Intraspecies Variation Research Articles

Update of the scientific opinion on tetrabromobisphenol A (TBBPA) and its derivatives in food.

The European Commission asked EFSA to update its 2011 risk assessment on tetrabromobisphenol A (TBBPA) and five derivatives in food. Neurotoxicity and carcinogenicity were considered as the critical effects of TBBPA in rodent studies. The available evidence indicates that the carcinogenicity of TBBPA occurs via non-genotoxic mechanisms. Taking into account the new data, the CONTAM Panel considered it appropriate to set a tolerable daily intake (TDI). Based on decreased interest in social interaction in male mice, a lowest observed adverse effect level (LOAEL) of 0.2 mg/kg body weight (bw) per day was identified and selected as the reference point for the risk characterisation. Applying the default uncertainty factor of 100 for inter- and intraspecies variability, and a factor of 3 to extrapolate from the LOAEL to NOAEL, a TDI for TBBPA of 0.7 μg/kg bw per day was established. Around 2100 analytical results for TBBPA in food were used to estimate dietary exposure for the European population. The most important contributors to the chronic dietary LB exposure to TBBPA were fish and seafood, meat and meat products and milk and dairy products. The exposure estimates to TBBPA were all below the TDI, including those estimated for breastfed and formula-fed infants. Accounting for the uncertainties affecting the assessment, the CONTAM Panel concluded with 90%-95% certainty that the current dietary exposure to TBBPA does not raise a health concern for any of the population groups considered. There were insufficient data on the toxicity of any of the TBBPA derivatives to derive reference points, or to allow a comparison with TBBPA that would support assignment to an assessment group for the purposes of combined risk assessment.

Overview of the Multispecies Ovary Tissue Histology Electronic Repository†.

The Multispecies Ovary Tissue Histology Electronic Repository (MOTHER) is a publicly accessible repository of ovary histology images. MOTHER includes hundreds of images from nonhuman primates, as well as ovary histology images from an expanding range of other species. Along with an image, MOTHER provides metadata about the image, and for selected species, follicle identification annotations. Ongoing work includes assisting scientists with contributing their histology images, creation of manual and automated (via machine learning) processing pipelines to identify and count ovarian follicles in different stages of development, and the incorporation of that data into the MOTHER database (MOTHER-DB). MOTHER will be a critical data repository storing and disseminating high-value histology images that are essential for research into ovarian function, fertility, and intra-species variability.

Validation study on the practical accuracy of wood species identification via deep learning from visible microscopic images

This study aimed to validate the accuracy of identifying Japanese hardwood species from microscopic cross-sectional images using convolutional neural networks (CNN). The overarching goal is to create a versatile model that can handle microscopic cross-sectional images of wood. To gauge the practical accuracy, a comprehensive database of microscopic images of Japanese hardwood species was provided by the Forest Research and Management Organization. These images, captured from various positions on wood blocks, different trees, and diverse production areas, resulted in substantial intra-species image variation. To assess the effect of data distribution on accuracy, two datasets, D1 and D2, representing a segregated and a non-segregated dataset, respectively—from 1,000 images (20 images from each of the 50 species) were compiled. For D1, distinct images were allocated to the training, validation, and testing sets. However, in D2, the same images were used for both training and testing. Furthermore, the influence of the evaluation methodology on the identification accuracy was investigated by comparing two approaches: patch evaluation and E2 image evaluation. The accuracy of the model for uniformly sized images was approximately 90%, whereas that for variably sized images it was approximately 70%.

