The Global Museum: natural history collections and the future of evolutionary science and public education
Natural history museums are unique spaces for interdisciplinary research and educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they can provide a place-based window to focus on integration of science and discovery, as well as a locus for community engagement. At the same time, like a synthesis radio telescope, when joined together through emerging digital resources, the global community of museums (the ‘Global Museum’) is more than the sum of its parts, allowing insights and answers to diverse biological, environmental, and societal questions at the global scale, across eons of time, and spanning vast diversity across the Tree of Life. We argue that, whereas natural history collections and museums began with a focus on describing the diversity and peculiarities of species on Earth, they are now increasingly leveraged in new ways that significantly expand their impact and relevance. These new directions include the possibility to ask new, often interdisciplinary questions in basic and applied science, such as in biomimetic design, and by contributing to solutions to climate change, global health and food security challenges. As institutions, they have long been incubators for cutting-edge research in biology while simultaneously providing core infrastructure for research on present and future societal needs. Here we explore how the intersection between pressing issues in environmental and human health and rapid technological innovation have reinforced the relevance of museum collections. We do this by providing examples as food for thought for both the broader academic community and museum scientists on the evolving role of museums. We also identify challenges to the realization of the full potential of natural history collections and the Global Museum to science and society and discuss the critical need to grow these collections. We then focus on mapping and modelling of museum data (including place-based approaches and discovery), and explore the main projects, platforms and databases enabling this growth. Finally, we aim to improve relevant protocols for the long-term storage of specimens and tissues, ensuring proper connection with tomorrow’s technologies and hence further increasing the relevance of natural history museums.
Bakker et al. (2020) The Global Museum: natural history collections and the future of evolutionary science and public education. PeerJ 8:e8225 https://doi.org/10.7717/peerj.8225
­Complete plastid genome sequences of two species of the Neotropical genus Brunellia (Brunelliaceae)
Here we present the first two complete plastid genomes for Brunelliaceae, a Neotropical family with a single genus, Brunellia. We surveyed the entire plastid genome in order to find variable cpDNA regions for further phylogenetic analyses across the family. We sampled morphologically different species, B. antioquensis and B. trianae, and found that the plastid genomes are 157,685 and 157,775 bp in length and display the typical quadripartite structure found in angiosperms. Despite the clear morphological distinction between both species, the molecular data show a very low level of divergence. The amount of nucleotide substitutions per site is one of the lowest reported to date among published congeneric studies (π = 0.00025). The plastid genomes have gene order and content coincident with other COM (Celastrales, Oxalidales, Malpighiales) relatives. Phylogenetic analyses of selected superrosid representatives show high bootstrap support for the ((C,M)O) topology. The N-fixing clade appears as the sister group of the COM clade and Zygophyllales as the sister to the rest of the fabids group.
Valencia-D et al. (2020) ­Complete plastid genome sequences of two species of the Neotropical genus Brunellia (Brunelliaceae). PeerJ 8:e8392 https://doi.org/10.7717/peerj.8392
LINC00844 promotes proliferation and migration of hepatocellular carcinoma by regulating NDRG1 expression
Background Aberrant expression of long noncoding RNAs are implicated in the pathogenesis of human malignancies. LINC00844 expression is dramatically downregulated in prostate cancer, and functional studies have revealed the association between the aberrant expression of LINC00844 and prostate cancer cell invasion and metastasis. However, the function and mechanism of action of LINC00844 in the pathogenesis of hepatocellular carcinoma (HCC) are poorly understood. Methods LINC00844 and N-Myc downstream-regulated 1 (NDRG1) expression in HCC tissues and cell lines was detected with real-time quantitative polymerase chain reaction (RT-qPCR) and western blot analysis. Correlations between LINC00844 expression level and clinicopathological features were investigated using the original data from The Cancer Genome Atlas (TCGA) database. HepG2 and HCCLM9 cell lines were transfected with Lv-LIN00844 virus to obtain LINC00844-overexpressing cell lines. Cell proliferation and cell invasion and migration were examined with the cell counting kit-8 (CCK-8) and transwell assay, respectively. Furthermore, the correlation between LINC00844 and NDRG1 expression was analysed using Pearson’s correlation analysis. Results LINC00844 expression was significantly downregulatedin HCC tissues and cell lines, and a statistical correlation was detected between low LINC00844 expression and sex (Female), advanced American Joint Committee on Cancer (AJCC) stage (III + IV), histological grade (G3 + G4), and vascular invasion (Micro and Macro). In vitro experiments showed that LINC00844 overexpression significantly repressed the proliferation, migration, and invasion of HCC cells. NDRG1 expression was higher in HCC tissues and LINC00844 could partly inhibit the expression of NDRG1.
