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Instruction based on active learning is being promoted in higher education by the creation of new collaborative teaching and learning spaces, but capacity does not yet exist for all courses to be held in these new spaces. In this study, we examined how students choose between sections of the same course, with the same materials and techniques used by the same instructor, delivered in a collaborative teaching and learning space compared with a lecture-theater space. We also measured how the factors used in enrollment decision-making, and the subsequent learning experiences in the chosen environment, are associated with student attitudes related to learning chemistry. We collected student survey data from undergraduate students enrolled in Organic Chemistry II using items from the Colorado Learning Attitudes toward Science Survey for Chemistry and questions about the enrollment process. Students also responded to in-class prompts at the end of the semester about several different factors that could have influenced their decision to enroll in their section of the course. We combined these student responses with other data to create structural equation models for how the design of the teaching and learning space is associated with decision-making factors or attitudes about learning chemistry. Our models showed correlations among space enrollment, aspects of student identity, decision-making factors, and attitudes toward learning chemistry. These results suggest that students are self-sorting between the various learning spaces, which demonstrates a need for further research into the drivers of these sorting patterns over time. more...

Institutions of higher education are seeking to support more active learning among faculty, and that support includes the creation of active learning spaces to support more student-centered course activities. However, incremental development of these learning spaces leads to a sorting of students between active and passive learning environments. This study collected repeat-measure data from undergraduate students enrolled in a two-semester course sequence to evaluate factors affecting student enrollment decisions and student attitudes toward learning. We integrated this combination of research tools using a QuantCrit analytic framework, which revealed student attitudes and decision-making processes that were generally stable over the study period for individuals, but very different when examining student enrollment groups over time. Limited access to active learning classrooms forced students to self-sort based on either their social networks or their attitudes toward learning. That, in turn, may create a marginalizing force that pushes out some students—most often women—from undergraduate programs. [ABSTRACT FROM AUTHOR] more...

BackgroundAn understanding of the evolution of global transcription regulators is essential for comprehending the complex networks of cellular metabolism that have developed among related organisms. The fur gene encodes one of those regulators - the ferric uptake regulator Fur - widely distributed among bacteria and known to regulate different genes committed to varied metabolic pathways. On the other hand, members of the Actinobacteria comprise an ecologically diverse group of bacteria able to inhabit various natural environments, and for which relatively little is currently understood concerning transcriptional regulation.ResultsBLAST analyses revealed the presence of more than one fur homologue in most members of the Actinobacteria whose genomes have been fully sequenced. We propose a model to explain the evolutionary history of fur within this well-known bacterial phylum: the postulated scenario includes one duplication event from a primitive regulator, which probably had a broad range of co-factors and DNA-binding sites. This duplication predated the appearance of the last common ancestor of the Actinobacteria, while six other duplications occurred later within specific groups of organisms, particularly in two genera: Frankia and Streptomyces. The resulting paralogues maintained main biochemical properties, but became specialised for regulating specific functions, coordinating different metal ions and binding to unique DNA sequences. The presence of syntenic regions surrounding the different fur orthologues supports the proposed model, as do the evolutionary distances and topology of phylogenetic trees built using both Neighbor-Joining and Maximum-Likelihood methods.ConclusionThe proposed fur evolutionary model, which includes one general duplication and two in-genus duplications followed by divergence and specialization, explains the presence and diversity of fur genes within the Actinobacteria. Although a few rare horizontal gene transfer events have been reported, the model is consistent with the view of gene duplication as a main force of microbial genomes evolution. The parallel study of Fur phylogeny across diverse organisms offers a solid base to guide functional studies and allows the comparison between response mechanisms in relation with the surrounding environment. The survey of regulators among related genomes provides a relevant tool for understanding the evolution of one of the first lines of cellular adaptability, control of DNA transcription. more...