Assessment of fish diversity in the East China Sea hairtail national aquatic germplasm resources conservation zone using DNA barcoding

Based on the fishery resource survey data from 2019 to 2022, the species composition and taxonomic diversity of fish in the East China Sea hairtail national aquatic germplasm resources conservation zone (ECSHZ) were studied through the analysis of 185 COI sequences. The results showed that the 185 fish samples collected belonged to 105 species, 21 orders, 46 families, and 89 genera in terms of their taxonomic status. There are discrepancies between morphological identification and genetic identification results for four fish species. The intraspecific genetic distance ranged from 0 % to 1.0 %, with an average value of 0.3 %. Meanwhile, the interspecies within genus distance ranged from 5.3 % to 22.7 %, with an average of 14.5 %. The outcomes of the division using Automatic Barcoding Gap Discovery (ABGD) and Bayesian phylogenetics and phylogeography (BPP) were concordant, identifying a total of 105 species groups. ABGD and BPP have shown that there was no overlap between intra-species variation and inter-species variation, supporting the existence of a barcoding gap. The results demonstrate the superiority of DNA barcoding in species identification. A phylogenetic tree was constructed using the maximum likelihood method based on the COI gene, which revealed certain limitations of COI in representing phylogenetic relationships at the genus and higher taxonomic levels. Another phylogenetic tree was constructed using 13 mitochondrial protein-coding genes with more genetic information, allowing for a better study of evolutionary relationships of ECSHZ fish species. The tree supported that Carangidae, Polynemidae, Paralichthyidae, Pleuronectidae, Sphyraenidae, and Cynoglossidae were clustered in an independent clade, with Priacanthidae and Lobotidae separating from Perciformes. This study offers DNA barcodes for ECSHZ fish species, providing crucial data support for conserving fish diversity.

Arctic phytoplankton microdiversity across the marginal ice zone: Subspecies vulnerability to sea-ice loss

Seasonal phytoplankton blooms are important Arctic phenomena, contributing to global primary production and biogeochemical cycling. The decline in sea-ice extent and thickness favors a longer open-water period with impacts on phytoplankton dynamics. Arctic net productivity is influenced by microalgae living associated with sea ice, with distinct species thought to be favored by ice-covered and ice-free waters. In this study, we investigated the phytoplankton community structure in Baffin Bay, a semi-enclosed sea where Arctic and North Atlantic water masses interact. We compared communities from the ice-free Atlantic-influenced eastern, the marginal ice zone, and the ice-covered Arctic-influenced western Baffin Bay. The community was characterized using 18S rRNA high-throughput amplicon sequencing and flow cytometry cell counting, and compared to environmental data collected during the Green Edge campaign. We sampled 16 stations grouped by sectors according to sea-ice cover. In the sectors associated with sea ice, phytoplankton formed a highly diverse community of smaller taxa, which contrasted with a low-diversity community in ice-free sectors, dominated by larger centric diatoms and Phaeocystis pouchetii adapted to high light/low nutrient conditions. Several phytoplankton species were flagged as indicators for the under-ice and marginal ice zone sectors, including ice-associated taxa such as the diatoms Melosira arctica and Pseudo-nitzschia seriata, but also subspecies representatives of the early-blooming alga Micromonas polaris and the cryptophyte Baffinella frigidus. The strong association of certain taxa with under-ice and marginal ice zone sectors, including Pterosperma sp., Chrysochromulina sp., Micromonas polaris, and B. frigidus, suggest that they might be indicators of diversity loss due to ongoing sea-ice changes in Baffin Bay. We report new intra-species variability of Micromonas polaris suggesting that seasonal specialists could wax and wane over the bloom and non-bloom periods, highlighting the need for detailed year-long studies and the importance of microdiversity when assessing the diversity and distribution of polar phytoplankton.

Bacterial surface lipoproteins mediate epithelial microinvasion by Streptococcus pneumoniae.

