The Earth's Magnetic Field: A Simple Measurement of its Strength

Although most teachers agree that a field trip is an important educational experience for their students, many struggle with finding a way to make it connect with their classroom curriculum. Creating an effective field trip involves creating an effective lesson plan and using the resources of the museum, zoo, or aquarium to foster inquiry and learning. By incorporating the learning cycle into their field trip, students are able to use their explorations with animal-based exhibits to develop basic life science concepts.     

Student‐led field studies of herbivory: Hands‐on experiences for remote (or in‐person) learning

Challenging students to independently design and implement experiments is a powerful way to teach the scientific method while engaging with STEM‐related course material. For ecology and organismal biology, such experiences often take the form of field work. The COVID‐19 pandemic presented formidable challenges for instructors of such courses: How can students conduct any experiments, much less ones of their own design, when they might not even have access to campus? Here we describe a student‐led field project exploring invertebrate herbivory in terrestrial plant systems. Designed to flexibly accommodate student groups working either in‐person, remotely, or both, the project would be suitable for invertebrate biology, plant biology, or general ecology courses at the college or high school level. We describe our implementation in two sections of a sophomore‐level course, provide specific advice based on our experiences, make suggestions for future improvements or adaptations, and provide all the written materials that instructors would need to implement this in their own teaching.     

Genotyping‐free parentage assignment using RAD‐seq reads

Parentage assignment is defined as the identification of the true parents of one focal offspring among a list of candidates and has been commonly used in zoological, ecological, and agricultural studies. Although likelihood‐based parentage assignment is the preferred method in most cases, it requires genotyping a predefined set of DNA markers and providing their population allele frequencies. In the present study, we proposed an alternative method of parentage assignment that does not depend on genotype data and prior information of allele frequencies. Our method employs the restriction site‐associated DNA sequencing (RAD‐seq) reads for clustering into the overlapped RAD loci among the compared individuals, following which the likelihood ratio of parentage assignment could be directly calculated using two parameters—the genome heterozygosity and error rate of sequencing reads. This method was validated on one simulated and two real data sets with the accurate assignment of true parents to focal offspring. However, our method could not provide a statistical confidence to conclude that the first ranked candidate is a true parent.     

Effective field trips in nature: the interplay between novelty and learning

Educational field trips are common practice in environmental education and education for sustainable development, well recognised by researchers for their potential to achieve cognitive and affective educational outcomes. One of the factors that influences learning during field trips is their novelty. The current study focuses on the interplay between novelty, preparation and environmental learning outcomes of 5th and 6th grade students during a typical field trip in Flanders. Our dependent variables are Inclusion of Nature in the Self, the two major ecological values Preservation and Utilisation and ecosystem knowledge. The sample includes 484 students (10–12 years old) and their 24 teachers. Key questions addressed are: (1) What is learned during the field trip? (2) What is the level of novelty for students during a field trip? (3) How does the novelty effect relate to learning? Results show that participation in the field trip leads to a substantial increase in ecosystem knowledge, but fails in reaching the affective goals set out by the field trip organisers. Our results furthermore provide support for the hypothesised non-linear relationship between novelty and knowledge gain, showing that while a little novelty is positive, too much novelty can stand in the way of learning.     

Providing interactive and field laboratories while teaching university marine biology classes in an era of COVID‐19

An entirely online upper‐division university marine invertebrates course modeled after a field experience‐intensive course that also provided interaction with live animals and research experience was offered at Rosario Beach Marine Laboratory in the summer of 2020. We describe online methods we used for providing field experiences to students participating online, as well as a workstation and interactive method for identification and detailed anatomical examination of live macroinvertebrates with students. Students were also involved as active participants in a field research project. Nearly all of the equipment involved is inexpensive or readily available in most university biology laboratories or classrooms.     

