ITiCSE Working Group 2011: Motivating All Our Students?

Academics expend a large amount of time and effort to sustain and enhance the motivation of undergraduate students. Typically based on a desire to ensure that all students achieve their full potential, approaches are based on an understanding that students who are highly motivated will learn more. Furthermore, institutional rewards accrue from effective use of academics’ time, along with financial benefits associated with high levels of retention and progression. This working group report, based on practice in Europe, Australasia and North America, builds on previous work. It provides an updated and revised literature review, analyses a larger collection of survey data and has sought to triangulate earlier findings with qualitative data from practitioner interviews. The report covers established approaches in teaching, support and extra-curricular activities. It tracks emerging practice such as streamed and differentiated teaching, and research based and authentic learning. It also considers contemporary innovations in student activities. Finally it reports on a repository of tips and techniques which has been established to support faculty wishing to change or review current methods

Towards defining the chloroviruses: a genomic journey through a genus of large DNA viruses

Background: Giant viruses in the genus Chlorovirus (family Phycodnaviridae) infect eukaryotic green microalgae. The prototype member of the genus, Paramecium bursaria chlorella virus 1, was sequenced more than 15 years ago, and to date there are only 6 fully sequenced chloroviruses in public databases. Presented here are the draft genome sequences of 35 additional chloroviruses (287 – 348 Kb/319 – 381 predicted protein encoding genes) collected across the globe; they infect one of three different green algal species. These new data allowed us to analyze the genomic landscape of 41 chloroviruses, which revealed some remarkable features about these viruses. Results: Genome colinearity, nucleotide conservation and phylogenetic affinity were limited to chloroviruses infecting the same host, confirming the validity of the three previously known subgenera. Clues for the existence of a fourth new subgenus indicate that the boundaries of chlorovirus diversity are not completely determined. Comparison of the chlorovirus phylogeny with that of the algal hosts indicates that chloroviruses have changed hosts in their evolutionary history. Reconstruction of the ancestral genome suggests that the last common chlorovirus ancestor had a slightly more diverse protein repertoire than modern chloroviruses. However, more than half of the defined chlorovirus gene families have a potential recent origin (after Chlorovirus divergence), among which a portion shows compositional evidence for horizontal gene transfer. Only a few of the putative acquired proteins had close homologs in databases raising the question of the true donor organism(s). Phylogenomic analysis identified only seven proteins whose genes were potentially exchanged between the algal host and the chloroviruses. Conclusion: The present evaluation of the genomic evolution pattern suggests that chloroviruses differ from that described in the related Poxviridae and Mimiviridae. Our study shows that the fixation of algal host genes has been anecdotal in the evolutionary history of chloroviruses. We finally discuss the incongruence between compositional evidence of horizontal gene transfer and lack of close relative sequences in the databases, which suggests that the recently acquired genes originate from a still largely un-sequenced reservoir of genomes, possibly other unknown viruses that infect the same hosts

\u3ci\u3eParamecium bursaria\u3c/i\u3e Chlorella Virus 1 Proteome Reveals Novel Architectural and Regulatory Features of a Giant Virus

The 331 kilobase pairs chlorovirus PBCV-1 genome was re-sequenced and annotated to correct errors in the original 15 year old sequence; forty codons was considered the minimum protein size of an open reading frame. PBCV-1 encodes 416 predicted protein encoding sequences and 11 tRNAs. A proteome analysis was also conducted on highly purified PBCV-1 virions using two mass-spectrometry based protocols. The mass spectrometry-derived data were compared to PBCV-1 and its host Chlorella variabilis NC64A predicted proteomes. Combined, these analyses revealed 148 unique virus-encoded proteins associated with the virion (about 35% of the coding capacity of the virus) and one host protein. Some of these proteins appear to be structural/architectural, whereas others have enzymatic, chromatin modification and signal transduction functions. Most (106) of these proteins have no known function or homologs in the existing gene databases except as orthologs with other chloroviruses, phycodnaviruses and nuclear-cytoplasmic large DNA viruses. The genes encoding these proteins are dispersed throughout the virus genome and most are transcribed late or early late in the infection cycle, which is consistent with virion morphogenesis

Motivating All our Students?

Academics expend a large amount of time and effort to sustain and enhance the motivation of undergraduate students. Typically based on a desire to ensure that all students achieve their full potential, approaches are based on an understanding that students who are highly motivated will learn more. Furthermore, institutional rewards accrue from effective use of academics' time, along with financial benefits associated with high levels of retention and progression. This working group report, based on practice in Europe, Australasia and North America, builds on previous work. It provides an updated and revised literature review, analyses a larger collection of survey data and has sought to triangulate earlier findings with qualitative data from practitioner interviews. The report covers established approaches in teaching, support and extra-curricular activities. It tracks emerging practice such as streamed and differentiated teaching, and research based and authentic learning. It also considers contemporary innovations in student activities. Finally it reports on a repository of tips and techniques which has been established to support faculty wishing to change or review current methods

Increasing Capacity to Detect Clusters of Rapid HIV Transmission in Varied Populations—United States

Molecular cluster detection analyzes HIV sequences to identify rapid HIV transmission and inform public health responses. We describe changes in the capability to detect molecular clusters and in geographic variation in transmission dynamics. We examined the reporting completeness of HIV-1 polymerase sequences in quarterly National HIV Surveillance System datasets from December 2015 to December 2019. Priority clusters were identified quarterly. To understand populations recently affected by rapid transmission, we described the transmission risk and race/ethnicity of people in clusters first detected in 2018-2019. During December 2015 to December 2019, national sequence completeness increased from 26% to 45%. Of the 1212 people in the 136 clusters first detected in 2018-2019, 69% were men who have sex with men (MSM) and 11% were people who inject drugs (PWID). State-by-state analysis showed substantial variation in transmission risk and racial/ethnic groups in clusters of rapid transmission. HIV sequence reporting has increased nationwide. Molecular cluster analysis identifies rapid transmission in varied populations and identifies emerging patterns of rapid transmission in specific population groups, such as PWID, who, in 2015-2016, comprised only 1% of people in such molecular clusters. These data can guide efforts to focus, tailor, and scale up prevention and care services for these populations