Streptococcus pneumoniae, a common colonizer of the upper respiratory tract, invades nasopharyngeal epithelial cells without causing disease in healthy participants of controlled human infection studies. We hypothesized that surface expression of pneumococcal lipoproteins, recognized by the innate immune receptor TLR2, mediates epithelial microinvasion. Mutation of lgt in serotype 4 (TIGR4) and serotype 6B (BHN418) pneumococcal strains abolishes the ability of the mutants to activate TLR2 signaling. Loss of lgt also led to the concomitant decrease in interferon signaling triggered by the bacterium. However, only BHN418 lgt::cm but not TIGR4 lgt::cm was significantly attenuated in epithelial adherence and microinvasion compared to their respective wild-type strains. To test the hypothesis that differential lipoprotein repertoires in TIGR4 and BHN418 lead to the intraspecies variation in epithelial microinvasion, we employed a motif-based genome analysis and identified an additional 525 a.a. lipoprotein (pneumococcal accessory lipoprotein A; palA) encoded by BHN418 that is absent in TIGR4. The gene encoding palA sits within a putative genetic island present in ~10% of global pneumococcal isolates. While palA was enriched in the carriage and otitis media pneumococcal strains, neither mutation nor overexpression of the gene encoding this lipoprotein significantly changed microinvasion patterns. In conclusion, mutation of lgt attenuates epithelial inflammatory responses during pneumococcal-epithelial interactions, with intraspecies variation in the effect on microinvasion. Differential lipoprotein repertoires encoded by the different strains do not explain these differences in microinvasion. Rather, we postulate that post-translational modifications of lipoproteins may account for the differences in microinvasion.IMPORTANCEStreptococcus pneumoniae (pneumococcus) is an important mucosal pathogen, estimated to cause over 500,000 deaths annually. Nasopharyngeal colonization is considered a necessary prerequisite for disease, yet many people are transiently and asymptomatically colonized by pneumococci without becoming unwell. It is therefore important to better understand how the colonization process is controlled at the epithelial surface. Controlled human infection studies revealed the presence of pneumococci within the epithelium of healthy volunteers (microinvasion). In this study, we focused on the regulation of epithelial microinvasion by pneumococcal lipoproteins. We found that pneumococcal lipoproteins induce epithelial inflammation but that differing lipoprotein repertoires do not significantly impact the magnitude of microinvasion. Targeting mucosal innate immunity and epithelial microinvasion alongside the induction of an adaptive immune response may be effective in preventing pneumococcal colonization and disease.

Transcriptome and functional analyses of phenotypic plasticity in sea grape Caulerpa okamurae.

Caulerpa is a marine green macroalga distinguished by a large single cell with multiple nuclei. It also exhibits remarkable morphological intraspecies variations, in response to diverse environmental types. However, the molecular mechanisms underlying this phenotypic plasticity remain poorly understood. In this work, we compare the transcriptomes of Caulerpa okamurae Weber Bosse, 1897 displaying altered phenotypes of cultivation and natural phenotypes and investigate significantly regulated genes and their biological functions using differential expression analyses. We observe light-harvesting complex upregulation and cellular framework stability downregulation in altered phenotypes compared to the natural phenotypes. Intertidal macrophytes reduce light capture to avoid photodamage and regulate their morphology to protect against wave damage. In contrast, the lower light conditions and the cultivation environment augment light capture and increase a morphology prioritizing light trapping. Moreover, the addition of simulated wave-sweeping stimuli induces a return to the natural morphology under high-light conditions, showing how mechanical stress affects morphological organization in C. okamurae. We provide detailed gene expression patterns in C. okamurae under varying light intensities and water conditions, suggesting a distinct influence on its morphological traits.

Improving rotational partners: Intraspecies variation for pea cover cropping traits

AbstractTo improve cover crops such as peas (Pisum sativum), as rotational partners, intraspecific variation for cover cropping traits such as nutrient mobilization, carbon deposition, and beneficial microbial recruitment must be identified. The majority of research on cover crops has focused on interspecies comparisons for cover cropping variation with minimal research investigating intraspecies variation. To address if variation of cover cropping traits is present within a cover cropping species, we grew 15 diverse accessions (four modern cultivars, three landraces, and eight wild accessions) of pea in a certified organic setting. We measured various cover cropping traits, such as nutrient mobilization, soil organic matter deposition, and microbial recruitment, and quantified the effect of pea accession on the growth and yield of a subsequently planted crop of corn (Zea mays). We discovered that the domestication history of pea has a significant impact on soil properties. Specifically, domesticated peas (modern cultivars and landraces) had higher average plant–soil feedback values for amounts of nitrogen, carbon, and manganese compared to wild peas. Additionally, no variation for prokaryotic recruitment (α‐ and β‐diversity) was observed within pea; however, we did observe significant variation for fungal recruitment (α‐ and β‐diversity) due to domestication and accession. Our results demonstrate that there is variation present in peas, and likely all crops, that can be selected to improve them as rotational partners to ultimately boost crop yields in sustainable agroecosystems.

