Search

Many efforts to improve science teaching in higher education focus on a few faculty members at an institution at a time, with limited published evidence on attempts to engage faculty across entire departments. We created a long-term, department-wide collaborative professional development program, Biology Faculty Explorations in Scientific Teaching (Biology FEST). Across 3 years of Biology FEST, 89% of the department’s faculty completed a weeklong scientific teaching institute, and 83% of eligible instructors participated in additional semester-long follow-up programs. A semester after institute completion, the majority of Biology FEST alumni reported adding active learning to their courses. These instructor self-reports were corroborated by audio analysis of classroom noise and surveys of students in biology courses on the frequency of active-learning techniques used in classes taught by Biology FEST alumni and nonalumni. Three years after Biology FEST launched, faculty participants overwhelmingly reported that their teaching was positively affected. Unexpectedly, most respondents also believed that they had improved relationships with departmental colleagues and felt a greater sense of belonging to the department. Overall, our results indicate that biology department–wide collaborative efforts to develop scientific teaching skills can indeed attract large numbers of faculty, spark widespread change in teaching practices, and improve departmental relations.

Active-learning pedagogies have been repeatedly demonstrated to produce superior learning gains with large effect sizes compared with lecture-based pedagogies. Shifting large numbers of college science, technology, engineering, and mathematics (STEM) faculty to include any active learning in their teaching may retain and more effectively educate far more students than having a few faculty completely transform their teaching, but the extent to which STEM faculty are changing their teaching methods is unclear. Here, we describe the development and application of the machine-learning-derived algorithm Decibel Analysis for Research in Teaching (DART), which can analyze thousands of hours of STEM course audio recordings quickly, with minimal costs, and without need for human observers. DART analyzes the volume and variance of classroom recordings to predict the quantity of time spent on single voice (e.g., lecture), multiple voice (e.g., pair discussion), and no voice (e.g., clicker question thinking) activities. Applying DART to 1,486 recordings of class sessions from 67 courses, a total of 1,720 h of audio, revealed varied patterns of lecture (single voice) and nonlecture activity (multiple and no voice) use. We also found that there was significantly more use of multiple and no voice strategies in courses for STEM majors compared with courses for non-STEM majors, indicating that DART can be used to compare teaching strategies in different types of courses. Therefore, DART has the potential to systematically inventory the presence of active learning with ∼90% accuracy across thousands of courses in diverse settings with minimal effort.

Instructor Talk—noncontent language used by instructors in classrooms—is a recently defined and promising variable for better understanding classroom dynamics. Having previously characterized the Instructor Talk framework within the context of a single course, we present here our results surrounding the applicability of the Instructor Talk framework to noncontent language used by instructors in novel course contexts. We analyzed Instructor Talk in eight additional biology courses in their entirety and in 61 biology courses using an emergent sampling strategy. We observed widespread use of Instructor Talk with variation in the amount and category type used. The vast majority of Instructor Talk could be characterized using the originally published Instructor Talk framework, suggesting the robustness of this framework. Additionally, a new form of Instructor Talk—Negatively Phrased Instructor Talk, language that may discourage students or distract from the learning process—was detected in these novel course contexts. Finally, the emergent sampling strategy described here may allow investigation of Instructor Talk in even larger numbers of courses across institutions and disciplines. Given its widespread use, potential influence on students in learning environments, and ability to be sampled, Instructor Talk may be a key variable to consider in future research on teaching and learning in higher education.

