An in-depth evaluation of metagenomic classifiers for soil microbiomes.

BACKGROUND: Recent endeavours in metagenomics, exemplified by projects such as the human microbiome project and TARA Oceans, have illuminated the complexities of microbial biomes. A robust bioinformatic pipeline and meticulous evaluation of their methodology have contributed to the success of these projects. The soil environment, however, with its unique challenges, requires a specialized methodological exploration to maximize microbial insights. A notable limitation in soil microbiome studies is the dearth of soil-specific reference databases available to classifiers that emulate the complexity of soil communities. There is also a lack of in-vitro mock communities derived from soil strains that can be assessed for taxonomic classification accuracy. RESULTS: In this study, we generated a custom in-silico mock community containing microbial genomes commonly observed in the soil microbiome. Using this mock community, we simulated shotgun sequencing data to evaluate the performance of three leading metagenomic classifiers: Kraken2 (supplemented with Bracken, using a custom database derived from GTDB-TK genomes along with its own default database), Kaiju, and MetaPhlAn, utilizing their respective default databases for a robust analysis. Our results highlight the importance of optimizing taxonomic classification parameters, database selection, as well as analysing trimmed reads and contigs. Our study showed that classifiers tailored to the specific taxa present in our samples led to fewer errors compared to broader databases including microbial eukaryotes, protozoa, or human genomes, highlighting the effectiveness of targeted taxonomic classification. Notably, an optimal classifier performance was achieved when applying a relative abundance threshold of 0.001% or 0.005%. The Kraken2 supplemented with bracken, with a custom database demonstrated superior precision, sensitivity, F1 score, and overall sequence classification. Using a custom database, this classifier classified 99% of in-silico reads and 58% of real-world soil shotgun reads, with the latter identifying previously overlooked phyla using a custom database. CONCLUSION: This study underscores the potential advantages of in-silico methodological optimization in metagenomic analyses, especially when deciphering the complexities of soil microbiomes. We demonstrate that the choice of classifier and database significantly impacts microbial taxonomic profiling. Our findings suggest that employing Kraken2 with Bracken, coupled with a custom database of GTDB-TK genomes and fungal genomes at a relative abundance threshold of 0.001% provides optimal accuracy in soil shotgun metagenome analysis.

Modeling the environmental fate of bracken toxin ptaquiloside: Production, release and transport in the rhizosphere.

Plants produce a diverse array of toxic compounds which may be released by precipitation, explaining their wide occurrence in surrounding soil and water. This study presents the first mechanistic model for describing the generation and environmental fate of a natural toxin, i.e. ptaquiloside (PTA), a carcinogenic phytotoxin produced by bracken fern (Pteridium aquilinum L. Kuhn). The newly adapted DAISY model was calibrated based on two-year monitoring performed in the period 2018-2019 in a Danish bracken population located in a forest glade. Several functions related to the fate of PTA were calibrated, covering processes from toxin generation in the canopy, wash off by precipitation and degradation in the soil. Model results show a good description of observed bracken biomass and PTA contents, supporting the assumption that toxin production can be explained by the production of new biomass. Model results show that only 4.4 % of the PTA produced in bracken is washed off by precipitation, from both canopy and litter. Model simulations showed that PTA degrades rapidly once in the soil, especially during summer due to the high soil temperatures. Leaching takes place in form of pulses directly connected to precipitation events, with maximum simulated concentrations up to 4.39 µg L-1 at 50 cm depth. Macropore transport is mainly responsible for the events with the highest PTA concentrations, contributing to 72 % of the total mass of PTA leached. Based on the results, we identify areas with high density of bracken, high precipitation during the summer and soils characterized by fast transport, as the most vulnerable to surface and groundwater pollution by phytotoxins.

Cross-species oncogenomics offers insight into human muscle-invasive bladder cancer.