Unraveling gluten protein compositions of einkorn, emmer, and spelt grown in the Lyon region in France

AbstractBackground and ObjectivesMinor species of wheat, including einkorn (Ei), emmer (Em), and spelt (Sp), are believed to have different gluten compositions compared to common wheat (CW). Given the limited research on these resources, and as a result of a collaboration with a collective of farmers, we aimed to provide insights into their gluten compositions. We focused on varieties readily accessible to farmers and bakers within the region of Lyon, France.FindingsWe compared gluten compositions in 31 wheat varieties, revealing significantly lower glutenin and protein aggregate contents in Ei and Em than in CW. Similar trends, though milder, were observed for Sp. Additionally, we observed intra‐species variability, especially for Em, and identified varieties within each species with noteworthy protein profiles.ConclusionsEach species showed characteristic protein contents, yet with intraspecies variability. Utilizing an innovative approach to analyze the full information provided by chromatograms, we successfully identified varieties with unusual characteristics.Significance and NoveltyThe specific protein compositions of Ei and Em, and to a lower extent Sp, may impact their processability and digestibility. Our study also highlights that considering complete chromatographic profiles can reveal differences that remain unnoticed when using traditional analytical approaches.

Intra-species variability in migratory movement of hawksbill turtles in the southwest Indian Ocean

Implementing effective conservation measures to manage migratory populations is challenging, especially in a relatively inaccessible dynamic environment such as the ocean. With limited financial and human resources, efforts must be intelligently prioritized to achieve conservation success and reduce uncertainties of conservation efforts. The southwest Indian Ocean (SWIO) hosts some of the world’s most important breeding grounds for the Critically Endangered hawksbill turtle Eretmochelys imbricata. However, knowledge gaps remain about the movement patterns of this species. Between 2007 and 2022, we deployed 17 satellite tags onto hawksbill turtles from scattered locations in the SWIO: 16 nesting females—Granitic Islands, Seychelles (n = 9); north Madagascar (n = 5); Moheli, Comoros (n = 1); Juan de Nova, Terres australes et antarctiques françaises (n = 1)—and 1 female bycaught in fisheries (east Madagascar). We found strong variability in migratory movements amongst individuals, particularly in terms of distance and movement persistence. Detailed analysis of movement persistence reveals that these individuals behave differently in neritic and oceanic habitats, with a lower movement persistence in neritic habitats. We identified a total of 12 foraging areas scattered throughout the SWIO, both in coastal and open-sea neritic habitats. These results reinforce the need to consider the importance of neritic habitats, for both migration and foraging, in conservation policies. The quantification of the degree of migratory variability is particularly important to developing conservation plans and strategies at both the national and international level, including the delineation of regional management units (RMUs) in the Indian Ocean.

