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opencc-by-4.0Jun 2020View details →

Fitness measures of maternal transplants (seed fitness) and of the F1 generation (rosette diameter) of three translocated populations of Arnica montana in southern Belgium

Fitness data measured in the framework of a genetic monitoring of translocated populations of the critically endangered Arnica montana. See Van Rossum et al. (2020) in Molecular Ecology for more details.

opencc-zeroJun 2020View details →

Data from: Transcriptomic plasticity of mesophotic corals among natural populations and transplants of Montastraea cavernosa in the Gulf of Mexico and Belize

While physiological responses to low-light environments have been studied among corals on mesophotic coral ecosystems worldwide (MCEs; 30–150 m), the mechanisms behind acclimatization and adaptation to depth are not well understood for most coral species. Transcriptomic approaches based on RNA sequencing are useful tools for quantifying gene expression plasticity, particularly in slow-growing species such as scleractinian corals, and for identifying potential functional differences among conspecifics. A tag-based RNA-Seq (Tag-Seq) pipeline was applied to quantify transcriptional variation in natural populations of the scleractinian coral Montastraea cavernosa from mesophotic and shallower environments across five sites in Belize and the Gulf of Mexico: Carrie Bow Cay, West and East Flower Garden Banks, Pulley Ridge, and Dry Tortugas. Regional site location was a stronger driver of gene expression patterns than depth. However, mesophotic corals among all sites shared similar regulation of metabolic and cell growth functional pathways that may represent common physiological responses to environmental conditions at depth. Additionally, in a transplant experiment at West and East Flower Garden Banks, colonies transplanted from mesophotic to shallower habitats diverged from the control mesophotic group over time, indicating depth-regulated plasticity of gene expression. When the shallower depth zone experienced a bleaching event, bleaching severity did not differ significantly between transplants and shallow controls, but gene expression patterns indicated variable regulation of stress responses among depth treatments. Coupled observational and experimental studies of gene expression among mesophotic and shallower M. cavernosa provide insights into the ability of this depth-generalist coral species to persist under varying environmental conditions.

opencc-zeroAug 2020View details →

Data from: Multi-population seedling and soil transplants show possible responses of a common tropical montane tree species (Weinmannia bangii) to climate change

A possible response of many plant species to global warming is migration to higher elevations. However, these migrations may not be required if species can tolerate higher temperatures, or may be prevented if there are other factors such as changes in soil conditions that make upslope areas unsuitable. We used a set of 3-year field transplant experiments in the remote Peruvian Andes to simulate two possible responses of an abundant tropical montane cloudforest tree species (Weinmania bangii) to global warming: (1) "upward migration", in which case seedlings of W. bangii's were grown at their current elevation/temperature but in soils transplanted from higher elevations; and (2) "migration failure", in which case seedlings were transplanted downslope along with their home soils into areas that are 1°C or 2°C warmer. We conducted separate experiments with populations from the upper/leading edge, middle and lower/trailing edges of W. bangii's elevational/thermal range to assess the influence of local adaptation on responses to changes in temperature or soil. We found that seedling survival and growth were not affected by changes in soil conditions, regardless of the origin population. However, seedling survival decreased with temperature. A simulated warming of 1°C caused a significant reduction in the survival of seedlings transplanted from the mid-range population, and 2°C warming caused a severe decrease in the survival of seedlings transplanted from both the mid-range and bottom-edge populations. Synthesis. Our findings reveal that rising temperatures are a serious threat to plants, especially in populations growing in the hotter portion of their species' range. At least in the case of W. bangii, novel soil conditions will not limit the establishment or growth of seedlings at higher elevations. As such, decreases in the survivorship at lower elevations may be offset through upward migrations as temperatures continue to increase.

opencc-zeroDec 2020View details →

Influence of polymorphisms in the vascular endothelial growth factor gene on allograft rejection after kidney transplantation: a meta-analysis

