The solitude of Henry David Thoreau

Typescript.Thesis (M.A.)--University of Illinois, 1915.Includes bibliographical references (leaves 115-122)

Unexpected exosites on the surface of matrix metalloproteinase-12 that fine-tune specificity for elastin and collagen V

Abstract only availableMMP-12 hydrolyzes collagens and elastin in normal physiological processes of development, wound repair, and reconstruction of the extracellular matrix. However, chronically elevated levels of MMP-12 activity can sustain disease states in certain tissues. Excessive MMP-12 activity upon elastic fibrils of lungs and arteries causes inflammation at those sites, resulting in emphysema, while excessive activity upon collagens triggers rupture of atheromatous plaques, which can lead to heart attack or stroke. Thus, research into the binding site interactions between MMP-12 and macromolecular substrates provides surface characterization of the enzyme and expedites the process of designing artificial inhibitor molecules to selectively inactivate MMP-12. The catalytic domain of MMP-12 spans amino acid residue 100 to 263, and this region is particularly important during hydrolysis of substrates. Three secondary binding sites within the catalytic domain were examined: phenylalanine 202 (F202), threonine 205 (T205), and histidine 206 (H206). Site-directed mutagenesis was performed at the aforementioned exosites to obtain single point mutations glutamine 202 (F202Q), lysine 205 (T205K), and histidine 206 (H206D). The MMP-12 mutants were expressed as the 18.2kDa catalytic domain in BL21 derived E. coli Rosetta™ 2 host strains. The mutated MMP-12 enzymes were isolated as insoluble inclusion bodies after lysis of E. coli cells using the French press. The inclusion bodies were solubilized in neutral 6M urea buffer, and preliminary purification with cation-exchange chromatography yielded a nucleic acid-free fraction of denatured enzyme. Refolding of the MMP-12 mutants was done by dialysis with serially diluted urea solution containing Tris-HCl buffer and CaCl2 at pH 7.5 without Zn++. ZnCl2 was added to the final dialysis buffer to complete the refolding process. Final purification of active renatured enzyme was achieved by another cation exchange chromatography run. Then, a Bio-Rad protein assay determined the concentration of the three MMP-12 mutants. Two types of flurometric-based kinetic experiments were performed to study changes in catalytic activity of the three MMP-12 mutants versus wild-type MMP-12: active site titration and substrate activity. Active site titration quantified the concentration of active sites for each MMP-12 mutant. The substrate runs for the substrates FS-6, fluorescently labeled elastin, and a triple helical peptide mimic of collagen V (THP-V) produced raw kinetics data, in the form of progress curves. Microcal Origin Pro 7.5 was used to analyze the data to give the kcat, the number of times each enzyme site converts substrate to product per second, and the Km, the concentration needed to achieve one half Vmax. Furthermore, dividing Kcat by Km revealed the amount of activity upon FS-6, elastin, and THP-V for each MMP-12 mutant with FS-6 as the control for mutated and wild-type MMP-12. Since the kcat/Km for wild-type MMP-12 was already known, comparison of activity upon THP-V and elastin between wild type MMP-12 and each MMP-12 mutant was achieved. Ongoing data collection suggests diminished catalytic activity upon elastin and THP-V in all three MMP-12 mutants (F202Q, T205K, and H206D) when compared to wild-type MMP-12, while showing no decrease in activity upon the general MMP substrate, FS-6. To date, data suggests that all three exosites are individually involved in fine-tuning MMP-12 specificity for elastin and triple helical peptide mimics of collagen V.NSF-REU Program in Biological Sciences & Biochemistr

Algal food and fuel coproduction can mitigate greenhouse gas emissions while improving land and water-use efficiency

The goals of ensuring energy, water, food, and climate security can often conflict.Microalgae (algae) are being pursued as a feedstockfor both food and fuels—primarily due to algae’s high areal yield and ability to grow on non-arable land, thus avoiding common bioenergy-food tradeoffs. However, algal cultivation requires significant energy inputs that may limit potential emission reductions.We examine the tradeoffs associated with producing fuel andfood from algae at the energy–food–water–climate nexus.We use the GCAM integrated assessment model to demonstrate that algalfood production can promote reductions in land-use change emissions through the offset of conventional agriculture. However,fuel production, either via co-production of algal food and fuel or complete biomass conversion to fuel, is necessary to ensure long-term emission reductions, due to the high energy costs of cultivation. Cultivation of salt– water algae for food products may lead to substantial freshwater savings; but, nutrients for algae cultivation will need to be sourced from waste streams to ensure sustainability. By reducing the land demand of food production, while simultaneously enhancingfood and energy security, algae can further enable the development of terrestrial bioenergy technologies including those utilizing carbon capture and storage. Our results demonstrate that large-scale algae research and commercialization efforts should focus on developing both food and energy products to achieve environmental goals.https://iopscience.iop.org/article/10.1088/1748-9326/11/11/114006/metaPublished versio

Jak-STAT regulation of male germline stem cell establishment during Drosophila embryogenesis

Germline stem cells (GSCs) in Drosophila are descendants of primordial germ cells (PGCs) specified during embryogenesis. The precise timing of GSC establishment in the testis has not been determined, nor is it known whether mechanisms that control GSC maintenance in the adult are involved in GSC establishment. Here, we determine that PGCs in the developing male gonad first become GSCs at the embryo to larval transition. This coincides with formation of the embryonic hub; the critical signaling center that regulates adult GSC behavior within the stem cell microenvironment (niche). We find that the Jak-STAT signaling pathway is activated in a subset of PGCs that associate with the newly-formed embryonic hub. These PGCs express GSC markers and function like GSCs, while PGCs that do not associate with the hub begin to differentiate. In the absence of Jak-STAT activation, PGCs adjacent to the hub fail to exhibit the characteristics of GSCs, while ectopic activation of the Jak-STAT pathway prevents differentiation. These findings show that stem cell formation is closely linked to development of the stem cell niche, and suggest that Jak-STAT signaling is required for initial establishment of the GSC population in developing testes. (C) 2009 Elsevier Inc. All rights reserved

