The COVID-19 paradox of online collaborative education: when you cannot physically meet, you need more social interactions

Collaborative learning is a teaching method that brings together students to discuss a topic important for a given course or curriculum and solve a related problem or create a product. By doing this, learners create knowledge together and gain 21^st –century skills such as communication, critical thinking, decision making, leadership and conflict management. Universities had to close their campuses and turn their education fully online in 2020 due to the COVID-19 pandemic, which created a forced step in the evolution of the digitalisation of collaborative teaching. How did TU Delft face this challenge? How did the students experience the online version of collaborative learning? How did distant learning affect their motivation? This article presents four student team projects investigating these questions from the collaborative learning perspective. One of the significant findings of these projects is the lack of socio-emotional interactions during online collaborative work. We present a few guidelines on how to enable these interactions when designing online or blended collaborative education.

Chaperone activity of ERD10 and ERD14, two disordered stress-related plant proteins

ERD10 and ERD14 (for early response to dehydration) proteins are members of the dehydrin family that accumulate in response to abiotic environmental stresses, such as high salinity, drought, and low temperature, in Arabidopsis (Arabidopsis thaliana). Whereas these proteins protect cells against the consequences of dehydration, the exact mode(s) of their action remains poorly understood. Here, detailed evidence is provided that ERD10 and ERD14 belong to the family of intrinsically disordered proteins, and it is shown in various assays that they act as chaperones in vitro. ERD10 and ERD14 are able to prevent the heat-induced aggregation and/or inactivation of various substrates, such as lysozyme, alcohol dehydrogenase, firefly luciferase, and citrate synthase. It is also demonstrated that ERD10 and ERD14 bind to acidic phospholipid vesicles without significantly affecting membrane fluidity. Membrane binding is strongly influenced by ionic strength. Our results show that these intrinsically disordered proteins have chaperone activity of rather wide substrate specificity and that they interact with phospholipid vesicles through electrostatic forces. We suggest that these findings provide the rationale for the mechanism of how these proteins avert the adverse effects of dehydration stresses.

A multicassette Gateway vector set for high throughput and comparative analyses in ciona and vertebrate embryos

Background

The past few years have seen a vast increase in the amount of genomic data available for a growing number of taxa, including sets of full length cDNA clones and cis-regulatory sequences. Large scale cross-species comparisons of protein function and cis-regulatory sequences may help to understand the emergence of specific traits during evolution.

Principal Findings

To facilitate such comparisons, we developed a Gateway compatible vector set, which can be used to systematically dissect cis-regulatory sequences, and overexpress wild type or tagged proteins in a variety of chordate systems. It was developed and first characterised in the embryos of the ascidian Ciona intestinalis, in which large scale analyses are easier to perform than in vertebrates, owing to the very efficient embryo electroporation protocol available in this organism. Its use was then extended to fish embryos and cultured mammalian cells.

Conclusion

This versatile vector set opens the way to the mid- to large-scale comparative analyses of protein function and cis-regulatory sequences across chordate evolution. A complete user manual is provided as supplemental material.

Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage

Alignment of orthologous vertebrate loci reveals that a significant proportion of conserved cis-regulatory elements have undergone shuffling during evolution.

Background

All vertebrates share a remarkable degree of similarity in their development as well as in the basic functions of their cells. Despite this, attempts at unearthing genome-wide regulatory elements conserved throughout the vertebrate lineage using BLAST-like approaches have thus far detected noncoding conservation in only a few hundred genes, mostly associated with regulation of transcription and development.

Results

We used a unique combination of tools to obtain regional global-local alignments of orthologous loci. This approach takes into account shuffling of regulatory regions that are likely to occur over evolutionary distances greater than those separating mammalian genomes. This approach revealed one order of magnitude more vertebrate conserved elements than was previously reported in over 2,000 genes, including a high number of genes found in the membrane and extracellular regions. Our analysis revealed that 72% of the elements identified have undergone shuffling. We tested the ability of the elements identified to enhance transcription in zebrafish embryos and compared their activity with a set of control fragments. We found that more than 80% of the elements tested were able to enhance transcription significantly, prevalently in a tissue-restricted manner corresponding to the expression domain of the neighboring gene.