Synthesis,HPLC Enantioresolution,and X‐ray Analysis of a New Series of C5‐methyl Pyridazines as N‐Formyl Peptide Receptor (FPR) Agonists

The synthesis of three racemates and the corresponding non‐chiral analogues of a C5‐methyl pyridazine series is described here, as well as the isolation of pure enantiomers and their absolute configuration assignment. In order to obtain optically active compounds, direct chromatographic methods of separation by HPLC‐UV were investigated using four chiral stationary phases (CSPs: Lux Amylose‐2, Lux Cellulose‐1, Lux Cellulose‐2 and Lux Cellulose‐3). The best resolution was achieved using amylose tris(5‐chloro‐2‐methylphenylcarbamate) (Lux Amylose‐2), and single enantiomers were isolated on a semipreparative scale with high enantiomeric excess, suitable for biological assays. The absolute configuration of optically active compounds was unequivocally established by X‐ray crystallographic analysis and comparative chiral HPLC‐UV profile. All compounds of the series were tested for formyl peptide receptor (FPR) agonist activity, and four were found to be active, with EC₅₀ values in the micromolar range. Chirality 25:400–408, 2013. © 2013 Wiley Periodicals, Inc.     

Chemical profiling of mycosporine‐like amino acids in twenty‐three red algal species

Rhodophyta produce a variety of chemically different mycosporine‐like amino acids (MAAs), compounds that are known as some of the strongest ultraviolet (UV) absorbing molecules in nature. Accordingly, they primarily act as photoprotectants against harmful levels of solar ultraviolet radiation in the UV‐A and UV‐B range. In order to get a deeper understanding of the chemical diversity of MAAs in red algae, pure standards of eleven mycosporine‐like amino acids were isolated from three different species (Agarophyton chilense, Pyropia plicata and Champia novae‐zelandiae) using various chromatographic methods. Their structures were confirmed by nuclear magnetic resonance and mass spectrometry. Four out of the eleven MAAs are reported for the first time in algae. In addition, a new high‐performance liquid chromatography method was developed for the separation of all isolated MAAs and successfully applied for the analysis of twenty‐three red algal species of marine origin. All of them contained MAAs, the most abundant compounds were shinorine, palythine, asterina‐330 and porphyra‐334. For some samples, the direct assignment of MAAs based on their UV spectra was not possible; therefore, the target analytes were enriched by a simple concentration step, followed by liquid chromatography‐mass spectrometry analysis of the extracts. This approach enabled a deeper insight into the MAA pattern of red algae, indicating that not only the four dominant ones are synthesized but also many others, which were often described as unknown compounds in previous studies.     

Flipper bands do not affect foraging‐trip duration of Magellanic Penguins

ABSTRACT Flipper bands are used to mark penguins because leg bands can injure their legs. However, concerns remain over the possible effects of flipper bands on penguins. We examined the effects of stainless‐steel flipper bands on the duration of foraging trips by Magellanic Penguins (Spheniscus magellanicus) at Punta Tombo, Argentina, using an automated detection system. We predicted that, if bands were costly and increased drag, flipper‐banded penguins would make longer foraging trips than those with small or no external markings. We tagged 121 penguins with radio‐frequency identification (RFID) tags and an additional external mark. We placed either a stainless‐steel band on the left flipper (N= 62) or a 2×10‐mm small‐animal ear tag in the outside web of the left foot (N= 59). We measured foraging‐trip durations (N= 376 trips) for 68 adult penguins with chicks from 15 December 2007 to 28 February 2008. Contrary to predictions, trip duration was similar for banded and web‐tagged penguins (P= 0.22) and for males and females (P= 0.52), with no interaction between tag type and sex (P= 0.52). No penguins marked in the 2007 breeding season and recaptured between 30 September and 30 November 2008 (N= 113) lost flipper bands or web tags, but three RFID tags failed between March and September 2008. Properly designed and applied flipper bands were a reliable marking method for Magellanic Penguins, had a lower failure rate than RFIDs, and did not affect foraging‐trip duration.     

Variation of cats under domestication: genetic assignment of domestic cats to breeds and worldwide random‐bred populations

Both cat breeders and the lay public have interests in the origins of their pets, not only in the genetic identity of the purebred individuals, but also in the historical origins of common household cats. The cat fancy is a relatively new institution with over 85% of its 40–50 breeds arising only in the past 75 years, primarily through selection on single‐gene aesthetic traits. The short, yet intense cat breed history poses a significant challenge to the development of a genetic marker–based breed identification strategy. Using different breed assignment strategies and methods, 477 cats representing 29 fancy breeds were analysed with 38 short tandem repeats, 148 intergenic and five phenotypic single nucleotide polymorphisms. Results suggest the frequentist method of Paetkau (single nucleotide polymorphisms = 0.78, short tandem repeats = 0.88) surpasses the Bayesian method of Rannala and Mountain (single nucleotide polymorphisms = 0.56, short tandem repeats = 0.83) for accurate assignment of individuals to the correct breed. Additionally, a post‐assignment verification step with the five phenotypic single nucleotide polymorphisms accurately identified between 0.31 and 0.58 of the misassigned individuals raising the sensitivity of assignment with the frequentist method to 0.89 and 0.92 for single nucleotide polymorphisms and short tandem repeats respectively. This study provides a novel multistep assignment strategy and suggests that, despite their short breed history and breed family groupings, a majority of cats can be assigned to their proper breed or population of origin, that is, race.     

