affinity species relative to their cold water affinity counterparts, and (iii) characterize the temporal change in the species’ functional trait assemblage. Our results strongly indicate a shift toward a novel fish assemblage between the late 1990s and 2000s. The context of changes within the most recent two decades is in stark contrast to those during the 1960s and 1970s, but similar to those during the previous warm period during the 1930s and 1940s. This novel assemblage is tightly linked to the warming temperatures in the region portrayed by the increased presence of warm‐water species and a higher incidence of pelagic, planktivorous species. The results indicate a clear influence of ocean temperature on the region's juvenile fish community that points to climate‐mediated effects on the species assemblages of an important fish nursery area.     

Influence of riparian forests on fish assemblages in temperate lowland streams

Environmental Biology of Fishes - The characteristics of riparian vegetation along streams vary with natural and anthropogenic factors. Deforestation for agricultural purposes has consequences for...     

Anthropogenic and natural size-related selection act in concert during brown trout (Salmo trutta) smolt river descent

Hydrobiologia - By hindering migration and inducing direct turbine mortality during downstream migration, hydropower is regarded as one of the most serious threats to anadromous salmonids. Yet,...     

Cattle grazing in CRP grasslands during the nesting season: effects on avian reproduction

Bird populations in grasslands have experienced declines coinciding with loss and fragmentation of prairies. The United States Department of Agriculture (USDA)-administered Conservation Reserve Program (CRP) is the most extensive grassland restoration program in North America and it has especially benefitted grassland birds. Grazing by domestic cattle has been restricted in CRP during avian nesting seasons despite the potential improvements in structuring habitat for a greater diversity of grassland bird species. Potential negative consequences of grazing in CRP grasslands include trampling of nests by cattle, reductions in nest concealment from predators, and attraction of brood-parasitic brown-headed cowbirds (Molothrus ater). We designed an experiment to test for effects of cattle grazing in CRP fields during the nesting season on nest survival and brood parasitism of 5 bird species that commonly nest in CRP grasslands: mourning dove (Zenaida macroura), grasshopper sparrow (Ammodramus savannarum), dickcissel (Spiza americana), and eastern (Sturnella magna) and western (S. neglecta) meadowlarks. Grazing was implemented during summers 2017 and 2018 on 17 of 36 fields followed by a year of rest on all fields in 2019. Of the 879 nests on grazed fields, only 4 were likely trampled by cattle (vs. 54% of all nests estimated as failing because of depredation). Experimental grazing (grazed vs. ungrazed fields) had variable effects on nest survival and cowbird parasitism among the bird species analyzed. Negative effects of grazing on daily nest survival of dickcissel and meadowlarks were apparent, at least in some years. We found no direct effects of grazing on nest survival of mourning dove or grasshopper sparrow. Probability and intensity (cowbird offspring/nest) of cowbird parasitism in dickcissel nests was higher on grazed versus ungrazed sites but only in conservation practice (CP) CP2 (vs. CP25 fields). Parasitism probability of grasshopper sparrow nests by cowbirds was higher on grazed fields in the 2 years after introduction of cattle in 2017. Greater vegetative concealment around nest sites was associated with reduced cowbird parasitism of meadowlark and grasshopper sparrow nests and higher nest survival for grasshopper sparrows. Reductions in vegetative height caused by longer-term or high-intensity grazing might therefore have negative consequences for some grassland birds by increasing nest site visibility and exposure to cowbird parasitism. Our results indicate that cattle grazing in CRP fields during the nesting season might have some negative effects on reproductive success of some grassland bird species, at least in the short term; however, the potential improvements of structuring habitat to accommodate more grassland bird species and increasing landowner participation in the CRP are considerable.     

Investigating the Conformational Response of the Sortilin Receptor upon Binding Endogenous Peptide- and Protein Ligands by HDX-MS

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