Publications by authors named "Maria Schneider"

176 Publications

Characterization and Biotechnological Potential of Intracellular Polyhydroxybutyrate by sp. B23 Using Cassava Peel as Carbon Source.

Polymers (Basel) 2021 Feb 25;13(5). Epub 2021 Feb 25.

Laboratory of Biotechnology of Enzymes and Biotransformations, Institute of Biological Sciences, Federal University of Pará, 66075-110 Belém, Pará, Brazil.

The possibility of utilizing lignocellulosic agro-industrial waste products such as cassava peel hydrolysate (CPH) as carbon sources for polyhydroxybutyrate (PHB) biosynthesis and characterization by Amazonian microalga sp. B23. was investigated. Cassava peel was hydrolyzed to reducing sugars to obtain increased glucose content with 2.56 ± 0.07 mmol/L. Prior to obtaining PHB, sp. B23 was grown in BG-11 for characterization and Z8 media for evaluation of PHB nanoparticles' cytotoxicity in zebrafish embryos. As results, microalga produced the highest amount of dry weight of PHB with 12.16 ± 1.28 (%) in modified Z8 medium, and PHB nanoparticles exerted some toxicity on zebrafish embryos at concentrations of 6.25-100 µg/mL, increased mortality (<35%) and lethality indicators as lack of somite formation (<25%), non-detachment of tail, and lack of heartbeat (both <15%). Characterization of PHB by scanning electron microscopy (SEM), X-ray diffraction (XRD), differential scanning calorimeter (DSC), and thermogravimetry (TGA) analysis revealed the polymer obtained from CPH cultivation to be morphologically, thermally, physically, and biologically acceptable and promising for its use as a biomaterial and confirmed the structure of the polymer as PHB. The findings revealed that microalgal PHB from sp. B23 was a promising and biologically feasible new option with high commercial value, potential for biomaterial applications, and also suggested the use of cassava peel as an alternative renewable resource of carbon for PHB biosynthesis and the non-use of agro-industrial waste and dumping concerns.
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http://dx.doi.org/10.3390/polym13050687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7956423PMC
February 2021

Epidemiology of human leptospirosis in urban and rural areas of Brazil, 2000-2015.

PLoS One 2021 4;16(3):e0247763. Epub 2021 Mar 4.

Department of International Health, Georgetown University, Washington, District of Columbia, United States of America.

Background: Leptospirosis is one of the most widespread zoonosis in the world and Brazil has the highest number of cases in Latin America. Transmission occurs mainly through exposure to water and soil contaminated by the urine of infected animals. The goals of this study are to describe the geographic distribution, demographic characteristics and exposure factors of urban and rural cases of leptospirosis, and identify spatial clusters in urban and rural areas of Brazil.

Methods/results: A retrospective epidemiological study was carried out using 16 years (2000-2015) of surveillance data from the Brazilian Ministry of Health. Cases were described by age, sex and race, and exposure factors were characterized in urban and rural areas. A spatial autocorrelation analysis was conducted using local Moran's I to identify urban and rural clusters of disease. On average 3,810 leptospirosis cases were reported annually with higher numbers in urban areas. National urban and rural incidence rates were the same (1.9 cases/100,000 population), however, regional differences were observed. Urban incidence rates were higher in the North and Northeast regions, while rural incidence rates were higher in the Southeast and South. The main exposure factor reported in urban and rural areas was exposure to places with signs of rodents, followed by flood in urban areas and agriculture and animal farming in rural areas. Clusters of leptospirosis were identified in densely populated urban areas of the North, Southeast and South regions, while rural clusters were concentrated in of the Southern region with large agriculture and animal farming practices.

Conclusions: This study highlights that leptospirosis is an important public health problem in both urban and rural areas of Brazil. The results provide decision-makers with detailed information about where disease incidence is high and can be used in the development of prevention and control strategies for priority areas and risk groups.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0247763PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7932126PMC
March 2021

Amazonia Seasons Have an Influence in the Composition of Bacterial Gut Microbiota of Mangrove Oysters ().

Front Genet 2020 12;11:602608. Epub 2021 Feb 12.

Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil.

The mangrove oysters () are molluscs native to the Amazonia region and their exploration and farming has increased considerably in recent years. These animals are farmed on beds built in the rivers of the Amazonia estuaries and, therefore, the composition of their microbiome should be directly influenced by environmental conditions. Our work aimed to evaluate the changes in bacterial composition of oyster's microbiota at two different seasons (rainy and dry). For this purpose, we amplified and sequenced the V3-V4 regions of the 16S rRNA gene. Sequencing was performed on the Illumina MiSeq platform. According to the rarefaction curve, the sampling effort was sufficient to describe the bacterial diversity in the samples. Alpha-diversity indexes showed that the bacterial microbiota of oysters is richer during the rainy season. This richness is possibly associated with the diversity at lower taxonomic levels, since the relative abundance of bacterial phyla in the two seasons remained relatively constant. The main phyla found include Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. Similar results were found for the species , and . Beta-diversity analysis showed that the bacterial composition of oyster's gut microbiota was quite different in the two seasons. Our data demonstrate the close relationship between the environment and the microbiome of these molluscs, reinforcing the need for conservation and sustainable management of estuaries in the Amazonia.
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http://dx.doi.org/10.3389/fgene.2020.602608DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7907636PMC
February 2021

An exploration of the protective effect of rodent species richness on the geographical expansion of Lassa fever in West Africa.