The ability of HIV to match levels of viral mRNA to the activation state of the host cell may play a role in its ability to persist as well as to replicate. This linkage depends on the function of the viral transcriptional regulatory protein, Tat, which increases the efficiency of RNA elongation (transcriptional processivity) in response to cellular activation. To quantify levels of Tat functionin vivo,a quantitative competitive RT-PCR assay was developed that reflects levels of TAR leader fragments (nonprocessive transcripts) and viral mRNA (processive transcripts), indicating low or high levels of Tat function, respectively. The abundance of these RNA species was measured in peripheral blood mononuclear cells (PBMC) of 22 HIV-1-positive individuals (CD4+T cell counts 63–934/mm3) and in established cell line models of HIV constitutive replication (H9IIIB) and reversible latency (U1 and ACH-2). In PBMC, the level of total viral transcripts ranged over four orders of magnitude; however, nonprocessive transcription predominated: 70% of PBMC samples had a ratio of processive to total transcripts of

Summary Myxococcus xanthus is a Gram-negative bacterium which has a complex life cycle that includes development (fruiting body formation). The gene for myxo-bacterial haemagglutinin, mbhA, is developmentally regulated and highly expressed. In this report we show that the mbhA mRNA is exceptionally stable for a prokaryotic organism, exhibiting a chemical half life (t1/2) of 150 min at 18 h of development. The mbhA mRNA was not stable in negetatively growing cells nor was it stable when expressed in Escherichia coli. We have used site–directed mutagenesis of the mbhA gene to analyse some of the determinants which mediate the stability of the mbhA transcript. Sequences within the 3′-untranslated region (3′-UTR) were found to be crucial for mRNA stability. This region of mRNA can potentially form an extremely stable stem-loop structure immediately adjacent to the translational stop codon. A deletion within this region caused a 10-fold increase in the decay rate of the transcript. Furthermore, conditions which were associated with reduced mbhA translation or mutations that caused premature termination of translation drastically reduced mRNA stability even in the presence of the wild type 3′-UTR. These results suggest that a significant aspect of mbhA mRNA stability involves a synergistic interaction of the translational machinery with sequence elements within the 3′-UTR.

The persistence of human immunodeficiency virus (HIV) in optimally treated infected individuals poses a major therapeutic problem. In latently infected cells, one of the observed phenotypes is absent elongation of viral transcription. Thus, the positive elongation factor b (P-TEFb), which is usually recruited by NF-κB or Tat, is not present on the HIV long terminal repeat (LTR). Although most attempts to activate these proviruses centered on NF-κB, we investigated effects of Tat. To this end, we generated transgenic mice, which secreted a chimera between Tat and the green fluorescent protein from β cells of the pancreas. This extracellular Tat distributed widely, entered nuclei of resting cells, and specifically transactivated the HIV LTR. No deleterious side effects of Tat were found. Next, we determined that Tat can activate latent proviruses in optimally treated infected individuals. In their cells, T-cell activation or exogenous Tat could induce viral replication equivalently. Thus, P-TEFb could activate the majority of the latent HIV, in this case by Tat.

Transcription of bacteriophage SP01 middle promoters is specifically initiated by a complex of the Bacillus subtilis host's RNA polymerase core (E) with the SP01 gene 28 transcription-regulating protein, gp28. Normal SP01 DNA contains hydroxymethyluracil (hmUra) in place of thymine and E.gp28 preferentially transcribes hmUra-containing DNA. Hybrid DNA molecules containing an SP01 middle promoter, PM25.1, have been constructed in which one DNA strand contains T and the other hmUra. The major feature of these reciprocal hybrid promoters is that one has, predominantly, T substituted for hmUra in the central −35 recognition sequence in the transcribed strand, while the other has, predominantly, T substituted for hmUra in the −10 recognition sequence in the non-transcribed strand. Binding by the E.gp28 RNA polymerase and transcription of these hybrid promoters and of the normal, all-hmUra, promoter have been compared. Both hybrid promoters are weaker than the normal PM25.1 promoter, but the hybrid promoter with T substituted in the −10 sequence is the weakest of the set. The DNase I footprint of the normal PM25.1 promoter shows temperature-dependent protection of a relatively long stretch of DNA downstream from the transcriptional start site, correlating with a thermal transition of transcriptional activity of promoter complexes. The stronger of the hybrid promoters also undergoes this transition, but the weaker does not. We discuss these findings in terms of protein-DNA interactions determining specificity for a modified nucleotide at this promoter.

