The genome of the green anole lizard and a comparative analysis with birds and mammals.

The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments. Among amniotes, genome sequences are available for mammals and birds, but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes. Also, A. carolinensis mobile elements are very young and diverse-more so than in any other sequenced amniote genome. The GC content of this lizard genome is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds. We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.

Maximizing Academic Integrity While Minimizing Stress in the Virtual Classroom.

The article documents students' experiences with the shift online at the onset of the COVID-19 pandemic and provides informed recommendations to STEM instructors regarding academic integrity and student stress. Over 500 students were surveyed on these topics, including an open-ended question. Students experienced more stress and perceived a greater workload in online courses and therefore preferred in-person courses overall. Personal awareness of cheating during online exams is positively correlated with the proportion of cheating a student perceives. Fear of getting caught is the best cheating deterrent while getting a better grade makes cheating most enticing. Randomization of questions and answer choices is perceived as a highly effective tool to reduce cheating and is reported as the least stress-inducing method. Inability to backtrack and time limits cause students the most stress. Students report that multiple choice questions are the least effective question type to discourage cheating and oral exam questions cause the most stress. Use of camera and lockdown browser or being video- and audio- recorded caused the majority of student stress. Yet, nearly 60% agree that the combination of camera and lockdown browser is an effective deterrent. Recommendations: (i) Be transparent regarding academic dishonesty detection methods and penalties. (ii) Use online invigilating tools. (iii) Synchronize exams and (iv) randomize exam questions. (v) Allow backtracking. (vi) Avoid converting in-person exams to online exams; instead, explore new ways of designing exams for the online environment.

Reconnecting Students and Faculty to Maximize Academic Integrity and Minimize Student Stress in the Virtual Classroom.

The article documents faculty experiences with the shift online due to the pandemic and provides recommendations to science, technology, engineering, and mathematics (STEM) instructors. Over 100 faculty members were surveyed on these topics and contrasted with previously reported student experiences. The online shift changed how faculty administered exams, ran courses, and acted to ensure academic integrity. For example, when exams went online, 73% of faculty reported spending more time preventing cheating. Concerning academic integrity and stress, faculty and students agreed with the exception of a few notable disconnects. Students reported greater workloads in online classes, while faculty maintained that the shift online did not change student workloads. Students perceived more online cheating than faculty. Overall, there seems to be a significant disconnect regarding faculty not realizing how much their actions may encourage or discourage cheating. Few faculty (<15%) indicated that being a tough grader or having test times too short is a motivating factor, but over 55% of students reported that these motivate students to cheat. Conversely, over 60% of students reported respect for their professors discourages them from cheating, while only 37% of faculty indicated the same. Over 70% of faculty and students indicated that fear of getting caught is a deterrent to cheating. Recommendations to reconnect include (i) faculty should use the finding that the number one deterrent of cheating is fear of getting caught; and (ii) faculty should maintain students' respect by being clear or overestimating workload requirements, carefully adjusting time for online exams, and setting clear expectations with uncomplicated exam questions consistent with the material taught.

Triage and Recovery of STEM Laboratory Skills.

The global COVID-19 pandemic left universities with few options but to turn to remote learning. With much effort, STEM courses made this change in modality; however, many laboratory skills, such as measurement and handling equipment, are more difficult to teach in an online learning environment. A cohort of instructors who are part of the NSF RCN-UBE funded Sustainable, Transformative Engagement across a Multi-Institution/Multidisciplinary STEM (STEM)2 Network (a working group of faculty from two community colleges and three 4-year universities) analyzed introductory biology and chemistry courses to identify essential laboratory skills that students will need in advanced courses. Seven essential laboratory proficiencies were derived from reviewing disciplinary guiding documents such as AAAS Vision and Change in Undergraduate Biology Education, the American Society for Microbiology Recommended Curriculum Guidelines for Undergraduate Microbiology Education, and the American Chemical Society Guidelines for Chemistry: data analysis, scientific writing, proper handling and disposal of laboratory materials, discipline-specific techniques, measurement, lab safety and personal protective equipment, and interpersonal and collaborative skills. Our analysis has determined that some of these skills are difficult to develop in a remote or online setting but could be recovered with appropriate interventions. Skill recovery procedures suggested include a skills "boot camp," department or college coordinated club events, and a triage course. The authors recommend that one of these three recovery mechanisms be offered to bridge this skill gap and better prepare STEM students for upper-level science courses and the real world.

The evolutionary dynamics of autonomous non-LTR retrotransposons in the lizard Anolis carolinensis shows more similarity to fish than mammals.