PLoS Negl Trop Dis 2021 Feb 1;15(2):e0009108. Epub 2021 Feb 1.

Institute of Health and Environment, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea.

Background: Lassa fever (LF) is one of the most devastating rodent-borne diseases in West Africa, causing thousands of deaths annually. The geographical expansion of LF is also a concern; cases were recently identified in Ghana and Benin. Previous ecological studies have suggested that high natural-host biodiversity reduces the likelihood of spillover transmission of rodent-borne diseases, by suppressing the activities of reservoir species. However, the association of biodiversity with the geographical expansion of LF has not been the subject of epidemiological studies.

Methodology/principal Findings: We conducted a spatial analysis based on sociodemographic, geographical, and ecological data, and found that higher rodent species richness was significantly associated with a lower risk of LF emergence in West Africa from 2008 to 2017 (Odds Ratio = 0.852, 95% Credible Interval = 0.745-0.971).

Conclusions/significance: The results reinforce the importance of the 'One Health' approach by demonstrating that a high level of biodiversity could benefit human health.
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http://dx.doi.org/10.1371/journal.pntd.0009108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7877741PMC
February 2021

Overview of snakebite in Brazil: Possible drivers and a tool for risk mapping.

PLoS Negl Trop Dis 2021 Jan 29;15(1):e0009044. Epub 2021 Jan 29.

Oswaldo Cruz Foundation (FIOCRUZ), Ministry of Health of Brazil, Rio de Janeiro, RJ, Brazil.

Snakebite envenoming affects close to 2.7 million people globally every year. In Brazil, snakebites are reported to the Ministry of Health surveillance system and cases receive antivenom free of charge. There is an urgent need to identify higher risk areas for antivenom distribution, and to develop prevention activities. The objective of this study is to provide an overview of the epidemiological situation of snakebite envenoming in Brazil and explore possible drivers; as well as to create a flowchart tool to support decision-makers identify higher risk areas. An ecological-type study was carried out using data by municipality (2013-2017). Study parts: 1) Create a geocoded database and perform a descriptive and cluster analysis; 2) Statistical analysis to measure the association of snakebite and possible environmental and socioeconomic drivers; 3) Develop a flowchart to support decision-makers and the application of this tool in one state (Rio Grande do Sul) as an example. An average of 27,120 snakebite cases per year were reported at the country level. Clusters of municipalities with high numbers of snakebites are mostly found in the Amazon Legal Region. The negative binomial regression model showed association with the snakebite case count: the type of major habitat, tropical or non-tropical; temperature; percentage of urbanization; precipitation; elevation; GDP per capita; a weaker relation with forest loss; and with venomous snake richness. The state where the instrument was applied reported 4,227 snakebites in the period. Most municipalities were considered as medium risk and 56/496 as high risk according to the tool created. Snakebite cases are distributed across the entire country with the highest concentration in the Legal Amazon Region. This creates a complex situation both for better understanding of the association of environmental and socioeconomic factors with snakebites and for the distribution and maintenance of antivenom to remote areas. Research into types of antivenom with a longer shelf life without the need for refrigeration is needed.
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http://dx.doi.org/10.1371/journal.pntd.0009044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7875335PMC
January 2021

Changes in the Vaginal Microbiome during the Pregnancy to Postpartum Transition.

Reprod Sci 2021 Jan 11. Epub 2021 Jan 11.

Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USA.

Substantial changes in the composition of the vaginal microbiome occur following the end of pregnancy. To identify potential drivers of microbiome changes in individual women during the pregnancy to postpartum transition, we evaluated vaginal samples from 48 pregnant women during their first and third trimesters and postpartum. We determined the species composition of vaginal communities and the vaginal fluid levels of compounds involved in mediating changes in host physiology and the immune system at each time point. We used linear mixed-effects models to characterize associations. Consistent with previous reports, but with a larger sample size, a US population, and variations in the dominant bacteria, the vaginal microbiome was found to be more diverse during the postpartum period. There was a lower abundance of Lactobacillus and significantly higher proportions of Streptococcus anginosus and Prevotella bivia. Moreover, we uniquely demonstrated that postpartum vaginal secretions were also altered postpartum. There were elevated levels of hyaluronan and Hsp70 and decreased levels of the D- and L-lactic acid isomers. We posit that these variations are consequences of alterations in the vagina after delivery that profoundly alter the host environment and, thus, lead to changes in the capability of different bacterial species to survive and proliferate.
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http://dx.doi.org/10.1007/s43032-020-00438-6DOI Listing
January 2021

Protective effect of predator species richness on human hantavirus infection incidence.

Sci Rep 2020 12 10;10(1):21744. Epub 2020 Dec 10.

Institute of Health and Environment, Graduate School of Public Health, Seoul National University, Seoul, South Korea.

Are predators of rodents beneficial for public health? This question focuses on whether predators regulate the spillover transmission of rodent-borne diseases. No clear answer has emerged because of the complex linkages across multiple trophic levels and the lack of accessible data. Although previous empirical findings have suggested ecological mechanisms, such as resource partitioning, which implies protective effects from predator species richness, epidemiological evidence is needed to bolster these arguments. Thus, we investigated the association between predator species richness and incidence of rodent-borne haemorrhagic fever with renal syndrome in the human population using district-level longitudinal data of 13 years for South Korea. With the exception of districts with low species richness, we found a significant negative association between the incidence of haemorrhagic fever with renal syndrome and the species richness of both avian and mammalian predators; the trends for both predator types were similar. Thus, biodiversity conservation may benefit public health.
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http://dx.doi.org/10.1038/s41598-020-78765-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7728771PMC
December 2020

Association between predator species richness and human hantavirus infection emergence in Brazil.

