Italian natural history museums on the verge of collapse?

The Italian natural history museums are facing a critical situation, due to the progressive loss of scientific relevance, decreasing economic investments, and scarcity of personnel. This is extremely alarming, especially for ensuring the long-term preservation of the precious collections they host. Moreover, a commitment in fieldwork to increase scientific collections and concurrent taxonomic research are rarely considered priorities, while most of the activities are addressed to public events with political payoffs, such as exhibits, didactic meetings, expositions, and talks. This is possibly due to the absence of a national museum that would have better steered research activities and overall concepts for collection management. We here propose that Italian natural history museums collaborate to instate a “metamuseum”, by establishing a reciprocal interaction network aimed at sharing budgetary and technical resources, which would assure better coordination of common long-term goals and scientific activities.     

植物引种驯化对近500年人类文明史的影响及其科学意义

近500年来, 植物引种驯化及其广泛栽培深刻改变了世界农业生产的格局, 对促进人类社会文明进步产生了深远的影响。无论在西方殖民地发展史还是在我国明清发展史中, 每一种重要栽培植物的成功引种和驯化, 都对历史进程产生了不可估量的作用。活植物收集是植物园的核心和“灵魂”, 传承了现代植物园几个世纪科学研究的脉络和成就。活植物收集是植物园科学研究的基础和支撑平台, 也是当前和未来发展的根本。基于活植物收集的植物园研究工作具有多学科综合的特征, 既对基础生物学研究具有重要意义, 也与经济繁荣、社会发展和人类日常生活密切相关。     

What does it mean to be wild? Assessing human influence on the environments of nonhuman primate specimens in museum collections

ObjectivesNatural history collections are often thought to represent environments in a pristine natural state—free from human intervention—the so‐called “wild.” In this study, we aim to assess the level of human influence represented by natural history collections of wild‐collected primates over 120 years at the Smithsonian Institution''s National Museum of Natural History (NMNH).Materials and MethodsOur sample consisted of 875 catarrhine primate specimens in NMNH collections, representing 13 genera collected in 39 countries from 1882 to 2004. Using archival and accession information we determined the approximate locations from which specimens were collected. We then plotted location coordinates onto publicly available anthrome maps created by Ellis et al. (Global Ecology and Biogeography, 2010, 19, 589), which delineate terrestrial biomes of human population density and land use worldwide since the 1700s.ResultsWe found that among primates collected from their native ranges, 92% were from an environment that had some level of human impact, suggesting that the majority of presumed wild‐collected primate specimens lived in an environment influenced by humans during their lifetimes.DiscussionThe degree to which human‐modified environments may have impacted the lives of primates currently held in museum collections has been historically ignored, implicating unforeseen consequences for collection‐based research. While unique effects related to commensalism with humans remain understudied, effects currently attributed to natural phenomena may, in fact, be related to anthropogenic pressures on unmanaged populations of primates.     

The Batrachian Barf Bowl: An authentic research experience using ecological data from frog diets

Authentic research experiences (AREs) are a powerful strategy for inspiring and retaining students in science, technology, engineering, and math (STEM) fields. However, recent demand for virtual learning has emphasized the need for remote AREs that also foster a sense of community and interpersonal connections among participants. Here, we describe an ARE activity that leverages digitized diet data from natural history collections to provide students with collaborative research experience across any learning environment. Using magnified photographs of frog stomach contents collected in the Peruvian Amazon, we designed an open‐source “bowl game” competition that challenges students to identify, measure, and compare diet items across vouchered frog specimens (“Batrachian Barf Bowl”). To demonstrate learning outcomes, we ran this activity with 39 herpetology class students from the University of Notre Dame and the University of Michigan. We used pre‐ and post‐activity assessments to evaluate effectiveness, scientific accuracy of results, and impact on student well‐being. With minimal preparation and training in invertebrate identification, students were successful in identifying hundreds of frog diet items to taxonomic order, although accuracy varied among clades (global accuracy ~70%). While we found no difference in science identity, community, or self‐efficacy between the two institutions at either time point (pre‐ and post‐activity), we found that well‐being was significantly higher for both sets of students after the activity. Overall, this approach offers a model for combining active learning with museum collections to provide experiential research opportunities that highlight the power of scientific collaboration.     

The influence of community recommendations on metadata completeness

Many communities use standard, structured documentation that is machine-readable, i.e. metadata, to make discovery, access, use, and understanding of scientific datasets possible. Organizations and communities have also developed recommendations for metadata content that is required or suggested for their data developers and users. These recommendations are typically specific to metadata representations (dialects) used by the community. By considering the conceptual content of the recommendations, quantitative analysis and comparison of the completeness of multiple metadata dialects becomes possible. This is a study of completeness of EML and CSDGM metadata records from DataONE in terms of the LTER recommendation for Completeness. The goal of the study is to quantitatively measure completeness of metadata records and to determine if metadata developed by LTER is more complete with respect to the recommendation than other collections in EML and in CSDGM. We conclude that the LTER records are broadly more complete than the other EML collections, but similar in completeness to the CSDGM collections.     