The genome of the lizard Anolis carolinensis (the green anole) is the first nonavian reptilian genome sequenced. It offers a unique opportunity to comparatively examine the evolution of amniote genomes. We analyzed the abundance and diversity of non-LTR (long terminal repeat) retrotransposons in the anole using the Genome Parsing Suite. We found that the anole genome contains an extraordinary diversity of elements. We identified 46 families of elements representing five clades (L1, L2, CR1, RTE, and R4). Within most families, elements are very similar to each other suggesting that they have been inserted recently. The rarity of old elements suggests a high rate of turnover, the insertion of new elements being offset by the loss of element-containing loci. Consequently, non-LTR retrotransposons accumulate in the anole at a low rate and are found in low copy number. This pattern of diversity shows some striking similarity with the genome of teleostean fish but contrasts greatly with the low diversity and high copy number of mammalian L1 elements, suggesting a fundamental difference in the way mammals and nonmammalian vertebrates interact with their genomic parasites. The scarcity of divergent elements in anoles suggests that insertions have a deleterious effect and are eliminated by natural selection. We propose that the low abundance of non-LTR retrotransposons in the anole is related directly or indirectly to a higher rate of ectopic recombination in the anole relative to mammals.

Evolutionary dynamics of rhomboid proteases in Streptomycetes.

BACKGROUND: Proteolytic enzymes are ubiquitous and active in a myriad of biochemical pathways. One type, the rhomboids are intramembrane serine proteases that release their products extracellularly. These proteases are present in all forms of life and their function is not fully understood, although some evidence suggests they participate in cell signaling. Streptomycetes are prolific soil bacteria with diverse physiological and metabolic properties that respond to signals from other cells and from the environment. In the present study, we investigate the evolutionary dynamics of rhomboids in Streptomycetes, as this can shed light into the possible involvement of rhomboids in the complex lifestyles of these bacteria. RESULTS: Analysis of Streptomyces genomes revealed that they harbor up to five divergent putative rhomboid genes (arbitrarily labeled families A-E), two of which are orthologous to rhomboids previously described in Mycobacteria. Characterization of each of these rhomboid families reveals that each group is distinctive, and has its own evolutionary history. Two of the Streptomyces rhomboid families are highly conserved across all analyzed genomes suggesting they are essential. At least one family has been horizontally transferred, while others have been lost in several genomes. Additionally, the transcription of the four rhomboid genes identified in Streptomyces coelicolor, the model organism of this genus, was verified by reverse transcription. CONCLUSIONS: Using phylogenetic and genomic analysis, this study demonstrates the existence of five distinct families of rhomboid genes in Streptomycetes. Families A and D are present in all nine species analyzed indicating a potentially important role for these genes. The four rhomboids present in S. coelicolor are transcribed suggesting they could participate in cellular metabolism. Future studies are needed to provide insight into the involvement of rhomboids in Streptomyces physiology. We are currently constructing knock out (KO) mutants for each of the rhomboid genes from S. coelicolor and will compare the phenotypes of the KOs to the wild type strain.

Transposable element evolution in Heliconius suggests genome diversity within Lepidoptera.

BACKGROUND: Transposable elements (TEs) have the potential to impact genome structure, function and evolution in profound ways. In order to understand the contribution of transposable elements (TEs) to Heliconius melpomene, we queried the H. melpomene draft sequence to identify repetitive sequences. RESULTS: We determined that TEs comprise ~25% of the genome. The predominant class of TEs (~12% of the genome) was the non-long terminal repeat (non-LTR) retrotransposons, including a novel SINE family. However, this was only slightly higher than content derived from DNA transposons, which are diverse, with several families having mobilized in the recent past. Compared to the only other well-studied lepidopteran genome, Bombyx mori, H. melpomene exhibits a higher DNA transposon content and a distinct repertoire of retrotransposons. We also found that H. melpomene exhibits a high rate of TE turnover with few older elements accumulating in the genome. CONCLUSIONS: Our analysis represents the first complete, de novo characterization of TE content in a butterfly genome and suggests that, while TEs are able to invade and multiply, TEs have an overall deleterious effect and/or that maintaining a small genome is advantageous. Our results also hint that analysis of additional lepidopteran genomes will reveal substantial TE diversity within the group.

The evolution and diversity of DNA transposons in the genome of the Lizard Anolis carolinensis.

DNA transposons have considerably affected the size and structure of eukaryotic genomes and have been an important source of evolutionary novelties. In vertebrates, DNA transposons are discontinuously distributed due to the frequent extinction and recolonization of these genomes by active elements. We performed a detailed analysis of the DNA transposons in the genome of the lizard Anolis carolinensis, the first non-avian reptile to have its genome sequenced. Elements belonging to six of the previously recognized superfamilies of elements (hAT, Tc1/Mariner, Helitron, PIF/Harbinger, Polinton/Maverick, and Chapaev) were identified. However, only four (hAT, Tc1/Mariner, Helitron, and Chapaev) of these superfamilies have successfully amplified in the anole genome, producing 67 distinct families. The majority (57/67) are nonautonomous and demonstrate an extraordinary diversity of structure, resulting from frequent interelement recombination and incorporation of extraneous DNA sequences. The age distribution of transposon families differs among superfamilies and reveals different dynamics of amplification. Chapaev is the only superfamily to be extinct and is represented only by old copies. The hAT, Tc1/Mariner, and Helitron superfamilies show different pattern of amplification, yet they are predominantly represented by young families, whereas divergent families are exceedingly rare. Although it is likely that some elements, in particular long ones, are subjected to purifying selection and do not reach fixation, the majority of families are neutral and accumulate in the anole genome in large numbers. We propose that the scarcity of old copies in the anole genome results from the rapid decay of elements, caused by a high rate of DNA loss.