BACKGROUND: In humans, muscle-invasive bladder cancer (MIBC) is highly aggressive and associated with a poor prognosis. With a high mutation load and large number of altered genes, strategies to delineate key driver events are necessary. Dogs and cats develop urothelial carcinoma (UC) with histological and clinical similarities to human MIBC. Cattle that graze on bracken fern also develop UC, associated with exposure to the carcinogen ptaquiloside. These species may represent relevant animal models of spontaneous and carcinogen-induced UC that can provide insight into human MIBC. RESULTS: Whole-exome sequencing of domestic canine (n = 87) and feline (n = 23) UC, and comparative analysis with human MIBC reveals a lower mutation rate in animal cases and the absence of APOBEC mutational signatures. A convergence of driver genes (ARID1A, KDM6A, TP53, FAT1, and NRAS) is discovered, along with common focally amplified and deleted genes involved in regulation of the cell cycle and chromatin remodelling. We identify mismatch repair deficiency in a subset of canine and feline UCs with biallelic inactivation of MSH2. Bovine UC (n = 8) is distinctly different; we identify novel mutational signatures which are recapitulated in vitro in human urinary bladder UC cells treated with bracken fern extracts or purified ptaquiloside. CONCLUSION: Canine and feline urinary bladder UC represent relevant models of MIBC in humans, and cross-species analysis can identify evolutionarily conserved driver genes. We characterize mutational signatures in bovine UC associated with bracken fern and ptaquiloside exposure, a human-linked cancer exposure. Our work demonstrates the relevance of cross-species comparative analysis in understanding both human and animal UC.

Structural and physicochemical properties of bracken fern (Pteridium aquilinum) starch.

Introduction: Bracken fern (Pteridium aquilinum) starch is a non-mainstream, litter-researched starch, thus the starch characteristics remain largely unknown. Methods: The structural and physicochemical properties of two bracken starches were systematically investigated, by use of various techniques that routinely applied in starch analysis. Results and Discussion: The starches had amylose contents of 22.6 and 24.7%, respectively. The starch granules possessed C-type polymorph with D (4,3) ranging from 18.6 to 24.5 µm. During gelatinization event, the bracken starches showed lower viscosity than typical for rice starch, and lower gelatinization temperature than typical for cereal starches. After gelatinization event, bracken starches formed much softer and sticky gel than rice and potato starch. The molecular weight and branching degree (indexed by Mw, Mn and Rz values) of bracken starches were much higher than starches of many other sources. The branch chain length distributions showed that the bracken starches were structurally similar to some rice varieties (e. g. BP033, Beihan 1#), as reflected by proportions of A, B1, B2, and B3 chains. Notable differences in some starch traits between the two bracken starches were recorded, e. g. amylose content, gel hardness, gelatinization temperature and traits of structural properties. This study provides useful information on the utilization of bracken starch in both food and non-food industries.

Recovery of upland acid grasslands after successful Pteridium aquilinum control: Long-term effectiveness of cutting, repeated herbicide treatment and bruising.

There is a clear need for the development of management strategies to control dominant, perennial weeds and restore semi-natural communities and an important part of this is to know how long control treatments take to be effective and how long they last after treatments stop. Here, we report the results from a 17-year long experiment where we compared the effects of five control treatments on dense Pteridium aquilinum (L. Kuhn) relative to an untreated experimental-control in Derbyshire, UK. The experiment was run in two phases. In Phase 1 (2005-2012) we controlled the P. aquilinum by cutting and bruising, both twice and thrice annually, and a herbicide treatment (asulam in year 1, followed by annual spot-re-treatment of all emergent fronds). In Phase 2 (2012-2021) all treatments were stopped, and the vegetation was allowed to develop naturally. Between 2005 and 2021 we monitored P. aquilinum performance annually and full plant species composition at intervals. Here, we concentrate on analysing the Phase 2 data where we used regression approaches to model individual species responses through time and unconstrained ordination to compare treatment effects on the entire species composition over both Phases. Remote sensing was also used to assess edge invasion in 2018. At the end of Phase 1, a good reduction of P. aquilinum and restoration of acid-grassland was achieved for the asulam and cutting treatments, but not for bruising. In Phase 2, P. aquilinum increased through time in all treated plots but the asulam and cutting ones maintained a much lower P. aquilinum performance for nine years on all measures assessed. There was a reduction in species richness and richness fluctuations, especially in graminoid species. However, multivariate analysis showed that the asulam and cutting treatments were stationed some distance from the untreated and bruising treatments with no apparent sign of reversions suggesting an Alternative Stable State had been created, at least over this nine-year period. P. aquilinum reinvasion was mainly from plot edges. The use of repeated P. aquilinum control treatments, either through an initial asulam spray with annual follow-up spot-spraying or cutting twice or thrice annually for eight years gave good P. aquilinum control and helped restore an acid-grassland community. Edge reinvasion was detected, and it is recommended that either whole-patch control be implemented or treatments should be continued around patch edges.

