Double-digest RAD-sequencing: do pre- and post-sequencing protocol parameters impact biological results?

Next-generation sequencing technologies have opened a new era of research in population genetics. Following these new sequencing opportunities, the use of restriction enzyme-based genotyping techniques, such as restriction site-associated DNA sequencing (RAD-seq) or double-digest RAD-sequencing (ddRAD-seq), has dramatically increased in the last decade. From DNA sampling to SNP calling, the laboratory and bioinformatic parameters of enzyme-based techniques have been investigated in the literature. However, the impact of those parameters on downstream analyses and biological results remains less documented. In this study, we investigated the effects of sevral pre- and post-sequencing settings on ddRAD-seq results for two biological systems: a complex of butterfly species (Coenonympha sp.) and several populations of common beech (Fagus sylvatica). Our results suggest that pre-sequencing parameters (i.e., DNA quantity, number of PCR cycles during library preparation) have a significant impact on the number of recovered reads and SNPs, on the number of unique alleles and on individual heterozygosity. In the same way, we found that post-sequencing settings (i.e., clustering and minimum coverage thresholds) influenced loci reconstruction (e.g., number of loci, mean coverage) and SNP calling (e.g., number of SNPs; heterozygosity) but had only a marginal impact on downstream analyses (e.g., measure of genetic differentiation, estimation of individual admixture, and demographic inferences). In addition, replication analyses confirmed the reproducibility of the ddRAD-seq procedure. Overall, this study assesses the degree of sensitivity of ddRAD-seq data to pre- and post-sequencing protocols, and illustrates its robustness when studying population genetics.

Applying different emotion regulation strategies while providing negative feedback: Introduction of a new laboratory protocol

One aim of creating a new laboratory protocol was to investigate stress responses while being confronted with a work-related task, that is, having to provide negative feedback. It was central to the development of the scenario to make potential testosterone and cortisol responses measurable. The first part of the protocol comprises the introduction to the cover story, that is, being a member of the assessors' team as part of a larger assessment center program aiming to estimate the proficiency of students prior to their entry into professional life. Watching a video of one of the assessment center's candidates and having to assess his performance in a self-presentation task was introduced to personally involve participants in the feedback conversation they had to conduct with the same candidate later on. A second aim was to introduce an experimental manipulation in the form of instructions and brief tutorials regarding different emotion regulation strategies to apply. Participants were randomly assigned to one out of four conditions: expressive suppression (keeping a neutral expression); cognitive reappraisal (staying task-oriented and emotionally distanced); affect utilization (moving towards and using emotions); or control condition. Distinguishing these ways to regulate one's emotions enabled us to reveal differential hormonal stress responses: Applying either cognitive reappraisal or affect utilization strategies alleviated temporary testosterone declines compared with the other two conditions. This method article contains details regarding the procedure as well as the following documents in their original wording: • Introduction to the cover story (being a member of the assessors' team, observation of the attendant's self-presentation, assessment dimensions) • Slides and audio instructions regarding experimental conditions (how to regulate emotions) • Documents handed out to assist participants in conducting the feedback conversation.

A biomedical Engineering Laboratory module for exploring involuntary muscle reflexes using Electromyography

Background

Undergraduate biomedical engineering (BME) students interested in pursuing a career in research and development of medical or physiological monitoring devices require a strong foundation in biosignal analysis as well as physiological theory. Applied learning approaches are reported to be effective for reinforcing physiological coursework; therefore, we propose a new laboratory protocol for BME undergraduate physiology courses that integrates both neural engineering and physiological concepts to explore involuntary skeletal muscle reflexes. The protocol consists of two sections: the first focuses on recruiting soleus motor units through transcutaneous electrical nerve stimulation (TENS), while the second focuses on exploring the natural stretch reflex with and without the Jendrassik maneuver. In this case study, third-year biomedical engineering students collected electromyographic (EMG) activity of skeletal muscle contractions in response to peripheral nerve stimulation using a BioRadio Wireless Physiology Monitor system and analyzed the corresponding signal parameters (latency and amplitude) using the MATLAB platform.