Impact of predicted climate change environmental conditions on the growth of Fusarium asiaticum strains and mycotoxins production on a wheat-based matrix

Fusarium asiaticum is a predominant fungal pathogen causing Fusarium Head Blight (FHB) in wheat and barley in China and is associated with approximately £201 million in annual losses due to grains contaminated with mycotoxins. F. asiaticum produces deoxynivalenol and zearalenone whose maximum limits in cereals and cereals-derived products have been established in different countries including the EU. Few studies are available on the ecophysiological behaviour of this fungal pathogen, but nothing is known about the impact of projected climate change scenarios on its growth and mycotoxin production. Therefore, this study aimed to examine the interacting effect of i) current and increased temperature (25 vs 30 °C), ii) drought stress variation (0.98 vs 0.95 water activity; aw) and iii) existing and predicted CO2 concentrations (400 vs 1000 ppm) on fungal growth and mycotoxin production (type B trichothecenes and zearalenone) by three F. asiaticum strains (CH024b, 82, 0982) on a wheat-based matrix after 10 days of incubation. The results showed that, when exposed to increased CO2 concentration (1000 ppm) there was a significant reduction of fungal growth compared to current concentration (400 ppm) both at 25 and 30 °C, especially at 0.95 aw. The multi-mycotoxin analysis performed by LC-MS/MS qTRAP showed a significant increase of deoxynivalenol and 15-acetyldeoxynivalenol production when the CH024b strain was exposed to elevated CO2 compared to current CO2 levels. Zearalenone production by the strain 0982 was significantly stimulated by mild water stress (0.95 aw) and increased CO2 concentration (1000 ppm) regardless of the temperature. Such results highlight that intraspecies variability exist among F. asiaticum strains with some mycotoxins likely to exceed current EU legislative limits under prospected climate change conditions.

Genotype-phenotype evaluation of the heterogeneity in biofilm formation by diverse Bacillus licheniformis strains isolated from dairy products

The spoilage bacterium Bacillus licheniformis has been identified as a quick and strong biofilm former in the dairy industry. In our previous study, intra-species variation in bacterial biofilms has been observed in diverse B. licheniformis strains from different genetic backgrounds; however, the mechanisms driving the observed heterogeneity of biofilms remain to be determined. In this study, the genotype-phenotype evaluation of the heterogeneity in biofilm formation of four B. licheniformis strains were examined. The heterogeneity in biofilm phenotype was accessed in aspects of bacterial growth and motility, cell viability, biofilm matrix production, and biofilm architectures. The underlying mechanisms of the intra-species variability in biofilms were also explored by whole genome resequencing (WGR). Results from bacterial motility tests showed a diverse motility among the strains, but there was no clear correlation between bacterial motility and biofilm formation. The cell viability results showed a different number of live cells in biofilms at the intra-species level. Analysis of chemical components in biofilm matrix demonstrated the great intra-species differences regarding extracellular matrix composition, and a negative correlation between biofilm formation on stainless steel and the protein: carbohydrate ratio in biofilm matrix was observed. Confocal laser scanning microscopy analysis also revealed the intra-species variability by showing great differences in general properties of B. licheniformis biofilms. WGR results identified important pathways involved in biofilm formation, such as two-component systems, quorum sensing, starch and sucrose metabolism, ABC transporters, glyoxylate and dicarboxylate metabolism, purine metabolism, and a phosphotransferase system. Overall, the above results emphasize the necessity of exploring the intra-species variation in biofilms, and would provide in-depth knowledge for designing efficient biofilm control strategies in the dairy industry.

Wildlife mortality risk posed by high and low traffic roads.

Wildlife mortality due to collisions with vehicles (roadkill) is one of the predominant negative effects exerted by roads on many wildlife species. Reducing roadkill is therefore a major component of wildlife conservation. Roadkill is affected by various factors, including road attributes and traffic volume. It is theorized that the effect of traffic volume on roadkill probability should be unimodal. However, empirical evidence for this theory is lacking. Using a large-scale roadkill database of 18 wildlife species in Israel, encompassing 2846km of roads over 10years, we explored the effects of traffic volume and road attributes (e.g., road lighting, verge vegetation) on roadkill probability with a multivariate generalized linear mixed model. A unimodal effect of traffic volume was identified for the striped hyena (Hyaena hyaena), whereas 5 species demonstrated a novel quadratic U-shaped effect (e.g., golden jackal [Canis aureus]). Four species showed a negative linear effect (e.g., wild boar [Sus scrofa]). We also identified varying effects of road attributes on roadkill. For instance, road lighting and roadside trees decreased roadkill for several species, whereas bus stops and concrete guardrails led to increased roadkill. The theorized unimodal effect of traffic volume may only apply to large, agile species, and the U-shaped effect could be related to intraspecies variability in traffic avoidance behavior. In general, we found that both high-traffic and low-traffic roads can pose a high mortality risk for wildlife. It is therefore important to monitor roadkill on low-traffic roads and adapt road attributes to mitigate roadkill. Road design for effective roadkill mitigation includes reducing the use of concrete guardrails and median barriers where possible and avoiding dense bushes in verge landscaping. These measures are complemented by employing wildlife detection systems, driver warnings, and seasonal speed reduction measures on low-traffic roads identified as roadkill hotspots.

