Total organic carbon measurements reveal major gaps in petrochemical emissions reporting.

Anthropogenic organic carbon emissions reporting has been largely limited to subsets of chemically speciated volatile organic compounds. However, new aircraft-based measurements revealed total gas-phase organic carbon emissions that exceed oil sands industry-reported values by 1900% to over 6300%, the bulk of which was due to unaccounted-for intermediate-volatility and semivolatile organic compounds. Measured facility-wide emissions represented approximately 1% of extracted petroleum, resulting in total organic carbon emissions equivalent to that from all other sources across Canada combined. These real-world observations demonstrate total organic carbon measurements as a means of detecting unknown or underreported carbon emissions regardless of chemical features. Because reporting gaps may include hazardous, reactive, or secondary air pollutants, fully constraining the impact of anthropogenic emissions necessitates routine, comprehensive total organic carbon monitoring as an inherent check on mass closure.

Chlamydia trachomatis glyceraldehyde 3-phosphate dehydrogenase: Enzyme kinetics, high-resolution crystal structure, and plasminogen binding.

Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is an evolutionarily conserved essential enzyme in the glycolytic pathway. GAPDH is also involved in a wide spectrum of non-catalytic cellular 'moonlighting' functions. Bacterial surface-associated GAPDHs engage in many host interactions that aid in colonization, pathogenesis, and virulence. We have structurally and functionally characterized the recombinant GAPDH of the obligate intracellular bacteria Chlamydia trachomatis, the leading cause of sexually transmitted bacterial and ocular infections. Contrary to earlier speculations, recent data confirm the presence of glucose-catabolizing enzymes including GAPDH in both stages of the biphasic life cycle of the bacterium. The high-resolution crystal structure described here provides a close-up view of the enzyme's active site and surface topology and reveals two chemically modified cysteine residues. Moreover, we show for the first time that purified C. trachomatis GAPDH binds to human plasminogen and plasmin. Based on the versatility of GAPDH's functions, data presented here emphasize the need for investigating the Chlamydiae GAPDH's involvement in biological functions beyond energy metabolism.

A simple and reliable method for determination of optimum pH in coupled enzyme assays.

Determination of the optimum pH in a coupled enzyme assay poses significant challenges because altering the pH of the reaction mixture can affect the performance of both enzymes. Here, we demonstrate a simple and reliable method to determine the pH optimum for pyruvate kinase using the pyruvate kinase/lactate dehydrogenase coupled enzyme assay. This simple and reliable method can be broadly adapted to determine the pH optimum for various enzymes that are assayed using a coupled enzyme assay.

An overview of structure, function, and regulation of pyruvate kinases.

In the last step of glycolysis Pyruvate kinase catalyzes the irreversible conversion of ADP and phosphoenolpyruvate to ATP and pyruvic acid, both crucial for cellular metabolism. Thus pyruvate kinase plays a key role in controlling the metabolic flux and ATP production. The hallmark of the activity of different pyruvate kinases is their tight modulation by a variety of mechanisms including the use of a large number of physiological allosteric effectors in addition to their homotropic regulation by phosphoenolpyruvate. Binding of effectors signals precise and orchestrated movements in selected areas of the protein structure that alter the catalytic action of these evolutionarily conserved enzymes with remarkably conserved architecture and sequences. While the diverse nature of the allosteric effectors has been discussed in the literature, the structural basis of their regulatory effects is still not well understood because of the lack of data representing conformations in various activation states. Results of recent studies on pyruvate kinases of different families suggest that members of evolutionarily related families follow somewhat conserved allosteric strategies but evolutionarily distant members adopt different strategies. Here we review the structure and allosteric properties of pyruvate kinases of different families for which structural data are available.

Active Learning in Flipped Life Science Courses Promotes Development of Critical Thinking Skills.

Although development of critical thinking skills has emerged as an important issue in undergraduate education, implementation of pedagogies targeting these skills across different science, technology, engineering, and mathematics disciplines has proved challenging. Our goal was to assess the impact of targeted interventions in 1) an introductory cell and molecular biology course, 2) an intermediate-level evolutionary ecology course, and 3) an upper-level biochemistry course. Each instructor used Web-based videos to flip some aspect of the course in order to implement active-learning exercises during class meetings. Activities included process-oriented guided-inquiry learning, model building, case studies, clicker-based think-pair-share strategies, and targeted critical thinking exercises. The proportion of time spent in active-learning activities relative to lecture varied among the courses, with increased active learning in intermediate/upper-level courses. Critical thinking was assessed via a pre/posttest design using the Critical Thinking Assessment Test. Students also assessed their own learning through a self-reported survey. Students in flipped courses exhibited gains in critical thinking, with the largest objective gains in intermediate and upper-level courses. Results from this study suggest that implementing active-learning strategies in the flipped classroom may benefit critical thinking and provide initial evidence suggesting that underrepresented and first-year students may experience a greater benefit.

