A5079779517- Microbial Community Ecology and Physiology
- Single-cell and spatial transcriptomics
- Mosquito-borne diseases and control
- Mercury impact and mitigation studies
- Polar Research and Ecology
- Malaria Research and Control
- Genomics and Phylogenetic Studies
- Wastewater Treatment and Nitrogen Removal
- Environmental DNA in Biodiversity Studies
- Multiple Myeloma Research and Treatments
- Hematological disorders and diagnostics
- Water Quality Monitoring Technologies
- Hematopoietic Stem Cell Transplantation
- Identification and Quantification in Food
- Water Quality Monitoring and Analysis
- T-cell and B-cell Immunology
- Immunotherapy and Immune Responses
- Advanced Nanomaterials in Catalysis
- Cell Image Analysis Techniques
- Microbial bioremediation and biosurfactants
- Marine Biology and Environmental Chemistry
- Cellular Automata and Applications
- Complement system in diseases
- Fungal and yeast genetics research
- Plant nutrient uptake and metabolism
Instituto Gulbenkian de Ciência
2020-2025
University of Turku
2023-2025
Turku Centre for Computer Science
2023-2025
Åbo Akademi University
2023-2025
Calouste Gulbenkian Foundation
2020-2021
Universidade do Porto
2018-2021
Centro Interdisciplinar de Investigação Marinha e Ambiental
2021
Bacterial diversity from McMurdo Dry Valleys in Antarctica, the coldest desert on earth, has become more easily assessed with development of High Throughput Sequencing (HTS) techniques. However, some remains inaccessible by power sequencing. In this study, we combine cultivation and HTS techniques to survey actinobacteria cyanobacteria along different soil endolithic micro-environments Victoria Valley Valleys. Our results demonstrate that distribution is driven environmental forces,...
SNF1-related Kinase 1 (SnRK1) is an evolutionarily conserved protein kinase with key functions in energy management during stress responses plants. To address a potential role of SnRK1 under favorable conditions, we performed metabolomic and transcriptomic characterization rosettes 20-d-old Arabidopsis (Arabidopsis thaliana) plants gain- loss-of-function mutants the regular diel cycle. Our results show that manipulation alters sucrose trehalose 6-phosphate (Tre6P) relationship, influencing...
Marine biofilms are known to influence the corrosion of metal surfaces in marine environment. Despite some recent research, succession bacterial communities colonizing artificial remains uncharacterized temporal settings. More specifically, it is not fully if colonizers similar or distinct different seasons year. In particular study early biofilms, which cells first adhere surfaces, crucial for development subsequent biofilm communities. this work, we used amplicon-based NGS (next-generation...
Current state-of-the-art integration methods for single-cell transcriptomics often struggle with imbalanced cell types across heterogeneous datasets, particularly when the datasets include similar but unshared types. Here, we introduce Coralysis, an R package featuring a multi-level algorithm to overcome these challenges. Coralysis enables sensitive integration, reference-mapping, and state identification demonstrating consistent performance diverse RNA-seq tasks outperforming are unevenly...
Whether jaundice, a common presentation of Plasmodium ( P .) falciparum malaria (1-3) arising from the accumulation circulating bilirubin, represents an adaptive or maladaptive response to spp. infection is not understood (1-3). We found that asymptomatic P. was associated with >10-fold higher ratio unconjugated bilirubin over parasite burden, compared symptomatic malaria. Genetic suppression synthesis by biliverdin reductase A (BVRA) (4) increased virulence and mortality in mice....
SUMMARY When pollen lands on a receptive stigma, it germinates and extends tube inside the transmitting tissue of pistil to deliver sperm cells for double fertilization. The growth triggers significant alterations in its gene expression. extent which these changes occur vegetative cell or extend transported by is unclear but important determine since are believed acquire competency fertilization during pollen–pistil interactions. To address questions, we compared transcriptomes Arabidopsis...
Abstract Motivation The analysis of cell migration using time-lapse microscopy typically focuses on track characteristics for classification and statistical evaluation behaviour. However, considerable heterogeneity can be seen in morphology microscope signal intensity features within the migrating populations. To utilise this information analysis, we introduce here an R package CellRomeR, designed phenotypic clustering cells based their morphological motility from images. Utilising machine...