Zhou et al. (2020) LINC00844 promotes proliferation and migration of hepatocellular carcinoma by regulating NDRG1 expression. PeerJ 8:e8394 https://doi.org/10.7717/peerj.8394
Teenage sleep and technology engagement across the week
Background Throughout the developed world, adolescents are growing up with increased access to and engagement with a range of screen-based technologies, allowing them to encounter ideas and people on a global scale from the intimacy of their bedroom. The concerns about digital technologies negatively influencing sleep are therefore especially noteworthy, as sleep has been proven to greatly affect both cognitive and emotional well-being. The associations between digital engagement and adolescent sleep should therefore be carefully investigated in research adhering to the highest methodological standards. This understood, studies published to date have not often done so and have instead focused mainly on data derived from general retrospective self-report questionnaires. The value of this work has been called into question by recent research showing that retrospective questionnaires might fail to accurately measure these variables of interest. Novel and diverse approaches to measurement are therefore necessary for academic study to progress. Methods This study analyses data from 11,884 adolescents included in the UK Millennium Cohort Study to examine the association between digital engagement and adolescent sleep, comparing the relative effects of retrospective self-report vs. time-use diary measures of technology use. By doing so, it provides an empirical lens to understand the effects of digital engagement both throughout the day and before bedtime and adds nuance to a research area primarily relying on retrospective self-report. Results The study finds that there is a small negative association relating digital engagement to adolescent sleep both on weekdays and weekend days (median standardized association βweekday = −0.06 and βweekend = −0.03). There is a more negative association between digital engagement and total sleep time on weekdays compared to weekend days (median standardized βweekday = −0.08, median standardized βweekend = −0.02), while there is no such difference when examining adolescents’ bedtime. Surprisingly, and contrary to our expectations, digital technology use before bedtime is not substantively associated with the amount of sleep and the tardiness of bedtime in adolescents. Conclusions Results derived from the use of transparent Specification Curve Analysis methods show that the negative associations in evidence are mainly driven by retrospective technology use measures and measures of total time spent on digital devices during the day. The effects are overall very small: for example, an additional hour of digital screen time per day was only related to a 9 min decrease in total time spent sleeping on weekdays and a 3 min decrease on weekends. Using digital screens 30 min before bed led to a 1 min decrease in total time spent sleeping on weekdays and weekends. The study shows that more work should be done examining how to measure digital screen time before interventions are designed.
Orben et al. (2020) Teenage sleep and technology engagement across the week. PeerJ 8:e8427 https://doi.org/10.7717/peerj.8427
Metabolic response of Scapharca subcrenata to heat stress using GC/MS-based metabolomics
Marine mollusks are commonly subjected to heat stress. To evaluate the effects of heat stress on the physiological metabolism of the ark shell Scapharca subcrenata, clams were exposed to different high temperatures (24, 28 and 32 °C) for 72 h. The oxygen consumption and ammonia excretion rates were measured at 2, 12, 24, 48 and 72 h. The results indicated that the metabolic rates of the ark shell significantly increased with increasing heat stress, accompanied by mortalities in response to prolonged exposure. A metabolomics approach based on gas chromatography coupled with mass spectrometry was further applied to assess the changes of metabolites in the mantle of the ark shell at 32 °C. Moreover, multivariate and pathway analyses were conducted for the different metabolites. The results showed that the heat stress caused changes in energy metabolism, amino acid metabolism, osmotic regulation, carbohydrate metabolism and lipid metabolism through different metabolic pathways. These results are consistent with the significant changes of oxygen consumption rate and ammonia excretion rate. The present study contributes to the understanding of the impacts of heat stress on intertidal bivalves and elucidates the relationship between individual-level responses and underlying molecular metabolic dynamics.