Purpose Reported associations of allograft rejection in kidney transplant patients with VEGF single nucleotide polymorphisms (SNPs) have been inconsistent between studies, which prompted a meta-analysis to obtain more precise estimates. Methods Using the PICO elements, kidney transplant patients (P) were compared by genotype data between rejectors (I) and non-rejectors (C) in order to determine the risk of allograft rejection (O) attributed to the VEGF SNPs. Literature search of four databases yielded seven articles. To calculate risks for allograft rejection, four SNPs were examined. Meta-analysis treatments included outlier and subgroup analyses, the latter was based on ethnicity (Indians/Caucasians) and rejection type (acute/chronic). Multiple comparisons were corrected with the Bonferroni test. Results Five highly significant outcomes (Pa < 0.01) survived Bonferroni correction, one of which showed reduced risk for the var allele (OR 0.61, 95% CI 0.45-0.82). The remaining four indicated increased risk for the wt allele where the chronic rejection (OR 2.10, 95% CI 1.36-3.24) and Indian (OR 1.44, 95% CI 1.13-1.84) subgroups were accorded susceptibility status. Conclusions Risk associations for renal allograft rejection were increased and reduced on account of the wt and var alleles, respectively. These findings could render the VEGF polymorphisms useful in the clinical genetics of kidney transplantation.

opencc-zeroDec 2020View details →

Data from: Climate limitation at the cold edge – contrasting perspectives from species distribution modelling and a transplant experiment

The role of climate in determining range margins is often studied using species distribution models (SDMs), which are easily applied but have well-known limitations, e.g. due to their correlative nature and colonization and extinction time lags. Transplant experiments can give more direct information on environmental effects, but often cover small spatial and temporal scales. We simultaneously applied an SDM using high-resolution spatial predictors and an integral projection (demographic) model based on a transplant experiment at 58 sites to examine the effects of microclimate, light and soil conditions on the distribution and performance of a forest herb, Lathyrus vernus, at its cold range margin in central Sweden. In the SDM, occurrences were strongly associated with warmer climates. In contrast, only weak effects of climate were detected in the transplant experiment, whereas effects of soil conditions and light dominated. The higher contribution of climate in the SDM is likely a result from its correlation with soil quality, forest type, and potentially historic land use, which were unaccounted for in the model. Predicted habitat suitability and population growth rate, yielded by the two approaches, were not correlated across the transplant sites. We argue that the ranking of site habitat suitability is probably more reliable in the transplant experiment than in the SDM because predictors in the former better describe understory conditions, but that ranking might vary among years, e.g. due to differences in climate. Our results suggest that L. vernus is limited by soil and light rather than directly by climate at its northern range edge, where conifers dominate forests and create suboptimal conditions of soil and canopy-penetrating light. A general implication of our study is that to better understand how climate change influences range dynamics, we should not only strive to improve existing approaches but also to use multiple approaches in concert.

opencc-zeroJan 2020View details →

Disentangling the effects of methanogen community and environment on peatland greenhouse gas production by a reciprocal transplant experiment

1. Northern peatlands consist of a mosaic of peatland types that vary spatially and temporally and differ in their methane (CH4) production. Microbial community composition and environment both potentially control the processes that release carbon from anoxic peat either as CH4 or carbon dioxide (CO2), a less potent greenhouse gas than CH4. However, the respective roles of these controls remain unclear, which prevents incorporating microbes in the predictions of peatland CH4 emissions. 2. Here, a reciprocal transplant experiment was carried out to separate the influences of microbial community and environment in CH4 and anaerobic CO2 production. Peat from an acidic Sphagnum bog and a sedge fen with higher pH was enclosed in membrane bags with a pore size of 0.2 µm, preventing microbial colonization from the outside, and transplanted in the field for two months. 3. Potential CH4 production was primarily controlled by the environment. The conditions in the bog suppressed the initially higher activity of fen methanogens and reduced CH4 production by 79%. Against expectations, the inhibition was not specific to acetate-using Methanotrichaceae. Reciprocal transplantation favoured Methanosarcinaceae and potentially methylotrophic methanogenesis in general. Bog methanogens, mostly hydrogenotrophic Methanoregulaceae, retained their community structure and activity in the fen with a slight increase (+37%) in CH4 production. 4. Anaerobic CO2 production was controlled by both the microbial community and the environment. Transplantation led to increased CO2 production in both bog (+50%) and fen peat (+57%) with distinct bacterial community, showing that the new environment directed more carbon to other anaerobic processes than methanogenesis. 5. Taken together, these results relate differences in CH4 production of bogs and fens to ecophysiology of specific methanogen groups. The sensitiveness of fen methanogens to the acidic conditions in Sphagnum bogs can help explain the decrease of CH4 emission in the typical boreal peatland succession from young fens to older bogs. Increase in anaerobic CO2 vs. CH4 production with transplantation shows that disturbances of boreal peatlands can activate poorly defined pathways of anaerobic decomposition.