The serine/threonine-specific Moloney murine leukemia virus (PIM) kinase family (i.e., PIM1, PIM2, and PIM3) has been extensively studied in tumorigenesis. PIM kinases are downstream of several cytokine signaling pathways that drive immune-mediated diseases. Uncontrolled T helper 17 (Th17) cell activation associated with the pathogenesis autoimmunity. However, detailed molecular function PIMs human Th17 regulation yet to be studied. In present study, we comprehensively investigated how three...
Abstract During sexual reproduction in flowering plants, the two haploid sperm cells (SCs) embedded within cytoplasm of a growing pollen tube are carried to embryo sac for double fertilization. Pollen development plants is dynamic process that encompasses changes at transcriptome and epigenome levels. While SCs Arabidopsis (Arabidopsis thaliana) well documented, previous analyses have mostly been based on gene-level expression. In-depth analysis, particularly extent alternative splicing (AS)...
T lymphocyte differentiation in the steady state is characterized by high cellular turnover whereby thymocytes do not self-renew. However, if deprived of competent progenitors, thymus can temporarily maintain thymopoiesis autonomously. This bears a heavy cost, because prolongation autonomy causes leukemia. Here, we show that, at an early stage, relies on double-negative 3 (DN3e) that acquire stem-cell-like properties. Following progenitor deprivation, DN3e become long lived, are required for...
Bacterial natural products (NPs) are still a major source of new drug leads. Polyketides (PKs) and non-ribosomal peptides (NRP) two pharmaceutically important families NPs recent studies have revealed Antarctica to harbor endemic polyketide synthase (PKS) peptide synthetase (NRPS) genes, likely be involved in the production novel metabolites. Despite this, diversity secondary metabolites genes is poorly explored. In this study, computational bioprospection approach was employed study...
Aerobic nitrification is a fundamental nitrogen biogeochemical process that links the oxidation of ammonia to removal fixed in eutrophicated water bodies. However, estuarine environments there an enormous variability physicochemical parameters can affect biological process. For instance, it known salinity performance, yet still lack information on ammonia-oxidizing communities behavior facing daily fluctuations. In this work, laboratory experiments using upstream and downstream sediments...
Bulk RNA sequencing of Plasmodium spp., the causative parasite malaria, fails to discriminate developmental-stage-specific gene regulation. Here, we provide a protocol that uses single-cell FACS-sorted Plasmodium-chabaudi-chabaudi-AS-infected red blood cells (iRBCs) characterize modulation expression during malaria stage. We describe steps for infecting mice, monitoring disease progression, preparing iRBCs, and iRBCs. then detail procedures analyzing scRNA-seq data. For complete details on...
ABSTRACT T lymphocyte differentiation in the thymus relies on high cellular turnover, and cell competition enforces thymocyte replenishment. If deprived of competent progenitors, can maintain thymopoiesis autonomously for several weeks but this bears a risk leukemia. Here we show that double negative 3 early (DN3e) thymocytes acquire stem like properties, which enables them to thymopoiesis. Specifically, DN3e proved be long-lived, they proliferated differentiated vivo , were necessary...
In estuaries the deposition of copper nanoparticles upon sediments can contribute to change metal availability and promote transcriptional response denitrifying bacteria.
SUMMARY Hypoglycemia is a clinical hallmark of severe malaria, the often-lethal presentation Plasmodium falciparum infection humans. Here we report that mice reduce blood glucose levels in response to via coordinated whereby labile heme, an alarmin produced hemolysis, induces anorexia and represses hepatic production (HGP). While protective against unfettered immune-mediated inflammation, organ damage anemia, when sustained over time heme-driven repression HGP can progress towards...
Abstract Effects of metallic nanoparticles (NPs) to the estuarine biota have mostly been shown for concentrations higher than those actually measured or predicted in these environments. To address this gap, a range expected occur environments (from 0.01 1 μg g-1) was employed microcosms studies assess impact Cu NPs denitrification pathway. That achieved by quantifying gene expression and potential rate sediments exposed up six days. Expression nitrite ( nirS ) nitrous oxide nosZ reductase...