Biology subjects

Ferreira, H.

Publications and source records attributed to Ferreira, H..

6 recordsLinked to original sources

bioRxiv2025

Characterisation of a temperate phage induced from Alicyclobacillus acidoterrestris DSM 3922T: the Alicyclobacillus phage MMB025

The fruit juice industry has increasingly faced spoilage incidents attributed to Alicyclobacillus (ACB) bacteria. These spore-forming bacteria produce off-flavours and odours that compromise product quality and lead to significant food waste. Their resistance to acidic pH and the pasteurisation processes commonly used in the food industry demands the investigation of new preservation strategies. Bacteriophage-related treatments have emerged as a promising alternative, being considered safe, green, and sustainable. In this study, the type strain A. acidoterrestris DSM 3922T and a food isolate, A. acidoterrestris MMB007, were used as hosts to isolate new ACB-targeting phages. A phage was isolated from a soil sample in contact with the type strain, purified, and characterised for its genetic and phenotypic features. The isolated phage, named Alicyclobacillus phage MMB025, belongs to the Caudoviricetes class and exhibits a narrow host range. Also, phage MMB025 was revealed to be stable under different environmental conditions, maintaining its lytic activity across a wide range of pH values (3 to 12) and high temperatures (up to 1 h at 60 {degrees}C). The hybrid assembly of short and long reads revealed a phage genome of 105,243 bp with a GC content of 43.25 %. Sequence mapping to the A. acidoterrestris DSM 3922 genome indicated phage DNA integration within the bacterial chromosome, disrupting the sigK open reading frame. This suggests that MMB025 may have originated from a prophage induction event potentially linked to sporulation regulation. Despite the limitations derived from its likely temperate nature, phage MMB025 remains a valuable source of lysins capable of specifically and effectively eliminating ACB bacteria. More importantly, this study highlights the potential of phages as an alternative preservation strategy against ACB bacteria. The phage MMB025 characterisation opens venues to develop strategies for mitigating ACB-related spoilage, thereby enhancing the sustainability of food production.

microbiology↗

bioRxiv2024

Embedding bioprinting of low viscous, photopolymerizable blood-based bioinks in a self-healing transparent supporting bath

Protein-based hydrogels have great potential to be used as bioinks for biofabrication-driven tissue regeneration strategies due to their innate bioactivity. Nevertheless, their use as bioinks in conventional 3D bioprinting is impaired due to their intrinsic low viscosity. Using embedding bioprinting, a liquid bioink is printed whithin a support that physically holds the patterned filament. Inspired by the recognized microencapsulation technique complex coacervation, we introduce crystal self-healing embedding bioprinting (CLADDING) based on a highly transparent crystal supporting bath. The suitability of distinct classes of gelatins was evaluated (i.e., molecular weight distribution, isoelectric point and ionic content), as well as the formation of gelatin-gum arabic microparticles as a function of pH, temperature, solvent and mass ratios. Characterizing and controlling this parametric window resulted in high yields of support bath with ideal self-healing properties for interaction with protein-based bioinks during bioprinting. This support bath achieved transparency, which boosted light permeation within the bath. CLADDING bioprinted constructs fully composed of platelet lysates encapsulating a co-culture of human mesenchymal stem cells and endothelial cells were obtained, demonstrating high-dense cellular network with excellent cell viability and stability over a month. CLADDING broadens the spectrum of photocrosslinkable materials with extremely low viscosity that can now be bioprinted with sensitive cells using embedding bioprinting without any additional support.

bioengineering↗

bioRxiv2023

Unveiling the role of osteosarcoma-derived secretome in premetastatic lung remodeling

Lung metastasis represents the leading cause of osteosarcoma-related death. Progress in preventing lung metastasis is pretty modest due to the inherent complexity of the metastatic process and the lack of suitable models. Herein, we provide mechanistic insights into how osteosarcoma systemically reprograms the lung microenvironment for metastatic outgrowth using metastatic mouse models and a multi-omics approach. We found that osteosarcoma-bearing mice or those preconditioned with cell-secretome harbour profound lung structural alteration with airways damage, inflammation, neutrophil infiltration, and remodelling of the extracellular matrix with deposition of fibronectin and collagen by stromal activated fibroblasts for tumour cell adhesion. These changes, supported by transcriptomic and histological data, promoted and accelerated the development of lung metastasis. Comparative proteome profiling of the cell secretome and mouse plasma identified a large number of proteins engaged in the extracellular-matrix organization, cell-matrix adhesion, neutrophil degranulation, and cytokine-mediated signalling, which were consistent with the observed lung microenvironmental changes. Moreover, we identified EFEMP1, a secreted extracellular matrix glycoprotein, as a potential risk factor for lung metastasis and a poor prognosis factor in osteosarcoma patients.

cancer biology↗

bioRxiv2022

Core genome MLST for epidemiological and evolutionary analyses of phytopathogenic Xanthomonas citri

