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  • 1
    Publication Date: 2024-01-12
    Description: Monitoring of airborne pollen concentrations provides an important source of information for the \nglobally increasing number of hay fever patients. Airborne pollen is traditionally counted under \nthe microscope, but with the latest developments in image recognition methods, automating this \nprocess has become feasible. A challenge that persists, however, is that many pollen grains cannot \nbe distinguished beyond the genus or family level using a microscope. Here, we assess the use of \nConvolutional Neural Networks (CNNs) to increase taxonomic accuracy for airborne pollen. As a case \nstudy we use the nettle family (Urticaceae), which contains two main genera ( \nUrtica \n and \nParietaria \n) \ncommon in European landscapes which pollen cannot be separated by trained specialists. While \npollen from \nUrtica \n species has very low allergenic relevance, pollen from several species of \nParietaria \nis severely allergenic. We collect pollen from both fresh as well as from herbarium specimens and \nuse these without the often used acetolysis step to train the CNN model. The models show that \nunacetolyzed Urticaceae pollen grains can be distinguished with 〉 \n98% accuracy. We then apply our \nmodel on before unseen Urticaceae pollen collected from aerobiological samples and show that the \ngenera can be confidently distinguished, despite the more challenging input images that are often \noverlain by debris. Our method can also be applied to other pollen families in the future and will thus \nhelp to make allergenic pollen monitoring more specific
    Keywords: Asthma ; Atmospheric science ; Computer science ; Environmental sciences ; Plant sciences ; Transmission light microscopy
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
    Format: application/pdf
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  • 2
    Publication Date: 2024-03-12
    Description: Premise: Most studies of the movement of orchid fruits and roots during plant development have focused on morphological observations; however, further genetic analysis is required to understand the molecular mechanisms underlying this phenomenon. A precise tool is required to observe these movements and harvest tissue at the correct position and time for transcriptomics research. Methods: We utilized three\xe2\x80\x90dimensional (3D) micro\xe2\x80\x93computed tomography (CT)scans to capture the movement of fast\xe2\x80\x90growing Erycina pusillaroots, and built an integrated bioinformatics pipeline to process 3D images into 3D time\xe2\x80\x90lapse videos. To record the movement of slowly developing E. pusilla and Phalaenopsis equestris fruits, two\xe2\x80\x90dimensional (2D) photographs were used. Results: The E. pusilla roots twisted and resupinated multiple times from early development. The first period occurred in the early developmental stage (77\xe2\x80\x9384 days after germination [DAG]) and the subsequent period occurred later in development(140\xe2\x80\x93154 DAG). While E. pusilla fruits twisted 45\xc2\xb0 from 56\xe2\x80\x9363 days after pollination (DAP), the fruits of P. equestris only began to resupinate a week before dehiscence (133 DAP) and ended a week after dehiscence (161 DAP). Discussion: Our methods revealed that each orchid root and fruit had an independent direction and degree of torsion from the initial to the final position. Our innovative approaches produced detailed spatial and temporal information on the resupination of roots and fruits during orchid development.
    Keywords: Erycina pusilla ; fruits ; high\xe2\x80\x90precision laser scanning ; Phalaenopsis equestris ; plant growth ; resupination ; roots ; twisting
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
    Format: application/pdf
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  • 3
    Publication Date: 2024-03-08
    Keywords: Erycina pusilla ; fruits ; high\xe2\x80\x90precision laser scanning ; Phalaenopsis equestris ; plant growth ; resupination ; roots ; twisting
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 4
    Publication Date: 2024-03-14
    Description: Animals with large energy requirements are forced to optimize their hunting strategy, which may result in differentiation of the diet between sexes and across seasons. Here, we examined spatiotemporal variation in the diet of both sexes of the Pond Bat Myotis dasycneme, a species known to have spatial segregation of sexes when the young are born and lactating. Fecal pellets were collected from live animals for a period of 15 years at various locations in the Netherlands. A total of 535 pellets were successfully analyzed by microscopy and an additional 160 pellets by DNA metabarcoding. Morphological and molecular analyses showed that the diet of pregnant and lactating pond bats differed significantly from the diet of females with no reproductive investment. Further analyses of the data showed that pregnant female pond bats are highly dependent on small prey and pupae, mainly nonbiting midges and mosquitoes (Diptera: Chironomidae and Culicidae). These insects can be found in large quantities in peatlands intersected with shallow waterways, the habitat type in which female pond bats were observed more often than males. Our results suggest that during pregnancy the spatial segregation of sexes coincides with sex-specific diets, which might reflect habitat selection based on energy requirements, in addition to lowered intraspecific competition.