One Health 2021 Jun 13;11:100196. Epub 2020 Nov 13.

Institute of Health and Environment, Graduate School of Public Health, Seoul National University, South Korea.

Hantavirus infection is a rodent-borne disease (RBD) transmitted by urine or feces (as the natural reservoirs) with an annual estimated worldwide incidence of ~150,000 cases. Previous ecological studies suggested that higher species richness of rodents could decrease the risk of RBDs in humans, because the regulatory pressure of predators could reduce contact among rodents, and between humans and rodents. Using surveillance data, we investigated the association of predator species richness with hantavirus infection emergence in 5562 Brazilian inland municipalities between 2007 and 2017. Multivariable logistic regression models were used for the analyses. Diurnal and non-diurnal predator species were independent explanatory variables in the models. Rodent species richness and demographic, socioeconomic, and environmental factors were used as covariates. During the study period, 1084 cases were reported in 429 municipalities. The results showed a reverse-U-shaped association between diurnal predator species richness and hantavirus infection emergence (odds ratio [OR] 0.463, 0.688, and 0.553 for the first [lowest], third, and fourth [highest] quartiles, respectively, using the second quartile as a reference), while higher non-diurnal predator species richness tended to be associated with higher emergence risk (OR 0.134, 1.065, and 2.708 for the first, third, and fourth quartiles, respectively). The difference in these associations illustrates the complexity of the effects of predator species richness on human RBDs, which require further investigation in follow-up studies. The results showed a close link between environmental factors and public health, emphasizing that the One Health concept should be employed to understand the dynamics of RBDs.
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http://dx.doi.org/10.1016/j.onehlt.2020.100196DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7701261PMC
June 2021

Optimization of Polyhydroxybutyrate Production by Amazonian Microalga sp. B23.

Biomolecules 2020 12 3;10(12). Epub 2020 Dec 3.

Laboratory of Biotechnology of Enzymes and Biotransformations, Institute of Biological Sciences, Federal University of Pará, 01 Augusto Corrêa Street, 66075-110 Belém, Pará, Brazil.

The present work established the optimization and production of biodegradable thermoplastic polyhydroxybutyrate (PHB) from Amazonian microalga sp. B23. The optimization was performed in eight different growth media conditions of sp. B23, supplemented with sodium acetate and sodium bicarbonate and total deprivation of sodium nitrate. B23 was stained with Nile Red, and PHB was extracted and quantified by correlating the amount of fluorescence and biopolymer concentration through spectrofluorimetry and spectrophotometry, respectively. Our results detected the production of PHB in sp. B23 and in all modified media. Treatment with increased acetate and bicarbonate and without nitrate gave the highest concentration of PHB, while the treatment with only acetate gave the lowest among supplemented media. Our results showed a great potential of sp. B23, the first Amazonian microalga reported on PHB production. The microalga was isolated from a poorly explored and investigated region and proved to be productive when compared to other cyanobacterial and bacterial species. Additionally, microalga biomass changes due to the nutritional conditions and, reversely, biopolymer is well-synthetized. This great potential could lead to the pursuit of new Amazonian microalgae species in the search for alternative polyesters.
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http://dx.doi.org/10.3390/biom10121628DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7761742PMC
December 2020

Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment.

Cell 2020 09 5;182(6):1419-1440.e23. Epub 2020 Aug 5.

Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany; German Center for Lung Research (DZL).

Coronavirus disease 2019 (COVID-19) is a mild to moderate respiratory tract infection, however, a subset of patients progress to severe disease and respiratory failure. The mechanism of protective immunity in mild forms and the pathogenesis of severe COVID-19 associated with increased neutrophil counts and dysregulated immune responses remain unclear. In a dual-center, two-cohort study, we combined single-cell RNA-sequencing and single-cell proteomics of whole-blood and peripheral-blood mononuclear cells to determine changes in immune cell composition and activation in mild versus severe COVID-19 (242 samples from 109 individuals) over time. HLA-DRCD11c inflammatory monocytes with an interferon-stimulated gene signature were elevated in mild COVID-19. Severe COVID-19 was marked by occurrence of neutrophil precursors, as evidence of emergency myelopoiesis, dysfunctional mature neutrophils, and HLA-DR monocytes. Our study provides detailed insights into the systemic immune response to SARS-CoV-2 infection and reveals profound alterations in the myeloid cell compartment associated with severe COVID-19.
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http://dx.doi.org/10.1016/j.cell.2020.08.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7405822PMC
September 2020

A plasma protein biomarker strategy for detection of small intestinal neuroendocrine tumors.

Neuroendocrinology 2020 Jul 28. Epub 2020 Jul 28.

Background: Small intestinal neuroendocrine tumors (SI-NETs) are difficult to diagnose in the early stage of disease. Current blood biomarkers such as chromogranin A (CgA) and 5-hydroxyindolacetic acid (5-HIAA) have low sensitivity and specificity. This is a first pre-planned interim analysis (NORDIC non-interventional, exploratory, EXPLAIN study (NCT02630654)). Its objective is to investigate if a plasma protein multi-biomarker strategy can improve diagnostic accuracy in SI-NETs.