The bacteriophage SPO1 gene 28-encoded protein, gp28, directs specific recognition of viral middle promoters in hydroxymethyluracil-containing DNA by the Bacillus subtilis host's RNA polymerase core. Using appropriately sensitive methods of detection, we have shown that discrimination against thymine-containing DNA is not absolute and that the gp28-containing RNA polymerase precisely initiates transcription at two thymine-containing SPO1 middle promoters.

SPO1 gene 28, which codes for the positive regulator of middle transcription, gp28, has been mapped by in vitro DNA-directed protein synthesis to a segment located between 89.5 and 91.5 kbp from the left end of the genome. Gene 27 is also located in this interval. One early promoter has been mapped to this region of the genome (P E 13 at 90.1 kbp) and early transcription of gene 28 could initiate there. Two other early promoters, P E 14 and P E 15, are located at 99.2 and 112.5 kbp from the left end. These three early promoters are significantly weaker in vitro than those early promoters which are located in the terminal repeat. The functions associated with P E 14 and P E 15 are unknown, but evidence is presented that P E 15 is utilized in vivo . Thirteen middle promoters have also been mapped within the region of the genome extending from 85 to 113.5 kbp. The middle promoters are interspersed with the three early promoters and in some cases, yield overlapping early and middle transcription. Such overlapping early and middle transcription units apparently generate at least some em class SPO1 RNA in vivo .

The genome of the Bacillus subtilis phage SP01 contains a 12.6-kilobase-pair terminal redundancy. The transcription units in this region, which are utilized in vitro by B. subtilis RNA polymerase holoenzme, have been mapped. In vitro transcripts were separated and characterized by gel electrophoresis. Since there is such a large number of promoters in this region, it was necessary to employ conditions of transcription under which only subsets of all the transcripts would be made. Selective synthesis was achieved by transcription of restriction fragments containing a small number of promoters and by dinucleotide priming. Transcription units were mapped by observing the shortening of transcripts that resulted from restriction enzyme cleavage of the template. The mapping indicates the presence of two blocks of overlapping transcription units, oriented so as to yield convergent transcription toward a bidirectional termination region. The frequency of readthrough at the bidirectional terminator is low. Several partial termination sites of differing efficiencies have also been identified, including two that are active only at low ribonucleoside triphosphate concentrations. We also describe an effect of NaCl concentration on the migration of RNA in gels, which is specific for only two of the SP01 early transcripts. This effect may indicate unusual secondary structures for these two RNA molecules.

Summary The bulk transfer-RNA of Bacillus subtilis contains approximately one thymine residue per molecule. The methyl group of the thymine does not become labeled when the organism is grown in the presence of [methyl-14C]methionine, although other methylated bases of the B. subtilis tRNA do become labeled.

Myxococcus xanthus, a Gram-negative bacterium, has a complex life cycle that includes fruiting-body formation, a primitive form of multicellular development. Myxobacterial hemagglutinin (MBHA) is a lectin that is induced during the aggregation phase of fruiting-body formation. We have cloned the gene for MBHA and determined its sequence by the dideoxy chain-termination technique. The sequence data show the probable sites for translational initiation and termination and suggest that MBHA does not contain a cleaved leader signal peptide. The DNA sequence shows four strong internal homologies. The deduced amino acid sequence shows that the protein (Mr 27,920) consists of four highly conserved domains each consisting of 67 amino acids. Thus MBHA is physically multivalent in structure, a requirement for all hemagglutinins.

Bacteriophage SP01 early transcripts come predominantly from the terminally repeated 12-kilobase-pair segments of its genome. Much less early RNA comes from a relatively large region of the genome which surrounds the early regulatory gene 28. (The gene 28 protein positively regulates viral middle gene expression.) The major sites at which Bacillus subtilis RNA polymerase holoenzyme binds to SP01 DNA and initiates RNA synthesis have been mapped and the direction of transcription from each of these promoter sites has been determined. There are 12 such sites spanning 11.1 kilobase pairs at each end of the SP01 genome and each set of 12 sites defines a complex set of convergent transcription units.