Xanthomonas citri subspecies citri (XCC) is the cause of bacterial citrus canker, responsible for major economic losses to the citrus industry that includes sweet orange, lime and grapefruit production in regions including South America, United States, China and Japan. Other X. citri subsp. and pathovars are responsible for diseases in crops such as soy bean, common bean, mango, pomegranate and cashew. Tracing the spread of X. citri disease has been performed using several different typing methods over the years but recent studies using genomic sequencing have been key to understanding evolutionary relationships within the species including fundamental differences between XCC pathotypes. In this study we developed a core genome multilocus typing scheme (cgMLST) for X. citri based upon 250 genomes comprising multiple examples of X. citri subsp. citri pathotypes A, A* and Aw, X. citri subsp. malvacearum and X. citri pathovars aurantifolii, fuscans, glycines, malvacearum, mangiferaeindicae, viticola, vignicola and single isolates of X. citri pathovars dieffenbachiae and punicae. This dataset included genomic sequencing of 100 novel XCC isolates. The cgMLST scheme, based upon 1618 core genes across 250 genomes, has been implemented at PubMLST (https://pubmlst.org/organisms/xanthomonas-citri/). Grapetree minimum-spanning, and iTOL Neighbour-joining phylogenies generated from cgMLST data resolved almost identical groupings of isolates to a core genome SNP - based neighbour joining phylogeny taking 4 min, 15 min and 36 h respectively. These resolved identical groupings of XCC pathotypes and X. citri subsp. and pathovars. X. citri cgMLST should prove to be an increasingly valuable resource for the study of this key species of plant pathogenic bacteria. Users can submit genomic and associated metadata to compare with previously characterised isolates at PubMLST.org to allow rapid characterization of local, national and global epidemiology of these pathogens and examine evolutionary relationships.

microbiology↗

bioRxiv2020

CitrusKB: A Comprehensive Knowledge Base for Transcriptome and Interactome of Citrus spp. Infected by Xanthomonas citri subsp. citri at Different Infection Stages

Citrus canker type A is a serious disease caused by Xanthomonas citri subsp. citri (X. citri), which is responsible for severe losses to growers and to the citrus industry worldwide. To date, no canker-resistant citrus genotypes are available, and there is limited information regarding the molecular and genetic mechanisms involved in the early stages of the citrus canker development. Here, we present the knowledge base for transcriptome of in vivo citrus interactome, the CitrusKB. This is the first in vivo interactome database for different citrus cultivars, and it was produced to provide a valuable source of information on citrus and their interaction with the citrus canker bacterium X. citri. The database provides tools for a user-friendly web interface to search and analyze a large amount of information regarding eight citrus cultivars with distinct levels of susceptibility to the disease and their interaction, at different stages of infection, with the citrus canker bacterium X. citri. Currently, CitrusKB comprises a reference citrus genome and its transcriptome, expressed transcripts, pseudogenes and predicted genomic variations (SNPs and SSRs). The updating process will continue by incorporating annotations and analysis tools. We expect that CitrusKB may substantially contribute to the area of citrus genomics. CitrusKB is accessible at http://bioinfo.deinfo.uepg.br/citrus. Users can download all the generated raw sequences and generated datasets by this study from the CitrusKB website.

genomics↗

bioRxiv2019

Neutrophil Extracellular Traps contribute to the pathogenesis of leprosy type 2 reactions

Up to 50% of patients with the multibacillary form of leprosy is expected to develop acute systemic inflammatory episodes known as type 2 reactions (T2R), thus aggravating their clinical status. Thalidomide rapidly improves T2R symptoms. But, due to its restricted use worldwide, novel alternative therapies are urgently needed. A hallmark of T2R lesions is the presence of a neutrophil-rich inflammatory infiltrate. In this study, the potential involvement of neutrophil extracellular traps (NETs) production in T2R pathogenesis was investigated. Abundant NETs were found in T2R skin lesions, and increased spontaneous NETs formation was observed in T2R peripheral neutrophils. Both the M. leprae whole-cell sonicate and the CpG-Hlp complex, mimicking a mycobacterial TLR9 ligand, were able to induce NETs production in vitro. Moreover, TLR9 expression was shown to be higher in T2R neutrophils, suggesting that DNA recognition via TLR9 may be one of the pathways triggering this process during T2R. Finally, treatment of T2R patients with thalidomide for 7 consecutive days resulted in decreasing all of the evaluated in vivo and ex vivo NETosis parameters. Altogether, our findings shed light on the pathogenesis of T2R, which, it is hoped, will contribute to the emergence of novel alternative therapies in the near future.\n\nAuthor summaryLeprosy is caused by a mycobacterium that has a predilection for skin and nerve cells. The chronic course of the disease may be interrupted by acute inflammatory episodes known as reactions, despite effective bacterial killing with antibiotics. Reactions aggravate patients clinical status and may become a medical emergency. Type 2 reactions (T2R) only occur in patients with high bacterial burden and is treated with thalidomide and/or corticosteroids. We are interested in understanding how inflammation is triggered and amplified during T2R. In this study we investigated the potential role of extracellular DNA released by neutrophils (known as NETs) in T2R, since they have been shown to cause inflammation. Abundant NETs were found in T2R skin lesions, and increased spontaneous NETs formation was observed in neutrophils present in the blood of T2R patients. Moreover, bacterial constituents were able to induce NETs production. Finally, treatment of T2R patients with thalidomide resulted in decreased NET formation. Altogether, our findings shed light on the pathogenesis of T2R, which, it is hoped, will contribute to the identification of biomarkers for early diagnosis and emergence of novel alternative therapies in the near future.

immunology↗