New approach for evaluating habitat stability using scarce records for both historical and contemporary specimens: a case study using Carabidae specimen records

Natural history collections, such as specimen records, are crucial resources for conservation and habitat management. However, these data are usually scarce compared to physical environmental data (e.g., digital terrain maps) that we often have little species data and a lot of physical environmental data with which to evaluate habitats. In this paper, we propose a method for evaluating habitat stability using scarce natural history records and abundant physical environmental data. We used both historical and contemporary specimen records of carabid beetles (areas in which records of the same species were recorded during both periods) and evaluated the attributes of these areas using terrain characteristics. We found two common terrain characteristics among the occupied areas: large total river length and low variation in elevation. These terrain characteristics suggest that habitats of carabid species have been conserved in disturbed and wet environments for a long time. These results are consistent with the ecological characteristics of carabid beetles. Our study shows that scarce natural history collections, combined with ingenuity, can be useful for evaluating habitats.     

Quantifying Auditory Temporal Stability in a Large Database of Recorded Music

“Moving to the beat” is both one of the most basic and one of the most profound means by which humans (and a few other species) interact with music. Computer algorithms that detect the precise temporal location of beats (i.e., pulses of musical “energy”) in recorded music have important practical applications, such as the creation of playlists with a particular tempo for rehabilitation (e.g., rhythmic gait training), exercise (e.g., jogging), or entertainment (e.g., continuous dance mixes). Although several such algorithms return simple point estimates of an audio file’s temporal structure (e.g., “average tempo”, “time signature”), none has sought to quantify the temporal stability of a series of detected beats. Such a method-a “Balanced Evaluation of Auditory Temporal Stability” (BEATS)–is proposed here, and is illustrated using the Million Song Dataset (a collection of audio features and music metadata for nearly one million audio files). A publically accessible web interface is also presented, which combines the thresholdable statistics of BEATS with queryable metadata terms, fostering potential avenues of research and facilitating the creation of highly personalized music playlists for clinical or recreational applications.     

Social tagging in the life sciences: characterizing a new metadata resource for bioinformatics

Background  

Academic social tagging systems, such as Connotea and CiteULike, provide researchers with a means to organize personal collections of online references with keywords (tags) and to share these collections with others. One of the side-effects of the operation of these systems is the generation of large, publicly accessible metadata repositories describing the resources in the collections. In light of the well-known expansion of information in the life sciences and the need for metadata to enhance its value, these repositories present a potentially valuable new resource for application developers. Here we characterize the current contents of two scientifically relevant metadata repositories created through social tagging. This investigation helps to establish how such socially constructed metadata might be used as it stands currently and to suggest ways that new social tagging systems might be designed that would yield better aggregate products.     

Sexuality and Genetic Identity in the Agaricus Section Arvenses

Twelve wild collections and one commercial strain were used to characterize breeding systems and to develop molecular identities in the Arvenses section of the genus Agaricus, which includes the “horse mushroom” A. arvensis. Two morphotypes were identified based on macro- and micromorphological features. However, not all collections could be delimited by conventional taxonomic characters. Sequencing of the small subunit intergenic spacer (ITS) region (368 to 370 bp) of the rRNA genes clearly resolved the 13 collections into two clusters consistent with the identified morphotypes. Single-spore progenies and mating type testers were established and used to test intra- and interstock compatibility. The two compatibility groups identified were consistent with ITS clusters. Compatibility group I stocks readily interbred within the constraints of a unifactorial heterothallic system with a multiallelic mating type factor. Compatibility group II had a more restricted breeding pattern, and interactions were difficult to predict on the basis of mating type. Morphological data, ITS sequences, and the ability to interbreed suggest that these collections are part of a complex of interrelated species. Single-spore, homokaryotic isolates from both compatibility groups were able to fruit in compost culture, and two of the collections may represent natural homokaryotic fruiting. We conclude that species from the section Arvenses have versatile unifactorial heterothallic life cycles that permit both interbreeding and homokaryotic fruiting.     