opencc-by-4.0Nov 2016View details →

High-resolution tracking of microbial colonization in Fecal Microbiota Transplantation experiments via metagenome-assembled genomes

This project contains anvi'o profiles and contigs databases that is used and/or referenced from the Lee STM and Khan SA, et al. study titled "High-resolution tracking of microbial colonization in Fecal Microbiota Transplantation experiments via metagenome-assembled genomes". The pre-print of this study is available via http://dx.doi.org/10.1101/090993. To be able to work with the data files you will need anvi'o v2.1.0 to be installed on your system. For installation instructions, or to have access to a Docker image for anvi'o, please visit this URL: http://merenlab.org/software/anvio Public data: <ul> <li>ANVIO-FMT-D-R01-R02-QUICK-VISUALIZATION.tar.gz: Data files for a quick visualization of the 97 MAGs and their distribution across the two FMT recipients. A run script in the archive explains how to use this data. </li> <li>ANVIO-FMT-D-R01-R02-MERGED-PROFILE.tar.gz: The merged anvi'o profile for the entire data, which also contains a collection of 97 MAGs identified in the donor. The profile database contains no hierarchical clustering of contigs, however, individual MAGs can be displayed via the following notation since the collection 'MAGs' describe the organization of contigs in each MAG referenced from the dataset `ANVIO-FMT-D-R01-R02-QUICK-VISUALIZATION`, as well as from the paper: "anvi-refine -c CONTIGS.db -p PROFILE.db -C MAGs -b FMT-Donor_MAG_00054". All MAG names are in the supplementary tables in our paper. </li> <li>ANVIO-FMT-D-R01-R02-MAGs-SUMMARY.tar.gz: A static HTML website that contains FASTA files for each MAG, and TAB-delimited matrices for coverage and detection values, and others. After unpacking, you can double-click the index.html file. </li> </ul>

opencc-zeroJan 2024View details →

Data from: Combining the resurrection approach with transplant experiments to investigate adaptation of plant populations to environmental change

Recent climatic changes, such as more frequent droughts and heatwaves, can lead to rapid evolutionary adaptations in plant populations. Such rapid evolution can be investigated using the resurrection approach by comparing plants raised from stored ancestral and contemporary seeds from the same population. This approach has so far only been used in common garden experiments, allowing it to reveal genetic differentiation but not adaptation. In this study, we performed a novel approach by testing for evolutionary adaptation in natural plant populations using a resurrection study in combination with in situ transplantations. We cultivated seedlings from ancestors (23–26 years old) and contemporary descendants of three perennial species (Melica ciliata, Leontodon hispidus and Clinopodium vulgare) from calcareous grasslands in the greenhouse and transplanted them back to their collection sites. In addition, we sowed seeds of ancestors and descendants of two species (L. hispidus and C. vulgare) to the collection sites in order to investigate germination rates. In transplanted M. ciliata seedlings, we observed lower mortality and larger plant size in descendants compared to ancestors. This indicates that descendants are better adapted than ancestors to the current environmental conditions, which proved to be exceptionally hot and dry during the study period. Descendants of C. vulgare seedlings tended to be smaller and descendants of L. hispidus seedlings produced fewer leaves compared to their ancestors in their contemporary environmental conditions. In C. vulgare and L. hispidus, we found evolution towards faster germination, and especially descendant seeds of C. vulgare were better adapted to the unfavourable conditions during the experimental period. Concluding, we demonstrate that our novel approach to combine resurrection ecology with transplant experiments is a promising avenue to rigorously test for evolutionary adaptations in changing environments.

opencc-zeroFeb 2024View details →

Macroinvertebrate and environmental responses to dredging and submerged macrophytes transplantation