Conclusion

Our work elucidates the importance of shuffling in the detection of cis-regulatory elements. It also elucidates how similarities across the vertebrate lineage, which go well beyond development, can be explained not only within the realm of coding genes but also in that of the sequences that ultimately govern their expression.

A simple method for the simultaneous separation of peripheral blood mononuclear and polymorphonuclear cells in the dog

A simple method for the simultaneous separation and purification of peripheral blood mononuclear cells (PBMC) and polymorphonuclear neutrophil cells (PMNC) was developed for comparative and functional studies in the immune system of the dog. Purity and cell viability were > 95%, yields were similar to those obtained by other techniques but without red blood cell contamination. Differential blood cell count studies of the isolated cells in blood samples of beagle dogs and German shepherd dogs demonstrated that the 1.077/1.119 double density centrifugation is an effective method of acquiring both highly purified blood mononuclear cells and polymorphonuclear cells as separate entities from the same sample. The interface between plasma and 1.077 contained an average 97% blood mononuclear cells vs. 3% polymorphonuclear cells, and the interface between 1.077 and 1.119 an average 96% polymorphonuclear cells vs. 4% blood mononuclear cells. These data indicate that Histopaque 1.077/1.119 double density gradient allows the purification and physical separation of lymphocytes and phagocytes from a blood sample in the dog, enabling the investigator to examine both cell types from the same sample simultaneously.

Familial differences in antibody response of broiler chickens to vaccination with attenuated and inactivated Newcastle disease virus vaccine

Genetic differences in immune response to Newcastle disease virus (NDV) were studied in 4-week-old broilers, vaccinated with attenuated (live) or inactivated NDV. The experiment included 370 chicks from two farms distributed among 22 sire families and 60 dam families. Results in chicks from both farms were similar. Survival after challenge was closely related to titer level. The genetic correlation between day-7 and day-12 titers (attenuated virus) was 1.0. Significant differences were found between sire families in both sorts of vaccinations. Heritabilities based on the sire variance components for attenuated and inactivated virus vaccinations were respectively 0.31 and 0.60. The genetic correlation between them was 0.49. Nevertheless, it is concluded that selection for response to NDV based on inactivated virus may be most effective in improving response to attenuated NDV vaccinations.

Isolation and properties of the replicase of encephalomyocarditis virus

The RNA-dependent RNA polymerase (replicase) of encephalomyocarditis (EMC) virus was found to be closely associated with the smooth membranes of infected BHK-21 cells. An RNA-dependent EMC replicase was extracted from the membranes with 0.15% sodium dodecyl sulfate (SDS) and 1,1,2-trichlorotri-fluoroethane (Genetron 113) and further purified by high-salt dextran-polyethylene glycol phase separation, sievorptive chromatography, and glycerol gradient sedimentation. The enzyme does not manifest strict specificity toward EMC RNA template. It can use also Qbeta RNA, rRNA of BHK cells, or poly(C). SDS-polyacrylamide gel electrophoresis of purified EMC replicase labeled with radioactive methionine revealed that, of all the stable EMC proteins, the enzyme contains predominantly the 56,000-dalton (E) polypeptide.

The assay of gosling hepatitis virus and antibody by spermagglutination and spermagglutination-inhibition. II. Spermagglutination-inhibition

Spermagglutination by gosling hepatitis virus was specifically inhibited by sera from sick and convalescent goslings exposed to experimental and natural infection, by hyperimmune horse serum and by sera from vaccinated geese. When compared with passive protection of goslings, neutralization of egg infectivity and precipitation techniques, the spermagglutination-inhibition technique was found to be a highly sensitive serological procedure for antibody detection and assay.

The assay of gosling hepatitis virus and antibody by spermagglutination and spermagglutination-inhibition. I. Spermagglutination

Agglutination of bovine spermatozoa by gosling hepatitis virus grown in embryonated eggs of 3 different hosts and from several different passage levels was demonstrated. A good agreement was found between the egg-infective and spermagglutinating titres of the virus. The reaction closely resembles that previously described for Newcastle disease virus, influenza virus and Mycoplasma. Gosling hepatitis virus differs however from the other spermagglutinating agents by its inability to agglutinate erythrocytes. Optimal physico-chemical requirements for the reaction were determined. The spermagglutination technique provides a rapid and simple method for assaying the virus. The method is also convenient and inexpensive owing to the availability of spermatozoa in pelleted form which can be stored frozen for long periods.