Methods: At time of diagnosis, prior any disease specific treatment was initiated, blood was collected from patients with advanced SI-NETs and 92 putative cancer-related plasma proteins from 135 patients were analyzed and compared with the results of age and gender matched controls (n=143), using multiplex proximity extension assay and machine learning techniques.

Results: Using a random forest model including 12 top ranked plasma proteins in patients with SI-NETs, the multi-biomarker strategy showed sensitivity (SEN) and specificity (SPE) of 89% and 91%, respectively, with negative predictive value (NPV) and positive predictive value (PPV) of 90% and 91%, respectively, to identify patients with regional or metastatic disease with an area under the receiver operator characteristic curve (AUROC) of 99%. In thirty patients with normal CgA concentrations the model provided diagnostic SPE of 98%, a SEN of 56%, and NPV 90%, PPV of 90%, and AUROC 97%, regardless of proton pump inhibitor intake.

Conclusion: This interim analysis demonstrate that a multi-biomarker/machine learning strategy improve diagnostic accuracy of patients with SI-NET at the time of diagnosis, especially in patients with normal CgA levels. The results indicate that this multi-biomarker strategy can be useful for early detection of SI-NETs at presentation and conceivably detect recurrence after radical primary resection.
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http://dx.doi.org/10.1159/000510483DOI Listing
July 2020

A systematic literature review of leptospirosis outbreaks worldwide, 1970-2012.

Rev Panam Salud Publica 2020 15;44:e78. Epub 2020 Jul 15.

Pan American Health Organization Washington DC United States of America Pan American Health Organization, Washington DC, United States of America.

Objective: This review describes the geographic and temporal distribution of, detection methods for, and other epidemiological features of published leptospirosis outbreaks, with the aim of informing efforts to standardize outbreak-reporting practices.

Methods: We conducted a systematic review of leptospirosis outbreaks reported in the scientific literature and ProMED during 1970-2012. Predefined criteria were used to identify and classify outbreaks and a standard form was used to extract information.

Results: During 1970-2012, we identified 318 outbreaks (average: 7 outbreaks/year; range: 1-19). Most outbreaks were reported in the Latin America and the Caribbean region (36%), followed by Southern Asia (13%), and North America (11%). Most outbreaks were located in tropical and subtropical ecoregions (55%). Quality classification showed that there was clear description of laboratory-confirmed cases in 40% of outbreaks. Among those, the average outbreak size was 82 cases overall (range: 2-2 259) but reached 253 cases in tropical/subtropical ecoregions. Common risk factors included outdoor work activities (25%), exposure to floodwaters (23%), and recreational exposure to water (22%). Epidemiologic investigation was conducted in 80% of outbreaks, mainly as case interviews. Case fatality was 5% overall (range: 0%-60%).

Conclusions: Outbreak reporting increased over the study period with outbreaks covering tropical and non-tropical regions. Outbreaks varied by size, setting, and risk factors; however, data reviewed often had limited information regarding diagnosis and epidemiology. Guidelines are recommended to develop standardized procedures for diagnostic and epidemiological investigations during an outbreak and for reporting.
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http://dx.doi.org/10.26633/RPSP.2020.78DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7363284PMC
July 2020

Occurrence, antibiotic-resistance and virulence of E. coli strains isolated from mangrove oysters (Crassostrea gasar) farmed in estuaries of Amazonia.

Mar Pollut Bull 2020 Aug 1;157:111302. Epub 2020 Jun 1.

Centro de Genômica e Biologia de Sistemas, Instituto de Ciências Biológicas, Universidade Federal do Pará, 66075-110 Belém, PA, Brazil; Laboratório de Engenharia Biológica, Parque de Ciência e Tecnologia Guamá, 66075-750 Belém, PA, Brazil.

Concentration of bacterial species indicative of fecal contamination in the gut of mangrove oysters (Crassostrea gasar) is a major concern for public health and food surveillance. Our work aimed to determine the occurrence, antibiotic-resistance, phylogenetic profile and virulence of Escherichia coli strains isolated from C. gasar farmed in four estuaries of Amazonia. Santo Antônio de Urindeua was the sampling point with the highest number of E. coli cells in oyster samples (10 per 100 g of sample). Twenty-four isolates (52.2%) showed resistance to cephalotin and 18 to amoxicillin (39.1%). Eighteen clonal populations were determined by rep-PCR and were mainly affiliated to the pathogenic and commensal phylo-groups B1 and D. The presence of elt genes suggests that 10 of these clones belong to the Enterotoxigenic Escherichia coli pathotype. Plasmids, mostly of the F incompatibility group, were detected in the majority of the strains. All isolates were susceptible to last-resort antibiotics.
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http://dx.doi.org/10.1016/j.marpolbul.2020.111302DOI Listing
August 2020

Corrigendum to: Bioinformatics: scalability, capabilities and training in the data-driven era.

Brief Bioinform 2021 Jan;22(1):610

Chief Technical Officer ELIXIR. E-mail:

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http://dx.doi.org/10.1093/bib/bbaa106DOI Listing
January 2021

Fibronectin Adsorption on Electrospun Synthetic Vascular Grafts Attracts Endothelial Progenitor Cells and Promotes Endothelialization in Dynamic In Vitro Culture.

Cells 2020 03 23;9(3). Epub 2020 Mar 23.

NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany.