Telomeric G-quadruplex-forming DNA fragments induce TLR9-mediated and LL-37-regulated invasion in breast cancer cells in vitro.

Toll-like receptor 9 (TLR9) is a cellular DNA-receptor widely expressed in cancers. We previously showed that synthetic and self-derived DNA fragments induce TLR9-mediated breast cancer cell invasion in vitro. We investigated here the invasive effects of two nuclease-resistant DNA fragments, a 9-mer hairpin, and a G-quadruplex DNA based on the human telomere sequence, both having native phosphodiester backbone. Cellular uptake of DNAs was investigated with immunofluorescence, invasion was studied with Matrigel-assays, and mRNA and protein expression were studied with qPCR and Western blotting and protease activity with zymograms. TLR9 expression was suppressed through siRNA. Although both DNAs induced TLR9-mediated changes in pro-invasive mRNA expression, only the telomeric G-quadruplex DNA significantly increased cellular invasion. This was inhibited with GM6001 and aprotinin, suggesting MMP- and serine protease mediation. Furthermore, complexing with LL-37, a cathelicidin-peptide present in breast cancers, increased 9-mer hairpin and G-quadruplex DNA uptake into the cancer cells. However, DNA/LL-37 complexes decreased invasion, as compared with DNA-treatment alone. Invasion studies were conducted also with DNA fragments isolated from neoadjuvant chemotherapy-treated breast tumors. Also such DNA induced breast cancer cell invasion in vitro. As with the synthetic DNAs, this invasive effect was reduced by complexing the neoadjuvant tumor-derived DNAs with LL-37. We conclude that 9-mer hairpin and G-quadruplex DNA fragments are nuclease-resistant DNA structures that can act as invasion-inducing TLR9 ligands. Their cellular uptake and the invasive effects are regulated via LL-37. Although such structures may be present in chemotherapy-treated tumors, the clinical significance of this finding requires further studying.

Addition of bases to the 5'-end of human telomeric DNA: influences on thermal stability and energetics of unfolding.

Telomeric DNA has been intensely investigated for its role in chromosome protection, aging, cell death, and disease. In humans the telomeric tandem repeat (TTAGGG)n is found at the ends of chromosomes and provides a novel target for the development of new drugs in the treatment of age related diseases such as cancer. These telomeric sequences show slight sequence variations from species to species; however, each contains repeats of 3 to 4 guanines allowing the G-rich strands to fold into compact and stable nuclease resistant conformations referred to as G-quadruplexes. The focus of this manuscript is to examine the effects of 5'-nucleotides flanking the human telomeric core sequence 5'-AGGG(TTAGGG) 3-3' (h-Tel22). Our studies reveal that the addition of the 5'-flanking nucleotides (5'-T, and 5'-TT) results in significant changes to the thermodynamic stability of the G-quadruplex structure. Our data indicate that the observed changes in stability are associated with changes in the number of bound waters resulting from the addition of 5'-flanking nucleotides to the h-Tel22 sequence as well as possible intermolecular interactions of the 5' overhang with the core structure.

Response to comment on "Radiative absorption enhancements due to the mixing state of atmospheric black carbon".

Jacobson argues that our statement that "many climate models may overestimate warming by BC" has not been demonstrated. Jacobson challenges our results on the basis that we have misinterpreted some model results, omitted optical focusing under high relative humidity conditions and by involatile components, and because our measurements consist of only two locations over short atmospheric time periods. We address each of these arguments, acknowledging important issues and clarifying some misconceptions, and stand by our observations. We acknowledge that Jacobson identified one detail in our experimental technique that places an additional constraint on the interpretation of our observations and reduces somewhat the potential consequences of the stated implications.

Radiative absorption enhancements due to the mixing state of atmospheric black carbon.

Atmospheric black carbon (BC) warms Earth's climate, and its reduction has been targeted for near-term climate change mitigation. Models that include forcing by BC assume internal mixing with non-BC aerosol components that enhance BC absorption, often by a factor of ~2; such model estimates have yet to be clearly validated through atmospheric observations. Here, direct in situ measurements of BC absorption enhancements (E(abs)) and mixing state are reported for two California regions. The observed E(abs) is small-6% on average at 532 nm-and increases weakly with photochemical aging. The E(abs) is less than predicted from observationally constrained theoretical calculations, suggesting that many climate models may overestimate warming by BC. These ambient observations stand in contrast to laboratory measurements that show substantial E(abs) for BC are possible.