Trabeculae carneae as models of the ventricular walls: implications for the delivery of oxygen

Trabeculae carneae are the smallest naturally arising collections of linearly arranged myocytes in the heart. They are the preparation of choice for studies of function of intact myocardium in vitro. In vivo, trabeculae are unique in receiving oxygen from two independent sources: the coronary circulation and the surrounding ventricular blood. Because oxygen partial pressure (PO₂) in the coronary arterioles is identical in specimens from both ventricles, whereas that of ventricular blood is 2.5-fold higher in the left ventricle than in the right ventricle, trabeculae represent a “natural laboratory” in which to examine the influence of “extravascular” PO₂ on the extent of capillarization of myocardial tissue. We exploit this advantage to test four hypotheses. (1) In trabeculae from either ventricle, a peripheral annulus of cells is devoid of capillaries. (2) Hence, sufficiently small trabeculae from either ventricle are totally devoid of capillaries. (3) The capillary-to-myocyte ratios in specimens from either ventricle are identical to those of their respective walls. (4) Capillary-to-myocyte ratios are comparable in specimens from either ventricle, reflecting equivalent energy demands in vivo, driven by identical contractile frequencies and comparable wall stresses. We applied confocal fluorescent imaging to trabeculae in cross section, subsequently using semi-automated segmentation techniques to distinguish capillaries from myocytes. We quantified the capillary-to-myocyte ratios of trabeculae from both ventricles and compared them to those determined for the ventricular free walls and septum. Quantitative interpretation was furthered by mathematical modeling, using both the classical solution to the diffusion equation for elliptical cross sections, and a novel approach applicable to cross sections of arbitrary shape containing arbitrary disposition of capillaries and non-respiring collagen cords.     

The contribution of small collections to species distribution modelling: A case study from Fuireneae (Cyperaceae)

The recent and rapid digitization of biodiversity data from natural history collection (NHC) archives has enriched collections based data repositories; this data continues to inform studies of species' geographic distributions. Here we investigate the relative impact of plant data from small natural history collections (collections with < 100,000 specimens) on species distributional models in an effort to document the potential of data from small NHCs to contribute to and inform biodiversity research. We modelled suitable habitat of five test case species from Fuireneae (Cyperaceae) in the United States using specimen records available via the Global Biodiversity Information Facility and that of data ready to mobilize from two regional small herbaria. Data were partitioned into three datasets based on their source: 1) collections-based records from large NHCs accessed GBIF, 2) collections-based records from small NHCs accessed from GBIF, and 3) collections-based records from two small regional herbaria not yet mobilized to GBIF. We extracted and evaluated the ecological niche represented for each of the three datasets by applying dataset occurrences to 14 environmental factors, and we modelled habitat suitability using Maxent to compare the represented distribution of the environmental values among the datasets. Our analyses indicate that the data from small NHCs contributed unique information in both geographic and environmental space. When data from small collections were combined with data from large collections, species models of the ecological niche resulted in more refined predictions of habitat suitability, indicating that small collections can contribute unique occurrence data which enhance species distribution models by bridging geographic collection gaps and shifting modelled predictions of suitable habitat. Inclusion of specimen records from small collections in ongoing digitization efforts is essential for generating informed models of a species' niche and distribution.     

A method for the epidemiologic study of early diabetes

A diabetic survey was conducted among 4048 subjects well enough to report for work, using a questionnaire covering past, present, family and obstetric history, and a capillary blood glucose determination at least 1½ hours after eating. A “positive screen” was obtained in 267 individuals, in 67 on the basis of elevated blood glucose value alone, in 179 on the basis of questionnaire responses alone, and in 21 by both criteria. Glucose tolerance tests were performed on 130 subjects (49% of eligible individuals) and yielded diabetic curves in 18, 6 and 33% respectively for the three categories of positive screening tests.It is suggested that the magnitude of the group with positive history only is such that future natural history studies must take this subsample into consideration.     

Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution,new validation tools,and implications for the future

As a discipline, structural biology has been transformed by the three-dimensional electron microscopy (3DEM) “Resolution Revolution” made possible by convergence of robust cryo-preservation of vitrified biological materials, sample handling systems, and measurement stages operating a liquid nitrogen temperature, improvements in electron optics that preserve phase information at the atomic level, direct electron detectors (DEDs), high-speed computing with graphics processing units, and rapid advances in data acquisition and processing software. 3DEM structure information (atomic coordinates and related metadata) are archived in the open-access Protein Data Bank (PDB), which currently holds more than 11,000 3DEM structures of proteins and nucleic acids, and their complexes with one another and small-molecule ligands (~ 6% of the archive). Underlying experimental data (3DEM density maps and related metadata) are stored in the Electron Microscopy Data Bank (EMDB), which currently holds more than 21,000 3DEM density maps. After describing the history of the PDB and the Worldwide Protein Data Bank (wwPDB) partnership, which jointly manages both the PDB and EMDB archives, this review examines the origins of the resolution revolution and analyzes its impact on structural biology viewed through the lens of PDB holdings. Six areas of focus exemplifying the impact of 3DEM across the biosciences are discussed in detail (icosahedral viruses, ribosomes, integral membrane proteins, SARS-CoV-2 spike proteins, cryogenic electron tomography, and integrative structure determination combining 3DEM with complementary biophysical measurement techniques), followed by a review of 3DEM structure validation by the wwPDB that underscores the importance of community engagement.     