Application of NMR spectroscopy for assignment of the absolute configuration of 8‐tert‐butyl‐2‐hydroxy‐7‐methoxy‐8‐methyl‐9‐oxa‐6‐azaspiro[4.5]dec‐6‐en‐10‐one

In order to assign the absolute configurations of 8‐tert‐butyl‐2‐hydroxy‐7‐methoxy‐8‐methyl‐9‐oxa‐6‐azaspiro[4.5]dec‐6‐en‐10‐one ( 2a , 2b ), their esters ( 5a , 5b , 5c , 5d ) with (R)‐ or (S)‐2‐methoxyphenylacetic acid ( 4a , 4b ) have been synthesized. The absolute configurations of these compounds have been determined on the basis of NOESY correlations between the protons of the tert‐butyl group and the cyclopentane fragment of the molecules. The crucial part of this analysis was assignment of the absolute configuration at C‐5. Additionally, by calculation of the chemical shift anisotropy, δ^RS, for the relevant protons, it was also possible to confirm the absolute configurations at the C‐2 centres of compounds 2a , 2b and 5a , 5b , 5c , 5d . Chirality, 25:422–426, 2013.© 2013 Wiley Periodicals, Inc.     

Design and implementation of a genomics field trip program aimed at secondary school students

With the rapid pace of advancements in biological research brought about by the application of computer science and information technology, we believe the time is right for introducing genomics and bioinformatics tools and concepts to secondary school students. Our approach has been to offer a full-day field trip in our research facility where secondary school students carry out experiments at the laboratory bench and on a laptop computer. This experience offers benefits for students, teachers, and field trip instructors. In delivering a wide variety of science outreach and education programs, we have learned that a number of factors contribute to designing a successful experience for secondary school students. First, it is important to engage students with authentic and fun activities that are linked to real-world applications and/or research questions. Second, connecting with a local high school teacher to pilot programs and linking to curricula taught in secondary schools will enrich the field trip experience. Whether or not programs are linked directly to local teachers, it is important to be flexible and build in mechanisms for collecting feedback in field trip programs. Finally, graduate students can be very powerful mentors for students and should be encouraged to share their enthusiasm for science and to talk about career paths. Our experiences suggest a real need for effective science outreach programs at the secondary school level and that genomics and bioinformatics are ideal areas to explore.     

Solid‐phase synthesis and screening of a library of C‐terminal arginine peptide aldehydes against Murray Valley encephalitis virus protease

Murray Valley encephalitis virus is a member of the flavivirus group, a large family of single‐stranded RNA viruses, which cause serious disease in all regions of the world. Unfortunately, no suitable antivirals are available, and there are commercial vaccines for only three flaviviruses. The solid‐phase synthesis of a library of 400 C‐terminal arginine peptide aldehydes and their screening against Murray Valley encephalitis virus protease are demonstrated. The library was utilised to elucidate several tripeptide sequences that can be used as inhibitors in further SAR studies. Copyright © 2012 European Peptide Society and John Wiley & Sons, Ltd.     

Bayesian propensity scores for high‐dimensional causal inference: A comparison of drug‐eluting to bare‐metal coronary stents

High‐dimensional data provide many potential confounders that may bolster the plausibility of the ignorability assumption in causal inference problems. Propensity score methods are powerful causal inference tools, which are popular in health care research and are particularly useful for high‐dimensional data. Recent interest has surrounded a Bayesian treatment of propensity scores in order to flexibly model the treatment assignment mechanism and summarize posterior quantities while incorporating variance from the treatment model. We discuss methods for Bayesian propensity score analysis of binary treatments, focusing on modern methods for high‐dimensional Bayesian regression and the propagation of uncertainty. We introduce a novel and simple estimator for the average treatment effect that capitalizes on conjugacy of the beta and binomial distributions. Through simulations, we show the utility of horseshoe priors and Bayesian additive regression trees paired with our new estimator, while demonstrating the importance of including variance from the treatment regression model. An application to cardiac stent data with almost 500 confounders and 9000 patients illustrates approaches and facilitates comparison with existing alternatives. As measured by a falsifiability endpoint, we improved confounder adjustment compared with past observational research of the same problem.     