BackgroundAn understanding of the evolution of global transcription regulators is essential for comprehending the complex networks of cellular metabolism that have developed among related organisms. The fur gene encodes one of those regulators - the ferric uptake regulator Fur - widely distributed among bacteria and known to regulate different genes committed to varied metabolic pathways. On the other hand, members of the Actinobacteria comprise an ecologically diverse group of bacteria able to inhabit various natural environments, and for which relatively little is currently understood concerning transcriptional regulation.ResultsBLAST analyses revealed the presence of more than one fur homologue in most members of the Actinobacteria whose genomes have been fully sequenced. We propose a model to explain the evolutionary history of fur within this well-known bacterial phylum: the postulated scenario includes one duplication event from a primitive regulator, which probably had a broad range of co-factors and DNA-binding sites. This duplication predated the appearance of the last common ancestor of the Actinobacteria, while six other duplications occurred later within specific groups of organisms, particularly in two genera: Frankia and Streptomyces. The resulting paralogues maintained main biochemical properties, but became specialised for regulating specific functions, coordinating different metal ions and binding to unique DNA sequences. The presence of syntenic regions surrounding the different fur orthologues supports the proposed model, as do the evolutionary distances and topology of phylogenetic trees built using both Neighbor-Joining and Maximum-Likelihood methods.ConclusionThe proposed fur evolutionary model, which includes one general duplication and two in-genus duplications followed by divergence and specialization, explains the presence and diversity of fur genes within the Actinobacteria. Although a few rare horizontal gene transfer events have been reported, the model is consistent with the view of gene duplication as a main force of microbial genomes evolution. The parallel study of Fur phylogeny across diverse organisms offers a solid base to guide functional studies and allows the comparison between response mechanisms in relation with the surrounding environment. The survey of regulators among related genomes provides a relevant tool for understanding the evolution of one of the first lines of cellular adaptability, control of DNA transcription. more...

NADH cytochrome b5 oxidoreductase (Ncb5or) is a cytosolic ferric reductase implicated in diabetes and neurological conditions. Ncb5or comprises cytochrome b5 (b5) and cytochrome b5 reductase (b5R) domains separated by a CHORD‐Sgt1 (CS) linker domain. Ncb5or redox activity depends on proper inter‐domain interactions to mediate electron transfer from NADH or NADPH via FAD to heme. While full‐length human Ncb5or has proven resistant to crystallization, we have succeeded in obtaining high‐resolution atomic structures of the b5 domain and a construct containing the CS and b5R domains (CS/b5R). Ncb5or also contains an N‐terminal intrinsically disordered region of 50 residues that has no homologs in other protein families in animals but features a distinctive, conserved L34MDWIRL40 motif also present in reduced lateral root formation (RLF) protein in rice and increased recombination center 21 in baker's yeast, all attaching to a b5 domain. After unsuccessful attempts at crystallizing a human Ncb5or construct comprising the N‐terminal region naturally fused to the b5 domain, we were able to obtain a high‐resolution atomic structure of a recombinant rice RLF construct corresponding to residues 25–129 of human Ncb5or (52% sequence identity; 74% similarity). The structure reveals Trp120 (corresponding to invariant Trp37 in Ncb5or) to be part of an 11‐residue α‐helix (S116QMDWLKLTRT126) packing against two of the four helices in the b5 domain that surround heme (α2 and α5). The Trp120 side chain forms a network of interactions with the side chains of four highly conserved residues corresponding to Tyr85 and Tyr88 (α2), Cys124 (α5), and Leu47 in Ncb5or. Circular dichroism measurements of human Ncb5or fragments further support a key role of Trp37 in nucleating the formation of the N‐terminal helix, whose location in the N/b5 module suggests a role in regulating the function of this multi‐domain redox enzyme. This study revealed for the first time an ancient origin of a helical motif in the N/b5 module as reflected by its existence in a class of cytochrome b5 proteins from three kingdoms among eukaryotes. [ABSTRACT FROM AUTHOR] more...

Filamentous actinobacteria from the genus Frankia and diverse woody trees and shrubs together form N2-fixing actinorhizal root nodule symbioses that are a major source of new soil nitrogen in widely diverse biomes 1. Three major clades of Frankia sp. strains are defined; each clade is associated with a defined subset of plants from among the eight actinorhizal plant families 2,3. The evolution arytrajectories followed by the ancestors of both symbionts leading to current patterns of symbiont compatibility are unknown. Here we show that the competing processes of genome expansion and contraction have operated in different groups of Frankia strains in a manner that can be related to the speciation of the plant hosts and their geographic distribution. We sequenced and compared the genomes from three Frankia sp. strains having different host plant specificities. The sizes of their genomes varied from 5.38 Mbp for a narrow host range strain (HFPCcI3) to 7.50Mbp for a medium host range strain (ACN14a) to 9.08 Mbp for a broad host range strain (EAN1pec.) This size divergence is the largest yet reported for such closely related bacteria. Since the order of divergence of the strains is known, the extent of gene deletion, duplication and acquisition could be estimated and was found to be inconcert with the biogeographic history of the symbioses. Host plant isolation favored genome contraction, whereas host plant diversification favored genome expansion. The results support the idea that major genome reductions as well as expansions can occur in facultatively symbiotic soil bacteria as they respond to new environments in the context of their symbioses. more...

An investigation was carried out to provide insight on possible factors important in the mechanisms of six-coordinate heme proteins that function as sensors of small molecules. The results suggest that differences in stability might be at least as important as differences in porphyrin solvent exposure in governing redox potentials of heme protein variants having identical heme ligation motifs. more...