Jiang et al. (2020) Metabolic response of Scapharca subcrenata to heat stress using GC/MS-based metabolomics. PeerJ 8:e8445 https://doi.org/10.7717/peerj.8445
Loss of Schlafen3 influences the expression levels of Schlafen family members in ileum, thymus, and spleen tissue
Background The Schlafen (Slfn) family proteins are important for regulation of cell growth, cell differentiation and cell cycle progression. We sought to distinguish Slfn family expression in Slfn3 knockout (KO) mice after RNA sequencing analysis of Slfn3KO vs. wildtype (WT) mice revealed varying expressions of Slfn family in ileal mucosa. Methods Quantitative PCR analysis of Slfn members was evaluated in ileal mucosa, thymus and spleen tissue since Slfn family members have roles in differentiating intestinal and immune cells. Results Ileal mucosa of Slfn3KO mice displayed a decrease in Slfn3, 4, 8 and 9 while Slfn1 and 5 increased in mRNA expression vs. WT mice. Thymic tissue had a Slfn9 increase and a Slfn4 decrease while splenic tissue had a Slfn8 and Slfn9 increase in Slfn3KO mice vs. WT mice. These differential expressions of Slfn members could indicate a feedback regulatory mechanism within the Slfn family. Indeed, MATCH™ tool from geneXplain predicted that all Slfn members have regions in their promoters for the Kruppel-like factor-6 transcription factor. In addition, NFAT related factors, ING4, ZNF333 and KLF4 are also predicted to bind in up to 6 of the 8 Slfn promoters. This study further describes a possible autoregulatory mechanism amongst the Slfn family members which could be important in how they regulate the differentiation of various cell types.
Vomhof-DeKrey et al. (2020) Loss of Schlafen3 influences the expression levels of Schlafen family members in ileum, thymus, and spleen tissue. PeerJ 8:e8461 https://doi.org/10.7717/peerj.8461
Light-harvesting chlorophyll a/b-binding protein-coding genes in jatropha and the comparison with castor, cassava and arabidopsis
The Lhc (light-harvesting chlorophyll a/b-binding protein) superfamily represents a class of antennae proteins that play indispensable roles in capture of solar energy as well as photoprotection under stress conditions. Despite their importance, little information has been available beyond model plants. In this study, we presents a first genome-wide analysis of Lhc superfamily genes in jatropha (Jatropha curcas L., Euphorbiaceae), an oil-bearing plant for biodiesel purpose. A total of 27 members were identified from the jatropha genome, which were shown to distribute over nine out of the 11 chromosomes. The superfamily number is comparable to 28 present in castor (Ricinus communis, Euphorbiaceae), but relatively less than 35 in cassava (Manihot esculenta, Euphorbiaceae) and 34 in arabidopsis (Arabidopsis thaliana) that experienced one or two recent whole-genome duplications (WGDs), respectively. In contrast to a high number of paralogs present in cassava and arabidopsis, few duplicates were found in jatropha as observed in castor, corresponding to no recent WGD occurred in these two species. Nevertheless, 26 orthologous groups representing four defined families were found in jatropha, and nearly one-to-one orthologous relationship was observed between jatropha and castor. By contrast, a novel group named SEP6 was shown to have been lost in arabidopsis. Global transcriptome profiling revealed a predominant expression pattern of most JcLhc superfamily genes in green tissues, reflecting their key roles in photosynthesis. Moreover, their expression profiles upon hormones, drought, and salt stresses were also investigated. These findings not only improve our knowledge on species-specific evolution of the Lhc supergene family, but also provide valuable information for further studies in jatropha.
Zhao et al. (2020) Light-harvesting chlorophyll a/b-binding protein-coding genes in jatropha and the comparison with castor, cassava and arabidopsis. PeerJ 8:e8465 https://doi.org/10.7717/peerj.8465
Moderation effects of food intake on the relationship between urinary microbiota and urinary interleukin-8 in female type 2 diabetic patients
Background Our previous study demonstrated that the composition of the urinary microbiota in female patients with type 2 diabetes mellitus (T2DM) was correlated with the concentration of urinary interleukin (IL)-8. As the composition of urine is mainly determined by diet, diet might mediate the correlation. Methods Seventy female T2DM patients and 70 healthy controls (HCs) were recruited. Midstream urine was used for the urine specimens. Urinary IL-8 was determined by enzyme-linked immunosorbent assay. A Chinese Food Frequency Questionnaire was used to collect food intake data. The independent variables in the hierarchical regression analysis were the relative abundances of the bacterial genera and species that were significantly different between the T2DM and HCs and between the T2DM patients with and without detectable urinary IL-8, and the bacterial genera associated with IL-8 concentration in the multiple regression model reported in our previous research. IL-8 concentration was the dependent variable, and nutrient intakes were moderator variables. Results Fiber and vitamin B3 and E intake exerted enhancing effects, and water intake exerted a buffering effect, on the positive relationship between the relative abundance of Ruminococcus and IL-8 concentration (p < 0.05). Cholesterol and magnesium intake exerted enhancing effects on the positive relationship between the relative abundance of Comamonas and IL-8 concentration (p < 0.05). Conclusion Modulating T2DM patients’ dietary patterns may prevent bladder inflammation.
Liu et al. (2020) Moderation effects of food intake on the relationship between urinary microbiota and urinary interleukin-8 in female type 2 diabetic patients. PeerJ 8:e8481 https://doi.org/10.7717/peerj.8481
Crypsis and convergence: integrative taxonomic revision of the Gehyra australis group (Squamata: Gekkonidae) from northern Australia
For over two decades, assessments of geographic variation in mtDNA and small numbers of nuclear loci have revealed morphologically similar, but genetically divergent, intraspecific lineages in lizards from around the world. Subsequent morphological analyses often find subtle corresponding diagnostic characters to support the distinctiveness of lineages, but occasionally do not. In recent years it has become increasingly possible to survey geographic variation by sequencing thousands of loci, enabling more rigorous assessment of species boundaries across morphologically similar lineages. Here we take this approach, adding new, geographically extensive SNP data to existing mtDNA and exon capture datasets for the Gehyra australis and G. koira species complexes of gecko from northern Australia. The combination of exon-based phylogenetics with dense spatial sampling of mitochondrial DNA sequencing, SNP-based tests for introgression at lineage boundaries and newly-collected morphological evidence supports the recognition of nine species, six of which are newly described here. Detection of discrete genetic clusters using new SNP data was especially convincing where candidate taxa were continuously sampled across their distributions up to and across geographic boundaries with analyses revealing no admixture. Some species defined herein appear to be truly cryptic, showing little, if any, diagnostic morphological variation. As these SNP-based approaches are progressively applied, and with all due conservatism, we can expect to see a substantial improvement in our ability to delineate and name cryptic species, especially in taxa for which previous approaches have struggled to resolve taxonomic boundaries.
Oliver et al. (2020) Crypsis and convergence: integrative taxonomic revision of the Gehyra australis group (Squamata: Gekkonidae) from northern Australia. PeerJ 8:e7971 https://doi.org/10.7717/peerj.7971
Investigating the effects of management practice on mammalian co-occurrence along the West Coast of South Africa
The subtle and cascading effects (e.g., altered interspecific interactions) that anthropogenic stressors have on local ecological assemblages often go unnoticed but are concerning given their importance in ecosystem function. For example, elimination of buffalo from the Serengeti National Park is suggested to have driven increased abundance of smaller antelope as a result of release from competition. The perceived low abundance of small antelope in the contractual Postberg section of the West Coast National Park (the park) has been an ongoing management concern which has been anecdotally attributed to predation by a mesopredator (the caracal, Caracal caracal). However, we hypothesized that the historical overstocking, and consequent overgrazing by larger-bodied managed ungulates would influence small antelope abundance. Using camera traps, we investigated species co-occurrence and temporal activity between small antelope, managed ungulates and caracals in Postberg as well as another part of the park (Langebaan) and a farm outside of the park. Results suggest that small antelope and managed ungulates have a high degree of temporal overlap (Δ = 0.74, 0.79 and 0.86 for the farm, Langebaan and Postberg respectively), while temporal partitioning between small antelope and caracal is apparent (Δ = 0.59). Further, small antelope and managed ungulates appear to occur independently of one another (SIF = 0.91–1 across areas). Managed ungulates were detected almost three times more frequently on fallow lands when compared to the more vegetated sites within the park suggesting that segregated food/cover resources allow for independent occurrence. Small antelope had a much higher probability of occurrence outside of the protected area (e.g., ψ = 0.192 and 0.486 for steenbok at Postberg, Langebaan compared to 0.841 on the farm), likely due to less variable (more intact) habitat outside of the protected area. There is not sufficient evidence to currently warrant management intervention for predators. The small size of the protected area provides limited scope for spatial replication thus reducing possibilities to infer the cause and effect for complex interactions (which would historically have taken place over much larger areas) with negative implications for adaptive management. We recommend continued monitoring over multiple seasons and a wider area to determine the spatial information requirements to inform management of small protected areas.
Winterton et al. (2020) Investigating the effects of management practice on mammalian co-occurrence along the West Coast of South Africa. PeerJ 8:e8184 https://doi.org/10.7717/peerj.8184