Genetic evidence for male‐biased dispersal in the Qinghai toad‐headed agamid Phrynocephalus vlangalii and its potential link to individual social interactions

Sex‐biased dispersal has profound impacts on a species' biology and several factors have been attributed to its evolution, including mating system, inbreeding avoidance, and social complexity. Sex‐biased dispersal and its potential link to individual social interactions were examined in the Qinghai toad‐headed agamid (Phrynocephalus vlangalii). We first determined the pattern of sex‐biased dispersal using population genetic methods. A total of 345 specimens from 32 sites in the Qaidam Basin were collected and genotyped for nine microsatellite DNA loci. Both individual‐based assignment tests and allele frequency‐based analyses were conducted. Females revealed much more genetic structure than males and all results were consistent with male‐biased dispersal. First‐generation migrants were also identified by genetic data. We then examined eight social interaction‐related morphological traits and explored their potential link to sex‐biased dispersal. Female residents had larger heads and longer tails than female migrants. The well‐developed signal system among females, coupled with viviparity, might make remaining on natal sites beneficial, and hence promote female philopatry. Dominant females with larger heads were more likely to stay. Contrary to females, male migrants had larger heads and belly patches than residents, suggesting that dispersal might confer selective advantages for males. Such advantages may include opportunities for multiple mating and escaping from crowded sites. Large belly patches and several other morphological traits may assist their success in obtaining mates during dispersal. Furthermore, a relatively high relatedness (R = 0.06) among females suggested that this species might have rudimentary social structure. Case studies in “less” social species may provide important evidence for a better understanding of sex‐biased dispersal.     

Overnight foraging trips by chick‐rearing Nazca Boobies Sula granti and the risk of attack by predatory fish

Most tropical booby species complete breeding foraging trips within daylight hours, thus avoiding nights at sea. Nazca Boobies Sula granti are unusual in this respect, frequently spending one or more nights away from the nest. We used GPS dataloggers, time‐depth recorders, and changes in body weight to characterize foraging trips and to evaluate potential influences on the decisions of 64 adult Nazca Boobies to spend a night at sea, or to return to their chicks on Isla Española, Galápagos, in daylight hours. The tagged birds foraged east of Isla Española, undertaking both single‐day (2–15 h, 67% of trips) and overnight trips (28 h–7.2 days, 33%), and executing 1–19 foraging plunge‐dives per single‐day trip. Birds might forage longer if they are in nutritional stress when they depart, but body weight at departure was not correlated with trip length. Birds might be expected to return from longer trips with more prey for young, but they returned from single‐day and overnight trips with similar body weights, consistent with previous indications that Nazca Boobies forage until accumulating a target value of prey weight. Birds with a lower dive frequency during the first 5 h of a trip were more likely to spend the night at sea, suggesting that they might choose to spend the night at sea if prey capture success was low. At night, birds almost never dived and spent most of their time resting on the water’s surface (11.8–12.1 h, > 99% of the time between civil sunset and civil dawn). Thus, the night is an unproductive time spent among subsurface predators under low illumination. The birds’ webbed feet provided evidence of this risk: 24% of birds were missing > 25% of their foot tissue, probably due to attacks by predatory fish, and the amount of foot tissue lost increased with age, consistent with a cumulative risk across the lifespan. In contrast, other tropical boobies (Blue‐footed Sula nebouxii and Brown Boobies Sula leucogaster), which do not spend the night on the water, showed no such damage. These results suggest that chick‐rearing Nazca Boobies accept nocturnal predation risk on occasions of low prey encounter during a foraging trip’s first day.     

Label‐free indicator‐free nucleic acid biosensors using carbon nanotubes

Carbon nanotubes (CNTs) are promising components for electrical biosensors due to their high surface‐to‐volume ratio and improved electron transfer properties. This review surveys CNT‐based label‐free indicator‐free biosensing strategies that have been demonstrated for the sensitive detection of nucleic acids. After an introduction to CNTs, the fabrication of biosensors and techniques for the immobilization of probe nucleic acids are outlined. Subsequently, two major label‐free strategies namely electrochemical transduction and field‐effect detection are presented. The focus is on direct detection methods that avoid labels, indicators, intercalating agents, mediators, and even secondary receptors. The review concludes with a comparison between the various biosensors and presents ways of engineering them so that they can be deployed in realistic diagnostic applications.     