The identification of a conserved Mc [b.sub.5] apoprotein (core 2) packing motif that plays a key role in stabilizing apoprotein conformation in the vicinity of Trp-22 is reported. Evidence indicates that the conserved Mc [b.sub.5] packing motif noted above contributes to the unusually extensive secondary structure exhibited by bovine Mc apo-[b.sub.5] in the area-denatured state. more...

Results indicate that leucine-71 plays a role in stabilizing the fold of the non-heme rat outer membrane microsomal cytochromes b(sub)5 in association with hydrophobic interactions involving isoleucine-25 and phenylalanine-58. more...

Research has been conducted on the cytochrome b (sub)5 from the rat hepatocyte associated with the liver mitochondria outer membrane. The factors responsible for the higher stability and slower hemin release and reorientation in the rat outer membrane protein have been investigated theoretically and experimentally. more...

A transition dynamical behavior is observed in the three synthetic 13-residue peptides as revealed by a disruption of the peptide backbone hydrogen bonding at the interface between alpha- and nascent pi-helical regions leading to a rearrangement among the charged side chains of the amino acid residues. more...

Research was conducted to examine the molecular diversity of Frankia species in plant root nodules using gene amplification and sequencing techniques. The gene sequence data from three host plants indicate that the distribution frequency varies greatly. more...

Research was conducted to examine the diversity and relationships among Frankia that infect family Rhamnaceae members. Partial and full-length 16S rDNAs from Frankia microsymbionts living in root nodules of Elaeagnaceae and Rhamnaceae families were isolated and sequenced. The close relationship between strains of Frankia that infect most plants belonging to the Elaeagnaceae and Rhamnaceae families indicate that the last common ancestor of both families was nodulated by Frankia strains similar to those occupying the nodules. more...

Peptide-sandwiched mesohemes (PSMs), a class of synthetic hemoprotein models, have been developed to look at the impact of heme-protein interactions on hemoprotein structure and function. Each PSM, numbered 1 to 5, is made up of two identical peptides covalently connected to the propionate groups of iron(III) mesoporphyrin IX through amide linkages with lysine (Lys) N-epsilon amines. In the folded forms of 1,2,4 and 5, both peptides adopt conformations with varying degrees of alpha-helix content. The folded forms of 3 and 5 were found to be less stable than the folded forms of 1, 2 and 4, even when 2,2,2-trifluoroethanol or 1-propanol are added to boost the helicity of the peptides. more...

Amplification of 16S rRNA sequences from plant-symbiotic nitrogen-fixing Frankia strains reveals identical sequences for nodules from Ceanothus griseus and P. tridentata and their resemblance to the endophyte of Dryas drummondii. The sequences for nodules from Coriaria arborea and Coriaria plumosa were identical along with a separate lineage. The Frankia strains in Discaria toumatou provide an exceptional sequence with a lineage close to bacteria infecting Elaeagnaceae. The amplification technique uses a very small amount of tissue and avoids digesting enzymes completely. more...

A water-soluble synthetic hemoprotein (1) is prepared, which has two short covalently attached peptides coordinate to the heme iron via histidine side chains. Circular dichroism (CD) studies indicates that the peptides in hemoproteins have 52% helical content in aqueous solution. Heme in 1 also exhibits CD features such as Soret band at 403 nm and the alpha- and beta-bands between 500 and 600 nm. Solvent studies suggest that the intensity of the CD Soret band is a function of intramolecular heme-peptide interaction. more...

A spin-labeled, fluorescent and photoactivatible amino acid is site-specifically incorporated into various surface and internal regions in the bacteriophage T4 lysozyme by using unnatural amino acid mutagenesis. T4 lysozyme mutants bearing the spin-labeled amino acid and the fluorescent amino acid are purified and spectrally characterized. more...

A study of the key residues Pro-34, Thr-35 and Ile-36 revealed the structural features needed for GTPase-activating protein (GAP) interaction and GTPase activity. The study employed the entire range of unnatural amino acid mutanenesis. GAP activation of Ras was curbed by the elimination of a single methyl group from Ile, proving that high specificity exists in protein-protein interaction. more...

Glutamine synthase (GS) is the central enzyme in nitrogen metabolism and exists in two forms, GSI and GSII, in Frankia alni CpI1. The F. alni CpI1 glnA gene, which codes for GSI, was isolated, characterized and expressed in Escherichia coli. DNA hybridization analysis showed that the glnA gene is adjacent to glnII, which codes for GSII. Several conserved sequences were identified, and it is proposed that the two genes are derived from the same ancestral gene via gene duplication. more...