Appropriate mechanical properties and fast endothelialization of synthetic grafts are key to ensure long-term functionality of implants. We used a newly developed biostable polyurethane elastomer (TPCU) to engineer electrospun vascular scaffolds with promising mechanical properties (E-modulus: 4.8 ± 0.6 MPa, burst pressure: 3326 ± 78 mmHg), which were biofunctionalized with fibronectin (FN) and decorin (DCN). Neither uncoated nor biofunctionalized TPCU scaffolds induced major adverse immune responses except for minor signs of polymorph nuclear cell activation. The in vivo endothelial progenitor cell homing potential of the biofunctionalized scaffolds was simulated in vitro by attracting endothelial colony-forming cells (ECFCs). Although DCN coating did attract ECFCs in combination with FN (FN + DCN), DCN-coated TPCU scaffolds showed a cell-repellent effect in the absence of FN. In a tissue-engineering approach, the electrospun and biofunctionalized tubular grafts were cultured with primary-isolated vascular endothelial cells in a custom-made bioreactor under dynamic conditions with the aim to engineer an advanced therapy medicinal product. Both FN and FN + DCN functionalization supported the formation of a confluent and functional endothelial layer.
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http://dx.doi.org/10.3390/cells9030778DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7140838PMC
March 2020

Cardiac Extracellular Vesicles (EVs) Released in the Presence or Absence of Inflammatory Cues Support Angiogenesis in Different Manners.

Int J Mol Sci 2019 Dec 17;20(24). Epub 2019 Dec 17.

Charité-Universitätsmedizin Berlin, BCRT-Berlin Institute of Health (BIH) Center for Regenerative Therapies, 10178 Berlin, Germany.

Cells release extracellular vesicles (EVs) to communicate in a paracrine manner with other cells, and thereby influence processes, such as angiogenesis. The conditioned medium of human cardiac-derived adherent proliferating (CardAP) cells was recently shown to enhance angiogenesis. To elucidate whether their released EVs are involved, we isolated them by differential centrifugation from the conditioned medium derived either in the presence or absence of a pro-inflammatory cytokine cocktail. Murine recipient cells internalized CardAP-EVs as determined by an intracellular detection of human proteins, such as CD63, by a novel flow cytometry method for studying EV-cell interaction. Moreover, endothelial cells treated for 24 h with either unstimulated or cytokine stimulated CardAP-EVs exhibited a higher tube formation capability on Matrigel. Interestingly, unstimulated CardAP-EVs caused endothelial cells to release significantly more vascular endothelial growth factor and interleukin (IL)-6, while cytokine stimulated CardAP-EVs significantly enhanced the release of IL-6 and IL-8. By nCounter miRNA expression assay (NanoString Technologies) we identified microRNA 302d-3p to be enhanced in unstimulated CardAP-EVs compared to their cytokine stimulated counterparts, which was verified by quantitative polymerase chain reaction. This study demonstrates that both CardAP-EVs are pro-angiogenic by inducing different factors from endothelial cells. This would allow to select potent targets for a safe and efficient therapeutic application.
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http://dx.doi.org/10.3390/ijms20246363DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6940836PMC
December 2019

A Polymorphonuclear Leukocyte Assay to Assess Implant Immunocompatibility.

Tissue Eng Part C Methods 2019 08;25(8):500-511

1Charité-Universitätsmedizin Berlin, BCRT-Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany.

Impact Statement: Polymorphonuclear leukocytes (PMNs) are essential in the first infection and host-versus-graft reactions. Strategies for adequate and standardized assays to test PMN activation by diverse types of matrices such as cardiovascular implants are urgently needed. To overcome this limitation, we established a straightforward PMN activation assay and validated lipopolysaccharide (LPS) as a reliable PMN activator that induces defined changes in surface marker expression and cytokine release. Biological "proof-of-principle" matrices demonstrated the feasibility of this PMN assay. Overall, this assay provides an instrument conducting an initial immunological assessment of biological implants prior their clinical application.
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http://dx.doi.org/10.1089/ten.TEC.2019.0105DOI Listing
August 2019

Bioinformatics: scalability, capabilities and training in the data-driven era.

Brief Bioinform 2019 03;20(2):735-736

University of Melbourne, Australia.

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http://dx.doi.org/10.1093/bib/bbz053DOI Listing
March 2019

The Marine Mammal Class II Major Histocompatibility Complex Organization.

Front Immunol 2019 4;10:696. Epub 2019 Apr 4.

Laboratory of Genomics and Biotechnology, Biological Sciences Institute, Federal University of Pará, Belém, Brazil.

Sirenians share with cetaceans and pinnipeds several convergent traits selected for the aquatic lifestyle. Living in water poses new challenges not only for locomotion and feeding but also for combating new pathogens, which may render the immune system one of the best tools aquatic mammals have for dealing with aquatic microbial threats. So far, only cetaceans have had their class II Major Histocompatibility Complex (MHC) organization characterized, despite the importance of MHC genes for adaptive immune responses. This study aims to characterize the organization of the marine mammal class II MHC using publicly available genomes. We located class II sequences in the genomes of one sirenian, four pinnipeds and eight cetaceans using NCBI-BLAST and reannotated the sequences using local BLAST search with exon and intron libraries. Scaffolds containing class II sequences were compared using dotplot analysis and introns were used for phylogenetic analysis. The manatee class II region shares overall synteny with other mammals, however most loci were translocated from the canonical location, past the extended class II region. Detailed analysis of the genomes of closely related taxa revealed that this presumed translocation is shared with all other living afrotherians. Other presumptive chromosome rearrangements in Afrotheria are the deletion of loci in Afrosoricida and deletion of in . Pinnipeds share the main features of dog MHC: lack of a functional pair of genes and inverted locus between and subregions. All cetaceans share the Cetartiodactyla inversion separating class II genes into two subregions: class IIa, with and genes, and class IIb, with non-classic genes and a pseudogene. These results point to three distinct and unheralded class II MHC structures in marine mammals: one canonical organization but lacking genes in pinnipeds; one bearing an inversion separating IIa and IIb subregions lacking genes found in cetaceans; and one with a translocation separating the most diverse class II gene from the MHC found in afrotherians and presumptive functional , and genes. Future functional research will reveal how these aquatic mammals cope with pathogen pressures with these divergent MHC organizations.
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http://dx.doi.org/10.3389/fimmu.2019.00696DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6459222PMC
September 2020