Evaluation and Monitoring of the Natural Toxin Ptaquiloside in Bracken Fern, Meat, and Dairy Products.

Ptaquiloside, a naturally occurring cancer-causing substance in bracken fern, has been detected in the meat and milk of cows fed a diet containing bracken fern. A rapid and sensitive method for the quantitative analysis of ptaquiloside in bracken fern, meat, and dairy products was developed using the QuEChERS method and liquid chromatography-tandem mass spectrometry. The method was validated according to the Association of Official Analytical Chemists guidelines and met the criteria. A single matrix-matched calibration method with bracken fern has been proposed, which is a novel strategy that uses one calibration for multiple matrices. The calibration curve ranged from 0.1 to 50 µg/kg and showed good linearity (r2 > 0.99). The limits of detection and quantification were 0.03 and 0.09 µg/kg, respectively. The intraday and interday accuracies were 83.5-98.5%, and the precision was <9.0%. This method was used for the monitoring and exposure assessment of ptaquiloside in all routes of exposure. A total of 0.1 µg/kg of ptaquiloside was detected in free-range beef, and the daily dietary exposure of South Koreans to ptaquiloside was estimated at up to 3.0 × 10-5 µg/kg b.w./day. The significance of this study is to evaluate commercially available products in which ptaquiloside may be present, to monitor consumer safety.

Risk Assessment and Risk Reduction of Ptaquiloside in Bracken Fern.

This study was conducted to determine the optimal boiling time to reduce ptaquiloside (PTA) and to carry out a risk assessment for PTA, a representative toxic substance found in bracken fern (BF; Pteridium aquilinum), which is frequently consumed as food in East Asian countries. High-performance liquid chromatography showed that the concentration of PTA in BF was reduced by up to 99% after boiling for 20 min. Risk assessment results showed that the cancer margin of exposure (MOE; ≥ 25,000 = safe) to PTA for an average daily exposure scenario after boiling BF for 20 min was considered safe. In addition, the non-cancer MOE (≥ 300 = safe) to PTA under an average daily exposure scenario after BF boiling for 20 min was considered safe. However, human exposure to PTA was considered unsafe under the non-boiled BF exposure and maximum daily exposure scenarios. Therefore, boiling BF for at least 20 min is recommended before consumption, to reduce exposure to PTA as much as possible.

An Unusual Small Bowel Phytobezoar Successfully Resolved by Double-balloon Enteroscopy.

We herein report a very unusual case of small bowel obstruction caused by phytobezoar in a 69-year-old woman who consumed a large amount of bracken. The patient presented with nausea and vomiting. Computed tomography revealed an air-filled foreign body in the jejunum that had likely caused the small bowel obstruction. A fibrous foreign body diagnosed as a phytobezoar was detected using double-balloon enteroscopy. The obstruction was successfully resolved by crushing the phytobezoar repeatedly using a snare. Small bowel obstructions caused by phytobezoars are often treated with surgical interventions. However, endoscopic fragmentation using a snare is a minimally invasive treatment alternative.

Health and Environmental Hazards of the Toxic Pteridium aquilinum (L.) Kuhn (Bracken Fern).

Bracken fern (Pteridium aquilinum (L.) Kuhn) is ubiquitous and acts as a cosmopolitan weed in pastures and similar environments. Despite its historical uses, it presents risks due to toxicity. This study, conducted in the second half of 2023, aimed to assess the environmental and health hazards of P. aquilinum, primarily focusing on its carcinogenic compound, ptaquiloside. The literature was comprehensively reviewed using diverse databases, including PubMed, Web of Science, Scopus, and Google Scholar. Information was synthesized from original research articles, meta-analyses, systematic reviews, and relevant animal studies. Animals grazing on bracken fern face annual production losses due to toxin exposure. The substantial impact on biodiversity, animal health, and human well-being arises from the presence of ptaquiloside and related compounds in milk, meat, and water, along with the increasing global prevalence of P. aquilinum and its swift colonization in acidic soil and fire-damaged areas. The objectives were to identify major bioactive compounds and explore their effects at molecular, cellular, pathological, and population levels. Various cooking techniques were considered to mitigate toxin exposure, although complete elimination remains unattainable. Therefore, the findings emphasize the need for cautious consumption. In conclusion, continued research is necessary to better understand and manage its environmental and health implications.