Culture Moderates the Relationship Between Emotional Fit and Collective Aspects of Well-Being

The present study examined how emotional fit with culture – the degree of similarity between an individual’ emotional response to the emotional response of others from the same culture – relates to well-being in a sample of Asian American and European American college students. Using a profile correlation method, we calculated three types of emotional fit based on self-reported emotions, facial expressions, and physiological responses. We then examined the relationships between emotional fit and individual well-being (depression, life satisfaction) as well as collective aspects of well-being, namely collective self-esteem (one’s evaluation of one’s cultural group) and identification with one’s group. The results revealed that self-report emotional fit was associated with greater individual well-being across cultures. In contrast, culture moderated the relationship between self-report emotional fit and collective self-esteem, such that emotional fit predicted greater collective self-esteem in Asian Americans, but not in European Americans. Behavioral emotional fit was unrelated to well-being. There was a marginally significant cultural moderation in the relationship between physiological emotional fit in a strong emotional situation and group identification. Specifically, physiological emotional fit predicted greater group identification in Asian Americans, but not in European Americans. However, this finding disappeared after a Bonferroni correction. The current finding extends previous research by showing that, while emotional fit may be closely related to individual aspects of well-being across cultures, the influence of emotional fit on collective aspects of well-being may be unique to cultures that emphasize interdependence and social harmony, and thus being in alignment with other members of the group

A meta-analysis of long-term effects of conservation agriculture on maize grain yield under rain-fed conditions

Conservation agriculture involves reduced tillage, permanent soil cover and crop rotations to enhance soil fertility and to supply food from a dwindling land resource. Recently, conservation agriculture has been promoted in Southern Africa, mainly for maize-based farming systems. However, maize yields under rain-fed conditions are often variable. There is therefore a need to identify factors that influence crop yield under conservation agriculture and rain-fed conditions. Here, we studied maize grain yield data from experiments lasting 5 years and more under rain-fed conditions. We assessed the effect of long-term tillage and residue retention on maize grain yield under contrasting soil textures, nitrogen input and climate. Yield variability was measured by stability analysis. Our results show an increase in maize yield over time with conservation agriculture practices that include rotation and high input use in low rainfall areas. But we observed no difference in system stability under those conditions. We observed a strong relationship between maize grain yield and annual rainfall. Our meta-analysis gave the following findings: (1) 92% of the data show that mulch cover in high rainfall areas leads to lower yields due to waterlogging; (2) 85% of data show that soil texture is important in the temporal development of conservation agriculture effects, improved yields are likely on well-drained soils; (3) 73% of the data show that conservation agriculture practices require high inputs especially N for improved yield; (4) 63% of data show that increased yields are obtained with rotation but calculations often do not include the variations in rainfall within and between seasons; (5) 56% of the data show that reduced tillage with no mulch cover leads to lower yields in semi-arid areas; and (6) when adequate fertiliser is available, rainfall is the most important determinant of yield in southern Africa. It is clear from our results that conservation agriculture needs to be targeted and adapted to specific biophysical conditions for improved impact

Innovative Visualizations Shed Light on Avian Nocturnal Migration

We acknowledge the support provided by COST–European Cooperation in Science and Technology through the Action ES1305 ‘European Network for the Radar Surveillance of Animal Movement’ (ENRAM) in facilitating this collaboration. We thank ENRAM members and researchers attending the EOU round table discussion ‘Radar aeroecology: unravelling population scale patterns of avian movement’ for feedback on the visualizations. We thank Arie Dekker for his feedback as jury member of the bird migration visualization challenge & hackathon hosted at the University of Amsterdam, 25–27 March 2015. We thank Willem Bouten and Kevin Winner for discussion of methodological design. We thank Kevin Webb and Jed Irvine for assistance with downloading, managing, and reviewing US radar data. We thank the Royal Meteorological Institute of Belgium for providing weather radar data.Globally, billions of flying animals undergo seasonal migrations, many of which occur at night. The temporal and spatial scales at which migrations occur and our inability to directly observe these nocturnal movements makes monitoring and characterizing this critical period in migratory animals’ life cycles difficult. Remote sensing, therefore, has played an important role in our understanding of large-scale nocturnal bird migrations. Weather surveillance radar networks in Europe and North America have great potential for long-term low-cost monitoring of bird migration at scales that have previously been impossible to achieve. Such long-term monitoring, however, poses a number of challenges for the ornithological and ecological communities: how does one take advantage of this vast data resource, integrate information across multiple sensors and large spatial and temporal scales, and visually represent the data for interpretation and dissemination, considering the dynamic nature of migration? We assembled an interdisciplinary team of ecologists, meteorologists, computer scientists, and graphic designers to develop two different flow visualizations, which are interactive and open source, in order to create novel representations of broad-front nocturnal bird migration to address a primary impediment to long-term, large-scale nocturnal migration monitoring. We have applied these visualization techniques to mass bird migration events recorded by two different weather surveillance radar networks covering regions in Europe and North America. These applications show the flexibility and portability of such an approach. The visualizations provide an intuitive representation of the scale and dynamics of these complex systems, are easily accessible for a broad interest group, and are biologically insightful. Additionally, they facilitate fundamental ecological research, conservation, mitigation of human–wildlife conflicts, improvement of meteorological products, and public outreach, education, and engagement.Yeshttp://www.plosone.org/static/editorial#pee

AI is a viable alternative to high throughput screening: a 318-target study

: High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery