Biodiversity Informatics
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The political economy of amphibian declines
Get PDFRecent conservation research stresses the importance of examining economic growth as an underlyingdriver of biodiversity loss. With exceptions, herpetological research on the causes of amphibian declines, endangerments,and extinction risks tends to focus on proximate rather than underlying drivers. This paper connects proximatecauses of amphibian declines to structural attributes of modern societies, specifically a growth-dependent economic system.Amphibian declines caused by habitat modification, climate change, contaminants, and commercial use are all inpart driven by “the treadmill of production” — capitalism’s systemic need to constantly expand. Recognizing the negativeimpacts of a growth-dependent economy on amphibians has important implications for conservation strategies
A predation attempt on a Three-spined Stickleback (Gasterosteus aculeatus) fry by a larval Santa Cruz Long-toed Salamander (Ambystoma macrodactylum croceum)
Get PDFVisual encounter surveys reveal a new population of Black Pine Snakes (Pituophis melanoleucus lodingi) in Mississippi
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Appropriate normalization is critical to improve reproducibility of tissue ChIP-seq
Get PDFChromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) is a powerful technology for studying genetic and epigenetic regulation. However, ChIP-seq data can be heavily affected by variations in chromatin amount and composition, ChIP enrichment, library preparation, and sequencing depth, affecting its overall reproducibility across biological replicates. Here, we evaluated four ChIP-seq normalization methods utilizing triplicate Foxa1 ChIP-seq data performed in prostate cancer tissues from three mice. We found that count-per-million (CPM) normalization, although not affecting peak calling in individual samples, is very useful for visualization and comparison of peak distribution and intensity across samples. By contrast, equal-read normalization improves both peak identification and intensity comparison. Moreover, spike-in normalization took advantage of spike-in chromatin ChIP to correct technical variations in ChIP-seq, including ChIP enrichment, sample preparation, and sequencing. Lastly, input-adjusted spike-in normalization further accounts for differences in input chromatin amount across samples, which is especially crucial for tissue ChIP-seq that often starts with different amounts of input chromatin. Overall, our study demonstrated that appropriate normalization is essential to improve the reproducibility and comparability of ChIP-seq experiments and highlighted the importance of input-adjusted spike-in normalization for tissue ChIP-seq.
First record of Rhinetula dentricus Friese (Hymenoptera: Halictidae: Halictini) from México
No full textRhinetula denticrus Friese is recorded for the first time in Mexico. During curatorial work, a specimen collected in 1980 from Cárdenas, Tabasco, Veracruz Biogeographic Province, was discovered, representing the northernmost known record of the genus in the Neotropical region. In addition, we provide new observations on the nesting habits of this species
Mortarboard Review: Montessori-Related Dissertations, 2024
Get PDFThis is the third article in an ongoing series, published annually, highlighting a selection of English-language dissertations from the previous calendar year related to Montessori philosophy and education. Twenty-one doctoral dissertations completed and approved during the 2024 calendar year were identified. The authors selected three dissertations to spotlight because they represent research that is novel, timely, and relevant to the current educational landscape
Ecological Niche Modeling Applications to Infectious Diseases
Get PDFEcological niche modeling (ENM) is a widely used analytical approach for predicting species distributions and has been applied to study spatial epidemiology of infectious diseases. Nevertheless, research evaluating the key components and assumptions of ENM in disease systems remains limited, raising concerns about its robustness, reproducibility, and transparency. To address this limitation, we conducted a systematic review and evaluated articles on ENM applications to infectious diseases between 2020 and 2022. We reviewed 78 articles to extract information following a standard protocol for reporting ENM analysis and summarized the information for each component (e.g., study subject, location, duration). The spatial extent of study areas varied from village to global scales, temporal duration ranged from 1 to 101 years, and the organismal levels ranged from individuals (57.7%) to populations (33.3%). Less frequently reported components included temporal autocorrelation tests (2.7%), algorithmic uncertainty (28.2%), temporal resolution (35.9%), background data selection (44.9%), coordinate reference system (41.0%), model performance from validation data (46.2%), and model averaging (20.5%). Our findings highlight a lack of consistency and transparency in disease ecology and disease biogeography studies, which may lead to misleading ENM applications in spatial epidemiology. Researchers and reviewers applying ENM to disease systems should clearly report key modeling components to ensure biologically sound outputs. This article identified trends and gaps in reporting ENM protocols for mapping disease transmission risk