Eutrophication of freshwater ecosystems is a major global problem, but restoration can be difficult due to ongoing problems relating to water pollution, sedimentary nutrient stores, and altered aquatic biodiversity. Mitigation of water quality stressors is often conducted alongside transplantation of submerged macrophytes and dredging, but knowledge of ecosystem response to post-dredging transplantation of submerged macrophytes is limited. Here, we report a long-term (2008-2018) in-situ monitoring study to evaluate the effects of two different restoration measures: dredging only (Dredged) and dredging with post-dredging transplantation of submerged macrophytes (Dredged with macrophytes) conducted in five subtropical eutrophic lakes in Lake Taihu basin, China. Water and sediment nutrients, bloom-forming algae Microcystis, and macroinvertebrate were monitored every two years for each treatment and compared with reference areas (Control) established in unrestored parts of the same lakes. Dredging only decreased sediment nutrients (nitrogen, phosphorus, total carbon, and water total phosphorus significantly, however, this effect diminished about five years later. Dredged with macrophytes had a stronger, longer-lasting positive effect on water quality than Dredged alone. Disturbance caused by dredging (without macrophytes transplantation) decreased the biomass of Microcystis, while transplantation of submerged macrophytes shortly after dredging did not contribute to the decrease of Microcystis biomass. The biomass of Microcystis in Dredged with macrophytes areas was always similar to Control over the period of our monitoring. A positive effect of submerged macrophytes transplantation post-dredging was found for macroinvertebrate abundance and diversity: Dredged with macrophytes areas had significantly higher macroinvertebrate biomass and richness than Dredged areas after 9 years' recovery. Macroinvertebrate richness in Dredged with macrophytes areas nearly doubled compared to Control; while Dredged areas were just restored to Control levels. Synthesis and applications. Our study provides an in-situ long-term field monitoring with new findings about the benefits and caution of submerged macrophytes transplantation post-dredging, and the effect of partial restoration, which could inform eutrophic waterbody restoration schemes.

opencc-by-4.0Oct 2024View details →

Regulatory T cell therapy is associated with distinct immune regulatory lymphocytic infiltrates in kidney transplants: Spatial transcriptomic dataset and images

The outputs of the NanoString GeoMx DSP platform were concatenated into three xlsx files, each illustrating a separate experiment along with their sample annotations. This technique analyzes protein or RNA abundance within regions of interest (ROIs) or specific cell segments selected based on histological features and immunofluorescence. In this repository, the concatenated GeoMx output files are presented, along with PowerPoint presentations for each biopsy that show immunofluorescence images of the selected ROIs and/or cell segments. <ul> <li>Protein_Full ROI: This experiment measured the abundance of 41 proteins in discrete regions of interest (ROIs) within transplant kidney biopsies.</li> <li>Protein_Rare cell: This experiment measured the abundance of 40 proteins in specific cell segments, such as CD4+FoxP3- cells vs. CD4+FoxP3+ cells, within transplant kidney biopsies.</li> <li>RNA: This experiment measured the abundance of 90 genes in discrete ROIs within transplant kidney biopsies.</li> </ul>

opencc-zeroFeb 2022View details →

Demonstration of local adaptation in maize landraces by reciprocal transplantation

Populations are locally adapted when they exhibit higher fitness than foreign populations in their native habitat. Maize landrace adaptations to highland and lowland conditions are of interest to researchers and breeders. To determine the prevalence and strength of local adaptation in maize landraces, we performed a reciprocal transplant experiment across an elevational gradient in Mexico. We grew 120 landraces, grouped into four populations (Mexican Highland, Mexican Lowland, South American Highland, South American Lowland), in Mexican highland and lowland common gardens and collected phenotypes relevant to fitness and known highland-adaptive traits such as anthocyanin pigmentation and macrohair density. 67k DArTseq markers were generated from field specimens to allow comparison between phenotypic patterns and population genetic structure. We found phenotypic patterns consistent with local adaptation, though these patterns differ between the Mexican and South American populations. Quantitative trait differentiation (QST) was greater than neutral allele frequency differentiation (FST) for many traits, signaling directional selection between pairs of populations. All populations exhibited higher fitness metric values when grown at their native elevation, and Mexican landraces had higher fitness than South American landraces when grown in these Mexican sites. As environmental distance between landraces' native collection sites and common garden sites increased, fitness values dropped, suggesting landraces are adapted to environmental conditions at their natal sites. Correlations between fitness and anthocyanin pigmentation and macrohair traits are stronger in the highland site than the lowland site, supporting their status as highland-adaptive. These results give substance to the long-held presumption of local adaptation of New World maize landraces to elevation and other environmental variables across North and South America.