Comparison of Metagenomics and Metatranscriptomics Tools: A Guide to Making the Right Choice.

The study of microorganisms is a field of great interest due to their environmental (e.g., soil contamination) and biomedical (e.g., parasitic diseases, autism) importance. The advent of revolutionary next-generation sequencing techniques, and their application to the hypervariable regions of the 16S, 18S or 23S ribosomal subunits, have allowed the research of a large variety of organisms more in-depth, including bacteria, archaea, eukaryotes and fungi. Additionally, together with the development of analysis software, the creation of specific databases (e.g., SILVA or RDP) has boosted the enormous growth of these studies. As the cost of sequencing per sample has continuously decreased, new protocols have also emerged, such as shotgun sequencing, which allows the profiling of all taxonomic domains in a sample. The sequencing of hypervariable regions and shotgun sequencing are technologies that enable the taxonomic classification of microorganisms from the DNA present in microbial communities. However, they are not capable of measuring what is actively expressed. Conversely, we advocate that metatranscriptomics is a "new" technology that makes the identification of the mRNAs of a microbial community possible, quantifying gene expression levels and active biological pathways. Furthermore, it can be also used to characterise symbiotic interactions between the host and its microbiome. In this manuscript, we examine the three technologies above, and discuss the implementation of different software and databases, which greatly impact the obtaining of reliable results. Finally, we have developed two easy-to-use pipelines leveraging Nextflow technology. These aim to provide everything required for an average user to perform a metagenomic analysis of marker genes with QIMME2 and a metatranscriptomic study using Kraken2/Bracken.

The Norsesquiterpene Glycoside Ptaquiloside as a Poisonous, Carcinogenic Component of Certain Ferns.

Previous studies related to the ptaquiloside molecule, a carcinogenic secondary metabolite known from the world of ferns, are summarised. Ptaquiloside (PTA) belongs to the group of norsesquiterpenes of the illudane type. The name illudane refers to the fungal taxa from which the first representatives of the molecular group were identified. Ptaquiloside occurs mainly in Pteridium fern species, although it is also known in other fern taxa. The species of the genus Pteridium are common, frequent invasive species on all continents, and PTA is formed in smaller or larger amounts in all organs of the affected species. The effects of PTA and of their derivatives on animals and humans are of great toxicological significance. Its basic chemical property is that the molecule can be transformed. First, with the loss of sugar moiety, ptaquilosine is formed, and then, under certain conditions, a dienone derivative (pteridienone) may arise. The latter can alkylate (through its cyclopropane groups) certain molecules, including DNA, in animal or human organisms. In this case, DNA adducts are formed, which can later have a carcinogenic effect through point mutations. The scope of the PTA is interdisciplinary in nature since, for example, molecules from plant biomass can enter the body of animals or humans in several ways (directly and indirectly). Due to its physico-chemical properties (excellent water solubility), PTA can get from the plant into the soil and then into different water layers. PTA molecules that enter the soil, but mainly water, undergo degradation (hydrolytic) processes, so it is very important to clarify the toxicological conditions of a given ecosystem and to estimate the possible risks caused by PTA. The toxicoses and diseases of the animal world (mainly for ruminant farm animals) caused by PTA are briefly described. The intake of PTA-containing plants as a feed source causes not only various syndromes but can also enter the milk (and meat) of animals. In connection with the toxicological safety of the food chain, it is important to investigate the transport of carcinogenic PTA metabolites between organisms in a reassuring manner and in detail. This is a global, interdisciplinary task. The present review aims to contribute to this.

Anaemia in Ruminants Caused by Plant Consumption.

Plant toxicology has affected animals throughout evolution. Plants have adapted themselves to the environment. This adaptation has led to the development of defensive strategies to avoid being consumed. Plants have several chemical compounds, which can cause deleterious effects on people or animals that consume them, causing a wide variety of clinical signs. Plants from various latitudes, both cultivated for human and animal feeding or decorative purpose and even wild growth plants are able to generate anaemia in ruminants. Coumarins or ptaquiloside predispose bleeding and haemorrhages, causing a haemorrhagic disease in affected animals. In this group, some important fodder plants, such sweet clover (Genus Melilotus spp.), or other weeds distributed worldwide, such as bracken fern (Pteridium aquilinum) of giant fennel (Ferula communis), are included. On the other hand, sulfur-containing chemicals (e.g., n-propyl disulfate and S-propyl cysteine sulfoxides (SMCOs)) may cause severe direct damage to the erythrocyte and their membrane, leading to their destruction and causing haemolytic anaemia in the animal. This review presents the most frequent intoxication by plants causing anaemia in ruminants. Toxic compounds, clinical signs, diagnosis and possible treatments are also presented.