Metal‐Organic Framework‐Derived Carbons for Battery Applications

The applications of carbon and carbon‐based materials with high porosity, high surface area, and functionalities based on metal‐organic framework precursors and/or templates have attracted significant research interest in recent years, particularly in the field of batteries. The chemical and physical properties of carbon and carbon‐based materials obtained by the heat treatment of various metal‐organic framework precursors or templates are improved to a certain extent. In this comprehensive review, the synthetic methods and electrochemical performance of carbon materials derived from metal‐organic frameworks (metal/carbon, metal oxide/carbon, nitrogen‐doped carbon, porous carbon, etc.) along with their applications in batteries are outlined.     

Using expert knowledge to incorporate uncertainty in cause‐of‐death assignments for modeling of cause‐specific mortality

Implicit and explicit use of expert knowledge to inform ecological analyses is becoming increasingly common because it often represents the sole source of information in many circumstances. Thus, there is a need to develop statistical methods that explicitly incorporate expert knowledge, and can successfully leverage this information while properly accounting for associated uncertainty during analysis. Studies of cause‐specific mortality provide an example of implicit use of expert knowledge when causes‐of‐death are uncertain and assigned based on the observer's knowledge of the most likely cause. To explicitly incorporate this use of expert knowledge and the associated uncertainty, we developed a statistical model for estimating cause‐specific mortality using a data augmentation approach within a Bayesian hierarchical framework. Specifically, for each mortality event, we elicited the observer's belief of cause‐of‐death by having them specify the probability that the death was due to each potential cause. These probabilities were then used as prior predictive values within our framework. This hierarchical framework permitted a simple and rigorous estimation method that was easily modified to include covariate effects and regularizing terms. Although applied to survival analysis, this method can be extended to any event‐time analysis with multiple event types, for which there is uncertainty regarding the true outcome. We conducted simulations to determine how our framework compared to traditional approaches that use expert knowledge implicitly and assume that cause‐of‐death is specified accurately. Simulation results supported the inclusion of observer uncertainty in cause‐of‐death assignment in modeling of cause‐specific mortality to improve model performance and inference. Finally, we applied the statistical model we developed and a traditional method to cause‐specific survival data for white‐tailed deer, and compared results. We demonstrate that model selection results changed between the two approaches, and incorporating observer knowledge in cause‐of‐death increased the variability associated with parameter estimates when compared to the traditional approach. These differences between the two approaches can impact reported results, and therefore, it is critical to explicitly incorporate expert knowledge in statistical methods to ensure rigorous inference.     

Taxonomy‐free molecular diatom index for high‐throughput eDNA biomonitoring

Current biodiversity assessment and biomonitoring are largely based on the morphological identification of selected bioindicator taxa. Recently, several attempts have been made to use eDNA metabarcoding as an alternative tool. However, until now, most applied metabarcoding studies have been based on the taxonomic assignment of sequences that provides reference to morphospecies ecology. Usually, only a small portion of metabarcoding data can be used due to a limited reference database and a lack of phylogenetic resolution. Here, we investigate the possibility to overcome these limitations using a taxonomy‐free approach that allows the computing of a molecular index directly from eDNA data without any reference to morphotaxonomy. As a case study, we use the benthic diatoms index, commonly used for monitoring the biological quality of rivers and streams. We analysed 87 epilithic samples from Swiss rivers, the ecological status of which was established based on the microscopic identification of diatom species. We compared the diatom index derived from eDNA data obtained with or without taxonomic assignment. Our taxonomy‐free approach yields promising results by providing a correct assessment for 77% of examined sites. The main advantage of this method is that almost 95% of OTUs could be used for index calculation, compared to 35% in the case of the taxonomic assignment approach. Its main limitations are under‐sampling and the need to calibrate the index based on the microscopic assessment of diatoms communities. However, once calibrated, the taxonomy‐free molecular index can be easily standardized and applied in routine biomonitoring, as a complementary tool allowing fast and cost‐effective assessment of the biological quality of watercourses.