Raw Data for the article: A retrospective molecular epidemiological scenario of carbapenemase-producing Klebsiella pneumoniae clinical isolates in a Sicilian transplantation hospital shows a swift polyclonal divergence among sequence types, resistome and virulome

In this work, we assessed and characterized the epidemiological scenario of carbapenem-resistant Klebsiella pneumoniae strains (CR-Kp) at IRCCS-ISMETT, a transplantation hospital in Palermo, Italy, from 2008 to 2017. A total of 288 K. pneumoniae clinical isolates were selected based on their resistance to carbapenems. Molecular characterization was also done in terms of the presence of virulence and resistance genes. All patients were inpatients from our facility and clinical isolates were collected from several sources, either from infection or colonization cases. We observed that, in agreement with the Italian epidemiological scenario, initially only ST258 and ST512 clade II (but not from clade I) were identified from 2008 to 2011. From 2012 onwards, other STs have been observed, including the clinically relevant ST101 and ST307, but also others not previously observed in other Italian health settings, such as ST220 and ST753. The presence of genes involved in resistance and virulence was confirmed, and a heterogeneous genetic resistance profile throughout the years was observed. Our work highlights that resistance genes are rapidly disseminating between different and novel K. pneumoniae clones which, combined with resistance to multiple antibiotics, can derive into more aggressive and pathogenic multidrug-resistant strains of clinical importance. Our results stress the importance of continuous surveillance of CR Enterobacterales in health facilities so that novel STs carrying resistance and virulence genes that may become increasingly pathogenic can be identified and adequate therapies to adopted to avoid their dissemination and derived pathologies.

Raw data for the article: Successful Use of Heterologous CMV-Reactive T Lymphocyte to Treat Severe Refractory Cytomegalovirus (CMV) Infection in a Liver Transplanted Patient: Correlation of the Host Antiviral Immune Reconstitution with CMV Viral Load and CMV miRNome

Cytomegalovirus (CMV) infection is the most significant viral infection in hosts with compromised immune systems as solid organ transplant patients. Despite significant progress being made in the prevention of CMV disease in these patients, further therapeutic strategies for CMV disease and for the CMV reactivation prevention are needed. Here, we describe the outcome of the infusion of in vitro expanded CMV-reactive T-cells, taken from a healthy CMV-seropositive donor, in a liver-transplanted recipient with a refractory recurrent CMV. In this particular case, adoptive transfer of allogenic CMV-reactive T-lymphocytes resulted in the clearance of CMV infection and resolution of the pathological manifestations of the patient. In the study we also investigated circulating miRNAs, both cellular and viral, as potential biomarkers during the course of CMV infection. The results indicate that the infusion of allogenic CMV-reactive T-cells can be an effective strategy to treat CMV infection recurrence when the generation of autologous virus specific T cell clones is not possible.

Raw Data for the article: Impaired anti-SARS-CoV-2 humoral and cellular immune response induced by Pfizer-BioNTech BNT162b2 mRNA vaccine in solid organ transplanted patients

SARS‐CoV‐2 vaccine is considered the primary health strategy able to end the current COVID‐19 pandemic. This viral infection impacts more severely solid organ transplant recipients (SOTRs) than general population, but the effect of vaccination in this subgroup of immunosuppressed patients is not known due to their exclusion from vaccination trials. Preliminary reports suggest a lower antibody production after BNT162b2 Pfizer/BioNTech mRNA‐vaccine,<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8222937/#ajt16702-bib-0001"> 1 </a>, <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8222937/#ajt16702-bib-0002">2 </a>, <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8222937/#ajt16702-bib-0003">3 </a>, <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8222937/#ajt16702-bib-0004">4 </a>but no data are currently available on the elicited virus‐specific T cell responses.