Efficient and Quality-Optimized Metagenomic Pipeline Designed for Taxonomic Classification in Routine Microbiological Clinical Tests.

Metagenomics analysis is now routinely used for clinical diagnosis in several diseases, and we need confidence in interpreting metagenomics analysis of microbiota. Particularly from the side of clinical microbiology, we consider that it would be a major milestone to further advance microbiota studies with an innovative and significant approach consisting of processing steps and quality assessment for interpreting metagenomics data used for diagnosis. Here, we propose a methodology for taxon identification and abundance assessment of shotgun sequencing data of microbes that are well fitted for clinical setup. Processing steps of quality controls have been developed in order (i) to avoid low-quality reads and sequences, (ii) to optimize abundance thresholds and profiles, (iii) to combine classifiers and reference databases for best classification of species and abundance profiles for both prokaryotic and eukaryotic sequences, and (iv) to introduce external positive control. We find that the best strategy is to use a pipeline composed of a combination of different but complementary classifiers such as Kraken2/Bracken and Kaiju. Such improved quality assessment will have a major impact on the robustness of biological and clinical conclusions drawn from metagenomic studies.

Does invasion by Pteridium aquilinum (Dennstaedtiaceae) affect the ecological succession in Atlantic Forest areas after a fire?

Pteridium aquilinum (Dennstaedtiaceae) colonization affects ecological and restoration processes. The knowledge of the impacts on the ecological succession by this species allows the use of restoration strategies in invaded environments. This work aimed to evaluate the floristic composition, diversity, structure, density, basal area, height, and diameter of natural regeneration in three areas of the Atlantic Forest in the Serra do Espinhaço Biosphere Reserve in an area invaded by P. aquilinum after a fire. Three environments with different coverage intensities by P. aquilinum were studied, and the plants over 10 cm in height or 5 cm in canopy diameter were measured. The floristic composition and diversity were analyzed using indices presented by Chao, Fisher, Margalef, Pielou, Shannon-Weaver, and Simpson, and similarity was evaluated by the Jaccard index. Species density, basal area, height, and canopy diameter classes were also evaluated. The floristic composition, diversity, structure of natural regeneration, density, and basal area were higher in post-fire areas with a lower coverage by P. aquilinum. The topsoil coverage with plant litter and the possible effect of P. aquilinum allelopathy probably reduced the species richness and diversity. The proportion of plants from the lowest height and canopy diameter classes was higher under moderate coverage by P. aquilinum. The reduction in the floristic composition, diversity, number of species, and basal area in post-fire areas colonized by P. aquilinum is probably due to this species aggressiveness. The population of this plant is high, accumulating large quantities of plant litter as a physical barrier preventing light and propagules from reaching the soil, reducing the germination of the seed bank and, consequently, the natural regeneration. The floristic composition, diversity, structure of natural regeneration, density, and basal area were lower in areas with higher coverage by P. aquilinum. The proportion of plants in the most significant height and canopy diameter classes was higher with reduced coverage by P. aquilinum. The P. aquilinum reduced forest succession in areas after a fire.

Sampling implications of variation in daily activity of the sheep tick, Ixodes ricinus at a coastal grassland site in the U.K.

The sheep tick, Ixodes ricinus L. (Acari: Ixodidae), is an important vector of many pathogens of medical and veterinary significance. Determining vector abundance is a requisite of assessing potential vector-borne disease risk. Estimation of tick abundance is often conducted by blanket drag sampling a site, conducted at one time point during the day. The time of day chosen for sampling can vary, is not widely standardized and is often unreported by the investigator. This study investigated whether the time of day chosen for sampling had an effect on tick collection at an open grassland coastal site in North Devon, U.K., during May 2019 to July 2019. Tick abundance for both adults and nymphs in the evening period was more than twice that found in the mid-day sampling period. Overall abundance differed with site aspect, ground temperature and relative humidity. This study shows that for this open grassland recreational site, the time of day chosen for sampling has important implications for tick collection and the assessment of the relative risk of human exposure to ticks and tick-borne infections.