    Keywords: Chiroptera ; environmental DNA (eDNA) ; high-throughput sequencing ; intraspecific competition ; metabarcoding ; Myotis dasycneme
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 5
    Publication Date: 2024-02-09
    Description: Fruits play a crucial role in seed dispersal. They open along dehiscence zones. Fruit dehiscence zone formation has been intensively studied in Arabidopsis thaliana. However, little is \nknown about the mechanisms and genes involved in the formation of fruit dehiscence zones \nin species outside the Brassicaceae. The dehiscence zone of A. thaliana contains a lignified \nlayer, while dehiscence zone tissues of the emerging orchid model Erycina pusilla include a \nlipid layer. Here we present an analysis of evolution and development of fruit dehiscence \nzones in orchids. We performed ancestral state reconstructions across the five orchid subfamilies to study the evolution of selected fruit traits and explored dehiscence zone developmental genes using RNA-seq and qPCR. We found that erect dehiscent fruits with nonlignified dehiscence zones and a short ripening period are ancestral characters in orchids. \nLignified dehiscence zones in orchid fruits evolved multiple times from non-lignified zones. \nFurthermore, we carried out gene expression analysis of tissues from different developmental stages of E. pusilla fruits. We found that fruit dehiscence genes from the MADS-box gene \nfamily and other important regulators in E. pusilla differed in their expression pattern from \ntheir homologs in A. thaliana. This suggests that the current A. thaliana fruit dehiscence \nmodel requires adjustment for orchids. Additionally, we discovered that homologs of A. thaliana genes involved in the development of carpel, gynoecium and ovules, and genes \ninvolved in lipid biosynthesis were expressed in the fruit valves of E. pusilla, implying that \nthese genes may play a novel role in formation of dehiscence zone tissues in orchids. Future \nfunctional analysis of developmental regulators, lipid identification and quantification can \nshed more light on lipid-layer based dehiscence of orchid fruits.
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
    Format: application/pdf
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  • 6
    Publication Date: 2024-05-02
    Description: Computer vision-based wood identification has been successfully applied to recognize tree species using digital images of wood sections or surfaces. However, this image-to-species approach can only recognize a limited number of species due to two main reasons: 1) the lack of a good reference database requiring high-quality standardized images from multiple individuals of hundreds or even thousands of traded timber species, and 2) species not included in the reference database cannot be identified without expert knowledge. Another bottleneck is that the feature extraction process used by these species recognition approaches is a black box, thereby creating a discrepancy between machine learning features and wood anatomical features. This discrepancy prevents wood anatomists from understanding how these machine-learning algorithms work. Here, we survey currently existing methods used in feature extraction, classification, and deep learning methods applied in wood identification along with their pitfalls and opportunities. As an example of how the field could move forward, we launch the idea of building an image-to-features-to-species identification approach based on microscopic wood images as well as text files comprising wood anatomical descriptions. If we can manage machine learning-based algorithms to recognize the main wood anatomical traits that experts use to identify species in a (semi-)automated way, this would boost wood identification in two ways: (1) extensive reference databases for each species would become less crucial as the databases are ordered at the trait level, (2) timber identification would become more feasible for species that have not yet been included in the reference database as long as wood anatomical descriptions are available.
    Keywords: feature incompatibility ; illegal logging ; species recognition
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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