Raw Data for the article: Liver Transplantation for Unresectable Intrahepatic Cholangiocarcinoma: The Role of Sequencing Genetic Profiling

Intrahepatic cholangiocarcinoma (iCCA) is a rare and aggressive primary liver tumor, characterized by a range of different clinical manifestations and by increasing incidence and mortality rates even after curative treatment with radical resection. In recent years, growing attention has been devoted to this disease and some evidence supports liver transplantation (LT) as an appropriate treatment for intrahepatic cholangiocarcinoma; evolving work has also provided a framework for better understanding the genetic basis of this cancer. The aim of this study was to provide a clinical description of our series of patients complemented with Next-Generation Sequencing genomic profiling. From 1999 to 2021, 12 patients who underwent LT with either iCCA or a combined hepatocellular and cholangiocellular carcinoma (HCC-iCCA) were included in this study. Mutations were observed in gene activating signaling pathways known to be involved with iCCA tumorigenesis (KRAS/MAPK, P53, PI3K-Akt/mTOR, cAMP, WNT, epigenetic regulation and chromatin remodeling). Among several others, a strong association was observed between the Notch pathway and tumor size (point-biserial rhopb = 0.93). Our results are suggestive of the benefit potentially derived from molecular analysis to improve our diagnostic capabilities and to devise new treatment protocols, and eventually ameliorate long-term survival of patients affected by iCCA or HCC-iCCA.

Raw Data for the article: Liver transplantation for unresectable intrahepatic cholangiocarcinoma: an Italian experience

Intrahepatic cholangiocarcinoma (iCCA) is an aggressive form of primary liver cancer treated exclusively with surgery. Its incidence in the western world is growing lately [<a href="https://link.springer.com/article/10.1007/s13304-021-01064-w#ref-CR1">1</a>] and the overall 5-year survival is poor due to late diagnosis, since patients rarely present a jaundice differently from patients affected by perihilar cholangiocarcinoma. Ideally liver resection and regional lymphadenectomy are the best treatments; however, these are unfortunately connotated by a 75% recurrence rate 5 years after surgery. Systemic chemotherapy offers a minimal response, as well as loco-regional therapy such as selective internal radiotherapy (SIRT), with a survival varying from 11 to 15 months between the two therapies

opencc-zeroMay 2022View details →

Kidney transplantation waiting times and risk of cardiovascular events and mortality: a retrospective observational cohort study in Taiwan

Objectives: Patients with end-stage renal disease (ESRD) are at a high risk of cardiovascular events (CVEs), and kidney transplantation (KT) has been reported to improve risk of CVEs and survival. As the association of KT timing on long-term survival and clinical outcomes remains unclear, we investigated the association of different KT waiting times on clinical outcomes. Design: Retrospective observational cohort study. Setting: We conducted an observational cohort study using data from the National Health Insurance Research Database in Taiwan. Adult patients who initiated kidney transplantation therapy from 1997 to 2013 were included. Participants: A total of 3562 adult patients who initiated uncomplicated KT therapy were included and categorized into four groups according to KT waiting times after ESRD: Group 1 (<1 year), Group 2 (1–3 years), Group 3 (3–6 years), and Group 4 (>6 years). Primary outcome measure: The main outcome was a composite of all-cause death, nonfatal myocardial infarction, or nonfatal stroke, based on the primary diagnosis in medical records during hospitalization. Results: Compared with Group 1, the adjusted risk of primary outcome events (all-cause death, nonfatal myocardial infarction, or nonfatal stroke) increased by 1.67 times in Group 2 (95% CI: 1.40–2.00; P <0.001), 2.17 times in Group 3 (95% CI: 1.73–2.71; P <0.001), and 3.10 times in Group 4 (95% CI: 2.21–4.35; P <0.001). The rates of primary outcome events were 6.7%, 13.4%, and 14.0% within five years, increasing to 19.5%, 26.3%, and 30.8% within 10 years in Groups 1, 2, and 3, respectively. Conclusions: Our results demonstrate that early KT is associated with superior long-term cardiovascular outcomes compared to late KT in selected ESRD patients receiving uncomplicated KT, suggesting that an early KT could be a better treatment option for ESRD patients who are eligible for transplantation.