Ocurrence enzootic hematuria in buffaloes in Brazil: epidemiological, clinical, and pathological aspects

ABSTRACT: It is reported the occurrence of enzootic hematuria (EH) in buffaloes in Brazil after performing an epidemiological survey and clinicopathological analises. To date, EH caused by ingestion of Pteridium esculentum subsp. arachnoideum, a radiomimetic plant popularly known as bracken fern, has not been described in this species in Brazil. Bovine EH is responsible for high economic losses in Brazils Southeast Region not only because of the deaths it causes, but also owing to its negative effect on productivity. In São José do Barreiro County, São Paulo, some farmers in areas with a high incidence of bovine EH have been replacing cattle with buffaloes, based on the premise that the latter would be more resistant to poisoning by ingestion of Pteridium spp. However, even though initial observations indicated that buffaloes are indeed less sensitive than cattle to the toxic principle of Pteridium spp., cases of hematuria in this species have been reported. According to preliminary date, EH only occurs in buffaloes over six years of age. Macroscopic examination revealed a thickened urinary vesicle mucosa, along with multiple foci of ulcerated, exophytic, verrucous, and pedunculated lesions. In one of the buffaloes studied, the bladder wall was ruptured and exhibited marked secondary inflammation. Histologically, neoplastic and non-neoplastic changes similar to those described in cattle poisoned by Pteridium spp. were observed. The neoplasms found included papilloma, carcinoma in situ, urothelial carcinoma (low and high grade), inverted, microcystic, and trabecular variants, urothelial carcinoma with divergent differentiation (squamous and glandular), squamous cell carcinoma, lymphangioma, hemangioma, and hemangiosarcoma. There was also coexistence of epithelial and mesenchymal neoplasms. Bovine papillomavirus particles were not detected by polymerase chain reaction in the bladder samples analyzed.

RESUMO: Descreve-se, através de levantamento epidemiológico e avaliação clínico-patológica, a ocorrência de hematúria enzoótica (HE) em búfalos no Brasil. Essa condição, causada pela ingestão da planta radiomimética Pteridium esculentum subsp. arachnoideum, conhecida popularmente como samambaia ou samambaia do campo, até então não havia sido descrita nessa espécie no Brasil. Na Região Sudeste, a HE bovina é responsável por elevadas perdas econômicas, devidas não apenas aos óbitos, mas também em função da queda de produtividade. No município de São José do Barreiro/SP, alguns produtores de áreas com alta incidência de HE bovina, vêm substituindo os bovinos por búfalos, com base na premissa de que estes seriam mais resistentes à intoxicação. Embora, de acordo com observações iniciais, os búfalos realmente sejam menos sensíveis que os bovinos ao princípio tóxico de Pteridium spp., ainda assim, tem-se verificado a ocorrência de casos de hematúria nessa espécie. De acordo com o levantamento inicial, a HE só ocorre em búfalos com idade a partir de seis anos. Ao exame macroscópico, verificou-se a mucosa da bexiga espessa, com múltiplos focos de lesões ulceradas, exofíticas, papiliformes, verrucosas, pedunculadas. Histologicamente, foram observadas alterações neoplásicas e não neoplásicas semelhantes às descritas nos bovinos com HE. Entre as neoplasias foram encontrados papiloma, carcinoma in situ, carcinoma urotelial (baixo e alto grau), variantes invertida, microcística e trabecular, carcinoma urotelial com diferenciação divergente (escamosa e glandular), carcinoma de células escamosas, linfangioma, hemangioma e hemangiossarcoma. Ocorreu também coexistência entre neoplasias epiteliais e mesenquimais. Não foram detectadas partículas de papilomavírus bovino pelo teste PCR nas amostras de bexiga analisadas.