Epithelial cell plasticity: breaking boundaries and changing landscapes

Epithelial tissues respond to a wide variety of environmental and genotoxic stresses. As an adaptive mechanism, cells can deviate from their natural paths to acquire new identities, both within and across lineages. Under extreme conditions, epithelial tissues can utilize “shape‐shifting” mechanisms whereby they alter their form and function at a tissue‐wide scale. Mounting evidence suggests that in order to acquire these alternate tissue identities, cells follow a core set of “tissue logic” principles based on developmental paradigms. Here, we review the terminology and the concepts that have been put forward to describe cell plasticity. We also provide insights into various cell intrinsic and extrinsic factors, including genetic mutations, inflammation, microbiota, and therapeutic agents that contribute to cell plasticity. Additionally, we discuss recent studies that have sought to decode the “syntax” of plasticity—i.e., the cellular and molecular principles through which cells acquire new identities in both homeostatic and malignant epithelial tissues—and how these processes can be manipulated for developing novel cancer therapeutics.     

Spatial Generalization in Operant Learning: Lessons from Professional Basketball

In operant learning, behaviors are reinforced or inhibited in response to the consequences of similar actions taken in the past. However, because in natural environments the “same” situation never recurs, it is essential for the learner to decide what “similar” is so that he can generalize from experience in one state of the world to future actions in different states of the world. The computational principles underlying this generalization are poorly understood, in particular because natural environments are typically too complex to study quantitatively. In this paper we study the principles underlying generalization in operant learning of professional basketball players. In particular, we utilize detailed information about the spatial organization of shot locations to study how players adapt their attacking strategy in real time according to recent events in the game. To quantify this learning, we study how a make \ miss from one location in the court affects the probabilities of shooting from different locations. We show that generalization is not a spatially-local process, nor is governed by the difficulty of the shot. Rather, to a first approximation, players use a simplified binary representation of the court into 2 pt and 3 pt zones. This result indicates that rather than using low-level features, generalization is determined by high-level cognitive processes that incorporate the abstract rules of the game.     

Genomic population structure associated with repeated escape of Salmonella enterica ATCC14028s from the laboratory into nature

Salmonella enterica serovar Typhimurium strain ATCC14028s is commercially available from multiple national type culture collections, and has been widely used since 1960 for quality control of growth media and experiments on fitness (“laboratory evolution”). ATCC14028s has been implicated in multiple cross-contaminations in the laboratory, and has also caused multiple laboratory infections and one known attempt at bioterrorism. According to hierarchical clustering of 3002 core gene sequences, ATCC14028s belongs to HierCC cluster HC20_373 in which most internal branch lengths are only one to three SNPs long. Many natural Typhimurium isolates from humans, domesticated animals and the environment also belong to HC20_373, and their core genomes are almost indistinguishable from those of laboratory strains. These natural isolates have infected humans in Ireland and Taiwan for decades, and are common in the British Isles as well as the Americas. The isolation history of some of the natural isolates confirms the conclusion that they do not represent recent contamination by the laboratory strain, and 10% carry plasmids or bacteriophages which have been acquired in nature by HGT from unrelated bacteria. We propose that ATCC14028s has repeatedly escaped from the laboratory environment into nature via laboratory accidents or infections, but the escaped micro-lineages have only a limited life span. As a result, there is a genetic gap separating HC20_373 from its closest natural relatives due to a divergence between them in the late 19^th century followed by repeated extinction events of escaped HC20_373.     

An Analysis of Factors Affecting Genotyping Success from Museum Specimens Reveals an Increase of Genetic and Morphological Variation during a Historical Range Expansion of a European Spider

Natural history collections house an enormous amount of plant and animal specimens, which constitute a promising source for molecular analyses. Storage conditions differ among taxa and can have a dramatic effect on the success of DNA work. Here, we analyze the feasibility of DNA extraction from ethanol preserved spiders (Araneae). We tested genotyping success using several hundred specimens of the wasp spider, Argiope bruennichi, deposited in two large German natural history collections. We tested the influence of different factors on the utility of specimens for genotyping. Our results show that not the specimen’s age, but the museum collection is a major predictor of genotyping success. These results indicate that long term storage conditions should be optimized in natural history museums to assure the utility of collections for DNA work. Using historical material, we also traced historical genetic and morphological variation in the course of a poleward range expansion of A. bruennichi by comparing contemporary and historical specimens from a native and an invasive population in Germany. We show that the invasion of A. bruennichi is tightly correlated with an historical increase of genetic and phenotypic variation in the invasive population.