Serovar-level identification of bacterial foodborne pathogens from full-length 16S rRNA gene sequencing.

The resolution of variation within species is critical for interpreting and acting on many microbial measurements. In the key foodborne pathogens Salmonella and Escherichia coli, the primary subspecies classification scheme used is serotyping: differentiating variants within these species by surface antigen profiles. Serotype prediction from whole-genome sequencing (WGS) of isolates is now seen as comparable or preferable to traditional laboratory methods where WGS is available. However, laboratory and WGS methods depend on an isolation step that is time-consuming and incompletely represents the sample when multiple strains are present. Community sequencing approaches that skip the isolation step are, therefore, of interest for pathogen surveillance. Here, we evaluated the viability of amplicon sequencing of the full-length 16S rRNA gene for serotyping Salmonella enterica and E. coli. We developed a novel algorithm for serotype prediction, implemented as an R package (Seroplacer), which takes as input full-length 16S rRNA gene sequences and outputs serovar predictions after phylogenetic placement into a reference phylogeny. We achieved over 89% accuracy in predicting Salmonella serotypes on in silico test data and identified key pathogenic serovars of Salmonella and E. coli in isolate and environmental test samples. Although serotype prediction from 16S rRNA gene sequences is not as accurate as serotype prediction from WGS of isolates, the potential to identify dangerous serovars directly from amplicon sequencing of environmental samples is intriguing for pathogen surveillance. The capabilities developed here are also broadly relevant to other applications where intraspecies variation and direct sequencing from environmental samples could be valuable.IMPORTANCEIn order to prevent and stop outbreaks of foodborne pathogens, it is important that we can detect when pathogenic bacteria are present in a food or food-associated site and identify connections between specific pathogenic bacteria present in different samples. In this work, we develop a new computational technology that allows the important foodborne pathogens Escherichia coli and Salmonella enterica to be serotyped (a subspecies level classification) from sequencing of a single-marker gene, and the 16S rRNA gene often used to surveil bacterial communities. Our results suggest current limitations to serotyping from 16S rRNA gene sequencing alone but set the stage for further progress that we consider likely given the rapid advance in the long-read sequencing technologies and genomic databases our work leverages. If this research direction succeeds, it could enable better detection of foodborne pathogens before they reach the public and speed the resolution of foodborne pathogen outbreaks.

Distinct genomic contexts predict gene presence-absence variation in different pathotypes of Magnaporthe oryzae.

Fungi use the accessory gene content of their pangenomes to adapt to their environments. While gene presence-absence variation contributes to shaping accessory gene reservoirs, the genomic contexts that shape these events remain unclear. Since pangenome studies are typically species-wide and do not analyze different populations separately, it is yet to be uncovered whether presence-absence variation patterns and mechanisms are consistent across populations. Fungal plant pathogens are useful models for studying presence-absence variation because they rely on it to adapt to their hosts, and members of a species often infect distinct hosts. We analyzed gene presence-absence variation in the blast fungus, Magnaporthe oryzae (syn. Pyricularia oryzae), and found that presence-absence variation genes involved in host-pathogen and microbe-microbe interactions may drive the adaptation of the fungus to its environment. We then analyzed genomic and epigenomic features of presence-absence variation and observed that proximity to transposable elements, gene GC content, gene length, expression level in the host, and histone H3K27me3 marks were different between presence-absence variation genes and conserved genes. We used these features to construct a model that was able to predict whether a gene is likely to experience presence-absence variation with high precision (86.06%) and recall (92.88%) in M. oryzae. Finally, we found that presence-absence variation genes in the rice and wheat pathotypes of M. oryzae differed in their number and their genomic context. Our results suggest that genomic and epigenomic features of gene presence-absence variation can be used to better understand and predict fungal pangenome evolution. We also show that substantial intra-species variation can exist in these features.