Seasonal changes in the song control nuclei of the Rufous-bellied Thrush, Turdus rufiventris (Oscine, Passeriformes, and Turdidae).

J Exp Zool B Mol Dev Evol 2019 05 19;332(3-4):92-98. Epub 2019 Apr 19.

Instituto de Ciências Biológicas, Centro de Genômica e Biologia de Sistemas, Universidade Federal do Pará, Belém, Brazil.

In vocal learning birds, memorization and song production rely on a set of telencephalic nuclei referred to as the song control system. Seasonal changes in song production are correlated with changes in the volume of the song control nuclei and are influenced by photoperiodic conditions and hormonal cues. The seasonal volume changes in the avian brain that controls singing are thought to involve regulation of neuronal replacement, which is a striking example of neuronal plasticity. The Rufous-bellied Thrush (Turdus rufiventris) is a seasonally breeding bird that actively sings during the spring and summer (breeding season) and is relatively silent in the fall, yet possible mechanisms behind the periodic changes in song production remain unknown. Here, we have examined two song control nuclei: High vocal center (HVC) and robust nucleus of arcopallium (RA) in fall males, spring males, and fall females of Rufous-bellied Thrush. The cytoarchitectonic organization was analyzed and quantified from Nissl-stained sections, and gene expression of song nuclei markers was examined by in situ hybridization during breeding and nonbreeding seasons. We observed a reduction in HVC volume and reductions in parvalbumin, and RGS4 expression in HVC and RA in males during the nonbreeding season. These findings provide evidence of seasonal changes in the song system of a representative tropical-breeding Turdidae species that does not maintain territories or mate bonding, setting the histological and molecular groundwork for future studies aimed at better understanding of song nuclei changes in seasonally breeding songbirds.
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http://dx.doi.org/10.1002/jez.b.22853DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6525033PMC
May 2019

Comparison of the Vaginal Microbiomes of Premenopausal and Postmenopausal Women.

Front Microbiol 2019 14;10:193. Epub 2019 Feb 14.

Department of Biological Sciences, University of Idaho, Moscow, ID, United States.

For decades hormone therapy (HT) has been prescribed to treat the symptoms of menopause, such as vaginal dryness, itching and burning. Here we sought to compare the vaginal microbiomes of postmenopausal women who received low dose estrogen therapy to those of premenopausal and postmenopausal women, and to do so in conjunction with assessing the alleviation of symptoms associated with vaginal atrophy. In this study vaginal swab samples were obtained from 45 women who were classified as either premenopausal, postmenopausal, or postmenopausal and undergoing HT. The vaginal microbiomes of these women were characterized by gene sequencing and bacterial abundances were quantified by qPCR. We found that the vaginal communities from our cohort could be divided into six clusters (A-F) based on differences in the composition and relative abundances of bacterial taxa. Communities in cluster A were dominated by , and those of cluster B were dominated by . Communities in cluster C had high proportions of , while those in cluster D were more even and included several co-dominant taxa. Communities in clusters E and F were dominated by and , respectively. The vaginal communities of most postmenopausal women receiving HT (10/15) were dominated by species of lactobacilli and belonged to clusters A, C, and F ( < 0.001). This sharply contrasts with vaginal communities of postmenopausal women without HT, most of which (10/15) were in cluster D, depleted of lactobacilli, and had about 10-fold fewer total bacteria ( < 0.05). The vaginal communities of women in each study group differed in terms of the dominant bacterial species composition and relative abundance. Those of postmenopausal women receiving HT significantly differed from those of postmenopausal women without HT and were most often dominated by species of . Noteworthy, HT greatly improved vaginal atrophy scores, decreased vaginal pH, and significantly increased bacterial numbers in comparison to postmenopausal women not receiving HT.
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http://dx.doi.org/10.3389/fmicb.2019.00193DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6382698PMC
February 2019

A One Health Approach to Investigating Serogroups and Their Spatial Distributions among Humans and Animals in Rio Grande do Sul, Brazil, 2013⁻2015.

Trop Med Infect Dis 2019 Feb 27;4(1). Epub 2019 Feb 27.

Pan American Health Organization (PAHO/WHO), Washington, DC 20037, USA.