Ocurrence enzootic hematuria in buffaloes in Brazil: epidemiological, clinical, and pathological aspects / Ocorrência de hematúria enzoótica em búfalos no Brasil: aspectos epidemiológicos, clínicos e patológicos

It is reported the occurrence of enzootic hematuria (EH) in buffaloes in Brazil after performing an epidemiological survey and clinicopathological analises. To date, EH caused by ingestion of Pteridium esculentum subsp. arachnoideum, a radiomimetic plant popularly known as "bracken fern", has not been described in this species in Brazil. Bovine EH is responsible for high economic losses in Brazil's Southeast Region not only because of the deaths it causes, but also owing to its negative effect on productivity. In São José do Barreiro County, São Paulo, some farmers in areas with a high incidence of bovine EH have been replacing cattle with buffaloes, based on the premise that the latter would be more resistant to poisoning by ingestion of Pteridium spp. However, even though initial observations indicated that buffaloes are indeed less sensitive than cattle to the toxic principle of Pteridium spp., cases of hematuria in this species have been reported. According to preliminary date, EH only occurs in buffaloes over six years of age. Macroscopic examination revealed a thickened urinary vesicle mucosa, along with multiple foci of ulcerated, exophytic, verrucous, and pedunculated lesions. In one of the buffaloes studied, the bladder wall was ruptured and exhibited marked secondary inflammation. Histologically, neoplastic and non-neoplastic changes similar to those described in cattle poisoned by Pteridium spp. were observed. The neoplasms found included papilloma, carcinoma in situ, urothelial carcinoma (low and high grade), inverted, microcystic, and trabecular variants, urothelial carcinoma with divergent differentiation (squamous and glandular), squamous cell carcinoma, lymphangioma, hemangioma, and hemangiosarcoma. There was also coexistence of epithelial and mesenchymal neoplasms. Bovine papillomavirus particles were not detected by polymerase chain reaction in the bladder samples analyzed.

Descreve-se, através de levantamento epidemiológico e avaliação clínico-patológica, a ocorrência de hematúria enzoótica (HE) em búfalos no Brasil. Essa condição, causada pela ingestão da planta radiomimética Pteridium esculentum subsp. arachnoideum, conhecida popularmente como "samambaia" ou "samambaia do campo", até então não havia sido descrita nessa espécie no Brasil. Na Região Sudeste, a HE bovina é responsável por elevadas perdas econômicas, devidas não apenas aos óbitos, mas também em função da queda de produtividade. No município de São José do Barreiro/SP, alguns produtores de áreas com alta incidência de HE bovina, vêm substituindo os bovinos por búfalos, com base na premissa de que estes seriam mais resistentes à intoxicação. Embora, de acordo com observações iniciais, os búfalos realmente sejam menos sensíveis que os bovinos ao princípio tóxico de Pteridium spp., ainda assim, tem-se verificado a ocorrência de casos de hematúria nessa espécie. De acordo com o levantamento inicial, a HE só ocorre em búfalos com idade a partir de seis anos. Ao exame macroscópico, verificou-se a mucosa da bexiga espessa, com múltiplos focos de lesões ulceradas, exofíticas, papiliformes, verrucosas, pedunculadas. Histologicamente, foram observadas alterações neoplásicas e não neoplásicas semelhantes às descritas nos bovinos com HE. Entre as neoplasias foram encontrados papiloma, carcinoma in situ, carcinoma urotelial (baixo e alto grau), variantes invertida, microcística e trabecular, carcinoma urotelial com diferenciação divergente (escamosa e glandular), carcinoma de células escamosas, linfangioma, hemangioma e hemangiossarcoma. Ocorreu também coexistência entre neoplasias epiteliais e mesenquimais. Não foram detectadas partículas de papilomavírus bovino pelo teste PCR nas amostras de bexiga analisadas.

Edible Far Eastern Ferns as a Dietary Source of Long-Chain Polyunsaturated Fatty Acids.

Young fronds of ferns are consumed as a vegetable in many countries. The aim of this study was to analyze three fern species that are available for sale in the Russian Far East as dietary sources in terms of fatty acids that are important for human physiology: arachidonic acid (20:4n-6, ARA), eicosapentaenoic acid (20:5n-3, EPA) and other valuable long-chain polyunsaturated fatty acids. The content of ARA and EPA was 5.5 and 0.5 mg/g dry weight, respectively, in Pteridium aquilinum, 4.1 and 1.1 in Matteuccia struthiopteris, and 2.2 and 0.8 in Osmundastrum asiaticum. Salted fronds of P. aquilinum contained less these fatty acids than the raw fronds, with a decrease of up to 49% for ARA and 65% for EPA. These losses were less pronounced or even insignificant in dried fronds. Cooked ferns preserved significant portions of the long-chain polyunsaturated fatty acids: cooked P. aquilinum contained 4.4 mg/g dry weight ARA and 0.3 mg/g dry weight EPA. The ferns may provide a supplemental dietary source of these valuable long-chain polyunsaturated fatty acids, especially for vegetarian diets.