Results/protocol validation

Electrical tibial nerve stimulation successfully recruited M-waves in all 8 student participants and F-waves in three student participants. The students used this data to learn about orthodromic and antidromic motor fiber activation as well as estimate the neural response latency and amplitude. With the stretch reflex, students were able to collect distinct signals corresponding to the tendon strike and motor response. From this, they were able to estimate the sensorimotor conduction velocity. Additionally, a significant increase in the stretch reflex EMG amplitude response was observed when using the Jendrassik maneuver during the knee-jerk response. A student exit survey on the laboratory experience reported that the class found the module engaging and helpful for reinforcing physiological course concepts.

Conclusion

This newly developed protocol not only allows BME students to explore physiological responses using natural and electrically-induced involuntary reflexes, but demonstrates that budget-friendly commercially available devices are capable of eliciting and measuring involuntary reflexes in an engaging manner. Despite some limitations caused by the equipment and students’ lack of signal processing experience, this new laboratory protocol provides a robust framework for integrating engineering and physiology in an applied approach for BME students to learn about involuntary reflexes, neurophysiology, and neural engineering.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13036-020-00248-z.

Organotypic 3D Skin Models: Human Epidermal Equivalent Cultures from Primary Keratinocytes and Immortalized Keratinocyte Cell Lines

The three-dimensional culturing of human keratinocytes at the air-liquid interface yields a fully stratified epidermis including a functional stratum corneum and thus enables the study on epidermal structure and function in the context of biomedical, toxicological and pharmaceutical sciences. Here we provide a step-by-step detailed protocol for the isolation of human primary keratinocytes and the development of human epidermal equivalents generated from primary keratinocytes or immortalized keratinocytes (N/TERT-1; N/TERT-2G), including widely accepted procedures for the analysis of barrier function, tissue morphology, cell proliferation, and gene expression.

In Vitro Culture of Embryos from LOPU-Derived Goat Oocytes

A high oocyte quality is the prerequisite for in vitro embryo production. Goat cumulus-oocyte complexes (COC) are mainly collected from slaughterhouse ovaries or by laparoscopic ovum pickup (LOPU) from live animals. Several features can influence the availability of good quality oocytes recovered by the LOPU technique. Interestingly, slaughterhouse and LOPU oocytes have different in vitro maturation kinetics and requirements, and thus, the IVP system must be adapted regarding the oocyte origin. Overall, the use of undefined media in the different steps makes interpretation of results more difficult, hampers their reproducibility, and introduces a sanitary risk. Thus, there is an effort worldwide to use simpler conditions for goat IVP. Although the success of IVP rates is relatively high, in vitro embryos differ from in vivo-derived ones in many aspects, resulting in lower viability. Therefore, strategies to improve in vitro embryo quality are crucial, such as the use of oviductal epithelium cells for coculture. Here we describe the main steps and culture media which can be utilized to produce embryos in vitro from LOPU or slaughterhouse oocytes in goats.

Improving Laboratory Assessment in Disorders of Sex Development through a Multidisciplinary Network

The aim of the European Reference Network for Rare Endocrine Disorders (Endo-ERN) is to ensure equal access to high-quality care for all those affected by a rare endocrine condition across Europe, such as a disorder/difference of sex development (DSD), both for children and adults. Although differences in resources, health care systems, and health insurances between the European countries are challenging and require political action, a European laboratory network within Endo-ERN could improve the diagnostic process in individuals with DSD, building on the work done by previous European collaborations such as the COST action DSDnet. In close collaboration, clinicians and laboratory specialists must make every effort to standardize diagnostic protocols, achieve necessary harmonization of various laboratory tests, e.g., the hCG stimulation test, and implement an external quality control system. This should ideally result in comparable quality across the network centers allowing the sharing of reference values. This would not only improve patient care but also greatly facilitate research.