Leptospirosis is an endemic zoonotic disease in Brazil and is widespread throughout rural populations in the state of Rio Grande do Sul. This study aimed to identify presumptive infecting serogroups in human and animal cases and describe their occurrences within the ecoregions of the state by animal species. Data for human and animal leptospirosis cases were gathered from the government's passive surveillance systems and presumptive infecting serogroups were identified based on a two-fold titer difference in serogroups in the microscopic agglutination test (MAT) panel. A total of 22 different serogroups were reported across both human and animal cases. Serogroup Icterohaemorrhagiae was the most common among humans, while serogroup Sejroe predominated among animal cases, particularly bovines. Each ecoregion had a large distribution of cases, with 51% of the human cases in the Parana⁻Paraiba ecoregion, and 81% of the animal cases in the Savannah ecoregion. Identifying and mapping the serogroups circulating using the One Health approach is the first step for further understanding the distribution of the disease in the state. This study has the potential to aid in guiding public health and agricultural practices, furthering the need for a human vaccine in high-risk populations to complement control and prevention efforts.
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http://dx.doi.org/10.3390/tropicalmed4010042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6473481PMC
February 2019

Structure of Hierridin C, Synthesis of Hierridins B and C, and Evidence for Prevalent Alkylresorcinol Biosynthesis in Picocyanobacteria.

J Nat Prod 2019 02 4;82(2):393-402. Epub 2019 Feb 4.

Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR) , University of Porto , Avenida General Norton de Matos, s/n , 4450-208 Matosinhos , Portugal.

Small, single-celled planktonic cyanobacteria are ubiquitous in the world's oceans yet tend not to be perceived as secondary metabolite-rich organisms. Here we report the isolation and structure elucidation of hierridin C, a minor metabolite obtained from the cultured picocyanobacterium Cyanobium sp. LEGE 06113. We describe a simple, straightforward synthetic route to the scarcely produced hierridins that relies on a key regioselective halogenation step. In addition, we show that these compounds originate from a type III PKS pathway and that similar biosynthetic gene clusters are found in a variety of bacterial genomes, most notably those of the globally distributed picocyanobacteria genera Prochlorococcus, Cyanobium and Synechococcus.
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http://dx.doi.org/10.1021/acs.jnatprod.8b01038DOI Listing
February 2019

Parrot Genomes and the Evolution of Heightened Longevity and Cognition.

Curr Biol 2018 12 6;28(24):4001-4008.e7. Epub 2018 Dec 6.

Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239, USA. Electronic address:

Parrots are one of the most distinct and intriguing groups of birds, with highly expanded brains [1], highly developed cognitive [2] and vocal communication [3] skills, and a long lifespan compared to other similar-sized birds [4]. Yet the genetic basis of these traits remains largely unidentified. To address this question, we have generated a high-coverage, annotated assembly of the genome of the blue-fronted Amazon (Amazona aestiva) and carried out extensive comparative analyses with 30 other avian species, including 4 additional parrots. We identified several genomic features unique to parrots, including parrot-specific novel genes and parrot-specific modifications to coding and regulatory sequences of existing genes. We also discovered genomic features under strong selection in parrots and other long-lived birds, including genes previously associated with lifespan determination as well as several hundred new candidate genes. These genes support a range of cellular functions, including telomerase activity; DNA damage repair; control of cell proliferation, cancer, and immunity; and anti-oxidative mechanisms. We also identified brain-expressed, parrot-specific paralogs with known functions in neural development or vocal-learning brain circuits. Intriguingly, parrot-specific changes in conserved regulatory sequences were overwhelmingly associated with genes that are linked to cognitive abilities and have undergone similar selection in the human lineage, suggesting convergent evolution. These findings bring novel insights into the genetics and evolution of longevity and cognition, as well as provide novel targets for exploring the mechanistic basis of these traits.
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http://dx.doi.org/10.1016/j.cub.2018.10.050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6393663PMC
December 2018

Congenital human toxoplasmosis caused by non-clonal Toxoplasma gondii genotypes in Argentina.

Parasitol Int 2019 Feb 7;68(1):48-52. Epub 2018 Oct 7.

Laboratorio de Inmunoparasitología, FCV-UNLP, La Plata, Argentina.

Toxoplasmosis, a worldwide distributed zoonosis, can be transmitted congenitally affecting fetuses and developing variable clinical signs. Different Toxoplasma gondii genotypes and infective dose are related factors with different clinical manifestations. Several studies indicate that atypical strains could produce more severe clinical manifestations compared to typical strains. Umbilical cord blood (n = 37) and placenta (n = 19) were collected at birth from women with acute T. gondii infection and processed for isolation by mice bioassay. Six isolates were obtained and identified as TgHm14-4Arg, TgHm15-02Arg, TgHm16-01Arg, TgHm16-02Arg, TgHm17-01Arg and TgHm17-02Arg. Three genotypes described previously on Toxo-DB were identified: #138 identified in chickens from Brazil, #182 isolated from eared doves from Brazil, #14 from wallaby kangaroos and chickens from Argentina, chickens from Brazil, Colombia, Chile and Venezuela, cats and dogs from Brazil and Colombia and also coyotes from USA indicating worldwide distribution of these genotypes. Two new allele combinations were obtained showing high genotypes diversity in Argentina. Four of the isolates (TgHm14-4Arg, TgHm15-02Arg, TgHm16-01Arg, TgHm16-02Arg) and two of them (TgHm17-01Arg, TgHm17-02Arg) produced chronic and acute infections in mice, respectively. Until now, seven T. gondii isolates have been obtained from humans in Argentina, and all were atypical or non-clonal genotypes. The identification of atypical strains causing congenital toxoplasmosis and circulating in our region, make important to perform the serological screenings according Argentine Consensus of Toxoplasmosis and to apply and monitoring treatments earlier in pregnancy. To achieve this aim, it is necessary to inform general population about T. gondii infection, diagnostics and control measures. These results should serve to generate awareness about congenital toxoplasmosis in South America.
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http://dx.doi.org/10.1016/j.parint.2018.10.002DOI Listing
February 2019

Comparative mitogenomic analyses of Amazona parrots and Psittaciformes.