New insights into the evolution of the fern family Dennstaedtiaceae from an expanded molecular phylogeny and morphological analysis.

Dennstaedtiaceae has 270 species, a worldwide distribution, and an edge-colonizing habit that is unusual among ferns. Aneuploidy, polyploidy, and hybrids are common in the family. Combining morphology, anatomy, chromosome number, and geographical distributions with our newly generated molecular phylogeny, we provide new insights into the evolution of the family. We paid special attention to Hypolepis. Our molecular dataset of five cpDNA markers is the most comprehensive to date, comprising 72 species (and a total of 98 taxa), of which 33 are Hypolepis (45 taxa). We also generated divergence-time estimates through BEAST with four fossil calibrations. We recovered three sub-families in Dennstaedtiaceae: Monachosoroideae (monogeneric), Dennstaedtioideae, and Hypolepidoideae. Monachosoroideae has a chromosome base number of x = 28; Hypolepidoideae of x = 26; while in Dennstaedtioideae this is still obscure, with different numbers ranging from 30 to 47. Dennstaedtioideae genera require re-circumscriptions because Dennstaedtia is polyphyletic. In Hypolepidoideae, the six genera are monophyletic. Within Hypolepis, seven geographically distinct clades were recovered; but we found no strong morphological characters to define them. Within the family, the long-creeping rhizome evolved with a change in habit: from shade-tolerant to edge-colonizers, to thicket-formers. Short or extremely large leaves are derived conditions. Sorus shape and position, glandular hairs, and prickles are homoplastic. Hybridization/allotetraploidy in Hypolepis can be suggested by the combined data. In our phylogenetic hypothesis, Dennstaedtiaceae originated around 135 Ma, with the split of Monachosoroideae around 94 Ma, and the split between Dennstaedtioideae/Hypolepidoideae around 78 Ma. All extant genera are inferred to be relatively young. Hypolepis started to diversify around 10 Ma, and it probably originated in east Asia and/or Oceania. Hypolepis reached the Neotropics twice: through elements of the Hypolepis rugosula clade (which originated at 7 Ma), and through the ancestor of the Neotropical clade, which originated at 3.1 Ma and was prickly.

Ptaquiloside and Pterosin B Levels in Mature Green Fronds and Sprouts of Pteridium arachnoideum.

Pteridium arachnoideum, a fern of the Pteridium aquilinum species complex found in South America, is responsible for several different syndromes of poisoning. Cases of bovine enzootic hematuria and upper alimentary squamous cell carcinoma are both frequent occurrences in Brazil, whereas only bovine enzootic hematuria is noted with any frequency around the world. The reason for the high frequency of upper alimentary squamous cell carcinoma in Brazil is not currently known. One possible explanation may be the higher levels of ptaquiloside and pterosin B in Brazilian Pteridium than those present in the plant in other countries. However, these levels have not yet been determined in P. arachnoideum. Thus, the present study aimed to measure and compare ptaquiloside and pterosin B levels in mature green fronds and sprouts of P. arachnoideum collected from different locations in Brazil. Samples of P. arachnoideum were collected from the states of Minas Gerais and Rio Grande do Sul. A total of 28 mature leaf samples and 23 sprout samples were used. The mean concentrations of ptaquiloside and pterosin B present in the mature green fronds of P. arachnoideum ranged from 2.49 to 2.75 mg/g and 0.68 to 0.88 mg/g, respectively; in P. arachnoideum sprouts, mean concentrations of ptaquiloside and pterosin B ranged from 12.47 to 18.81 mg/g, and 4.03 to 10.42 mg/g for ptaquiloside and pterosin B, respectively. Thus, ptaquiloside and pterosin B levels in P. arachnoideum samples collected in Brazil were higher in sprouts than in mature green fronds, as observed in other countries. However, there was no variation in ptaquiloside levels among plants collected from different cities in Brazil. The high frequency of upper alimentary squamous cell carcinoma in Brazilian cattle may not be attributed to greater levels of ptaquiloside and pterosin B in P. arachnoideum than in other Pteridium species in other countries.