The chronic wound milieu changes essential oils' antibiofilm activity—an in vitro and larval model study

Essential Oils (EOs) are currently being researched as potential antibiofilm agents to combat infections related to chronic wound biofilms. As documented in the literature, EOs’ in vitro antibacterial properties are often assessed using standard microbiological media and conditions that do not accurately reflect the actual environment of a chronic wound. To address this issue, In vitro Wound Milieu (IVWM) medium, which closely resembles the environment of a chronic wound, was applied for culturing S. aureus biofilms (n = 12) in this research. Biofilms cultivated in the standard Tryptic Soy Broth (TSB) medium served as a control for the experiment. Key biofilm features were analyzed and compared. Subsequently, staphylococci were exposed to the activity of thyme or rosemary EOs (T-EO and R-EO, respectively). As proof of concept, the cytotoxicity of T-EO and its antimicrobial in vivo activity were assessed using a G. mellonella larvae model. Key features of biofilm-forming cells were lower in the IVWM than in the TSB medium: biomass (up to 8 times), metabolic activity (up to 9 times), cell number (up to 100 times), and the live/dead cells ratio. Conversely, biofilm thickness was higher (up to 25%) in IVWM. These differences translated into varied responses of the biofilms to EOs exposure. The application of T-EO led to a greater reduction (up to 2 times) in 67% of biofilm-forming strains in IVWM compared to the TSB medium. Conversely, exposure to R-EO resulted in a higher reduction (up to 2.6 times) of 83% of biofilm-forming strains in TSB than in IVWM. The application of T-EO was not only non-toxic to G. mellonella larvae but also increased the survival of larvae infected with staphylococci (from 48 to 85%). Our findings suggest that EOs not only show promise as agents for treating biofilm-related wound infections but also that providing conditions reflecting the specific niche of the human body is of paramount importance in influencing the results obtained. However, before clinical application, challenges related to the methods of assessing their activity, microbial intra-species variability, and different levels of activity of various EOs should be analyzed and standardized.

The Impact of Various Types of Cooking on the Fate of Hg and Se in Predatory Fish Species

This study addresses the effect of various cooking approaches on total Hg (HgT) and total Se (SeT) contents in three predatory fish species. For this purpose, samples of swordfish, dogfish, and tuna from regular French (fish) markets were cooked by boiling, steaming, grilling, and frying, respectively. The levels of HgT and SeT in raw and cooked samples were determined by inductively coupled plasma-mass spectrometry. The data showed a significant increase in HgT and SeT levels between raw and cooked samples (33% of the samples for SeT and 67% for HgT) due to the water loss during the cooking. High intra-species variation related to HgT and SeT levels was found. Considering the level of exposure to HgT through fish consumption and taking also into account the possible protective effect of Se (expressed here via the Se/Hg molar ratio), the safest cooking approach corresponds to grilled swordfish, fried tuna, and steamed dogfish, which show Se/Hg molar ratios of (1.0 ± 0.5), (4.3 ± 4.2), and (1.0 ± 0.6), respectively.