Genet Mol Biol 2018 Jul/Sept.;41(3):593-604

Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.

Amazon parrots are long-lived birds with highly developed cognitive skills, including vocal learning. Several parrot mitogenomes have been sequenced, but important aspects of their organization and evolution are not fully understood or have limited experimental support. The main aim of the present study was to describe the mitogenome of the blue-fronted Amazon, Amazona aestiva, and compare it to other mitogenomes from the genus Amazona and the order Psittaciformes. We observed that mitogenomes are highly conserved among Amazon parrots, and a detailed analysis of their duplicated control regions revealed conserved blocks. Population level analyses indicated that the specimen analyzed here seems to be close to A. aestiva individuals from Bahia state. Evolutionary relationships of 41 Psittaciformes species and three outgroups were inferred by BEAST. All relationships were retrieved with high support.
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http://dx.doi.org/10.1590/1678-4685-GMB-2017-0023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6136379PMC
February 2017

Best practice data life cycle approaches for the life sciences.

F1000Res 2017;6:1618. Epub 2017 Aug 31.

Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia.

Throughout history, the life sciences have been revolutionised by technological advances; in our era this is manifested by advances in instrumentation for data generation, and consequently researchers now routinely handle large amounts of heterogeneous data in digital formats. The simultaneous transitions towards biology as a data science and towards a 'life cycle' view of research data pose new challenges. Researchers face a bewildering landscape of data management requirements, recommendations and regulations, without necessarily being able to access data management training or possessing a clear understanding of practical approaches that can assist in data management in their particular research domain. Here we provide an overview of best practice data life cycle approaches for researchers in the life sciences/bioinformatics space with a particular focus on 'omics' datasets and computer-based data processing and analysis. We discuss the different stages of the data life cycle and provide practical suggestions for useful tools and resources to improve data management practices.
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http://dx.doi.org/10.12688/f1000research.12344.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6069748PMC
August 2017

New susceptibility loci for cutaneous melanoma risk and progression revealed using a porcine model.

Oncotarget 2018 Jun 12;9(45):27682-27697. Epub 2018 Jun 12.

INSERM, UMR-946, Genetic Variation and Human Diseases Unit, Paris, France.

Despite major advances, it is estimated that a large part of melanoma predisposing genes remains to be discovered. Animal models of spontaneous diseases are valuable tools and experimental crosses can be used to identify and fine-map new susceptibility loci associated with melanoma. We performed a Genome-Wide Association Study (GWAS) of melanoma occurrence and progression (clinical ulceration and presence of metastasis) in a porcine model of spontaneous melanoma, the MeLiM pig. Five loci on chromosomes 2, 5, 7, 8 and 16 showed genome-wide significant associations ( < 5 × 10) with either one of these phenotypes. Suggestive associations ( < 5 × 10) were also found at 16 additional loci. Moreover, comparison of the porcine results to those reported by human melanoma GWAS indicated shared association signals notably at and loci but also nearby , FTO, and TMEM loci. Extensive search of the literature revealed a potential key role of genes at the identified porcine loci in tumor invasion (, PLEKHA5, , and ) and immune response modulation (, and ) of the progression phenotypes. These biological processes are consistent with the clinico-pathological features of MeLiM tumors and can open new routes for future melanoma research in humans.
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http://dx.doi.org/10.18632/oncotarget.25455DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6021234PMC
June 2018

Environmental and socioeconomic drivers in infectious disease.

Lancet Planet Health 2018 05;2(5):e198-e199

North Carolina State University, College of Veterinary Medicine, Department of Population Health and Pathobiology, Raleigh, NC 27606, USA.

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http://dx.doi.org/10.1016/S2542-5196(18)30069-XDOI Listing
May 2018

Towards a Novel Patch Material for Cardiac Applications: Tissue-Specific Extracellular Matrix Introduces Essential Key Features to Decellularized Amniotic Membrane.

Int J Mol Sci 2018 Mar 29;19(4). Epub 2018 Mar 29.

Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 13353 Berlin, Germany.

There is a growing need for scaffold material with tissue-specific bioactivity for use in regenerative medicine, tissue engineering, and for surgical repair of structural defects. We developed a novel composite biomaterial by processing human cardiac extracellular matrix (ECM) into a hydrogel and combining it with cell-free amniotic membrane via a dry-coating procedure. Cardiac biocompatibility and immunogenicity were tested in vitro using human cardiac fibroblasts, epicardial progenitor cells, murine HL-1 cells, and human immune cells derived from buffy coat. Processing of the ECM preserved important matrix proteins as demonstrated by mass spectrometry. ECM coating did not alter the mechanical characteristics of decellularized amniotic membrane but did cause a clear increase in adhesion capacity, cell proliferation and viability. Activated monocytes secreted less pro-inflammatory cytokines, and both macrophage polarization towards the pro-inflammatory M1 type and T cell proliferation were prevented. We conclude that the incorporation of human cardiac ECM hydrogel shifts and enhances the bioactivity of decellularized amniotic membrane, facilitating its use in future cardiac applications.
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http://dx.doi.org/10.3390/ijms19041032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5979550PMC
March 2018