A phased genome assembly of a Colombian Trypanosoma cruzi TcI strain and the evolution of gene families

Chagas is an endemic disease in tropical regions of Latin America, caused by the parasite Trypanosoma cruzi. High intraspecies variability and genome complexity have been challenges to assemble high quality genomes needed for studies in evolution, population genomics, diagnosis and drug development. Here we present a chromosome-level phased assembly of a TcI T. cruzi strain (Dm25). While 29 chromosomes show a large collinearity with the assembly of the Brazil A4 strain, three chromosomes show both large heterozygosity and large divergence, compared to previous assemblies of TcI T. cruzi strains. Nucleotide and protein evolution statistics indicate that T. cruzi Marinkellei separated before the diversification of T. cruzi in the known DTUs. Interchromosomal paralogs of dispersed gene families and histones appeared before but at the same time have a more strict purifying selection, compared to other repeat families. Previously unreported large tandem arrays of protein kinases and histones were identified in this assembly. Over one million variants obtained from Illumina reads aligned to the primary assembly clearly separate the main DTUs. We expect that this new assembly will be a valuable resource for further studies on evolution and functional genomics of Trypanosomatids.

Proteomic Investigation of Cape Cobra (Naja nivea) Venom Reveals First Evidence of Quaternary Protein Structures.

Naja nivea (N. nivea) is classed as a category one snake by the World Health Organization since its envenomation causes high levels of mortality and disability annually. Despite this, there has been little research into the venom composition of N. nivea, with only one full venom proteome published to date. Our current study separated N. nivea venom using size exclusion chromatography before utilizing a traditional bottom-up proteomics approach to unravel the composition of the venom proteome. As expected by its clinical presentation, N. nivea venom was found to consist mainly of neurotoxins, with three-finger toxins (3FTx), making up 76.01% of the total venom proteome. Additionally, cysteine-rich secretory proteins (CRISPs), vespryns (VESPs), cobra venom factors (CVFs), 5'-nucleotidases (5'NUCs), nerve growth factors (NGFs), phospholipase A2s (PLA2), acetylcholinesterases (AChEs), Kunitz-type serine protease inhibitor (KUN), phosphodiesterases (PDEs), L-amino acid oxidases (LAAOs), hydrolases (HYDs), snake venom metalloproteinases (SVMPs), and snake venom serine protease (SVSP) toxins were also identified in decreasing order of abundance. Interestingly, contrary to previous reports, we find PLA2 toxins in N. nivea venom. This highlights the importance of repeatedly profiling the venom of the same species to account for intra-species variation. Additionally, we report the first evidence of covalent protein complexes in N. nivea venom, which likely contribute to the potency of this venom.

Molecular Characterization of Spirometra erinaceieuropaei from Jungle Cat (Felis chaus) in North of Iran.

The aim of this study is to conduct a molecular characterization of Spirometra tapeworm from jungle cat (Felis chaus) in Guilan Province, north of Iran using DNA sequence analysis of the mitochondrial cytochrome c oxidase subunit 1 (Cox1) and 12S rDNA sequences. Morphological features of the adult tapeworm of Spirometra were evaluated using specific staining and light microscopy. The molecular characterization was performed using partial Cox1 and 12S rDNA regions. Genetic diversity was calculated and phylogenetic trees of the obtained sequences were constructed. Morphological features were compatible with previous description of adult Spirometra erinaceieuropaei. The Cox1 sequence of the specimen showed 100% similarity with S. erinaceieuropaei sequences in GenBank from Korea, China and Iran. Also, the 12S rDNA sequence revealed 99.7% similarity with S. erinaceieuropaei isolates from China and Japan. Intra-species variation within isolates of S. erinaceieuropaei was 0-1.4% and 0-4.6% for Cox1 and 12S rDNA genes, respectively. This is the first report of molecular characterization of S. erinaceieuropaei in jungle cat, F. chaus in Iran. Jungle cat probably plays a major role as reservoir host in maintaining of this parasite in this area with favorable climate condition. Needs for further assessment on the role of appropriate hosts, especially intermediate/paratenic hosts as well as the potential risk of human infectivity with sparganosis is emphasized.