Molecular dynamics simulations reveal that AEDANS is an inert fluorescent probe for the study of membrane proteins

Computer simulations were carried out of a number of AEDANS-labeled single cysteine mutants of a small reference membrane protein, M13 major coat protein, covering 60% of its primary sequence. M13 major coat protein is a single membrane-spanning, α-helical membrane protein with a relatively large water-exposed region in the N-terminus. In 10-ns molecular dynamics simulations, we analyze the behavior of the AEDANS label and the native tryptophan, which were used as acceptor and donor in previous FRET experiments. The results indicate that AEDANS is a relatively inert environmental probe that can move unhindered through the lipid membrane when attached to a membrane protein

Structural Heterogeneity and Quantitative FRET Efficiency Distributions of Polyprolines through a Hybrid Atomistic Simulation and Monte Carlo Approach

Förster Resonance Energy Transfer (FRET) experiments probe molecular distances via distance dependent energy transfer from an excited donor dye to an acceptor dye. Single molecule experiments not only probe average distances, but also distance distributions or even fluctuations, and thus provide a powerful tool to study biomolecular structure and dynamics. However, the measured energy transfer efficiency depends not only on the distance between the dyes, but also on their mutual orientation, which is typically inaccessible to experiments. Thus, assumptions on the orientation distributions and averages are usually made, limiting the accuracy of the distance distributions extracted from FRET experiments. Here, we demonstrate that by combining single molecule FRET experiments with the mutual dye orientation statistics obtained from Molecular Dynamics (MD) simulations, improved estimates of distances and distributions are obtained. From the simulated time-dependent mutual orientations, FRET efficiencies are calculated and the full statistics of individual photon absorption, energy transfer, and photon emission events is obtained from subsequent Monte Carlo (MC) simulations of the FRET kinetics. All recorded emission events are collected to bursts from which efficiency distributions are calculated in close resemblance to the actual FRET experiment, taking shot noise fully into account. Using polyproline chains with attached Alexa 488 and Alexa 594 dyes as a test system, we demonstrate the feasibility of this approach by direct comparison to experimental data. We identified cis-isomers and different static local environments as sources of the experimentally observed heterogeneity. Reconstructions of distance distributions from experimental data at different levels of theory demonstrate how the respective underlying assumptions and approximations affect the obtained accuracy. Our results show that dye fluctuations obtained from MD simulations, combined with MC single photon kinetics, provide a versatile tool to improve the accuracy of distance distributions that can be extracted from measured single molecule FRET efficiencies

Toll-like receptors (TLRs) and mannan-binding lectin (MBL): On constant alert in a hostile environment

In the beginning were neither B cells nor T cells nor antibodies, but innate immune defense alone. The primary functional theme of innate immunity is the distinction between self and non-self, which is maintained by a vast number of cellular and subcellular components. In this context, the immense importance of the Toll-like receptors (TLRs) is well established. Positive (Darwinian) selection seems to be acting on the ligand-binding domains of these molecules, suggesting a selection pattern similar to that previously observed in the MHC proteins. In sharp contrast to TLRs, the biological significance of mannan-binding lectin (MBL) is controversial, and, concerning humans, it has been suggested that low concentration of MBL in serum represents a selective advantage. In this mini-review, based on a doctoral thesis, evolutionary aspects of TLRs and MBL are discussed

The environmental impacts of palm oil in context

Delivering the Sustainable Development Goals (SDGs) requires balancing demands on land between agriculture (SDG 2) and biodiversity (SDG 15). The production of vegetable oils, and in particular palm oil, illustrates these competing demands and trade-offs. Palm oil accounts for 40% of the current global annual demand for vegetable oil as food, animal feed, and fuel (210 million tons (Mt)), but planted oil palm covers less than 5-5.5% of total global oil crop area (ca. 425 Mha), due to oil palm’s relatively high yields5. Recent oil palm expansion in forested regions of Borneo, Sumatra, and the Malay Peninsula, where >90% of global palm oil is produced, has led to substantial concern around oil palm’s role in deforestation. Oil palm expansion’s direct contribution to regional tropical deforestation varies widely, ranging from 3% in West Africa to 47% in Malaysia. Oil palm is also implicated in peatland draining and burning in Southeast Asia. Documented negative environmental impacts from such expansion include biodiversity declines, greenhouse gas emissions, and air pollution. However, oil palm generally produces more oil per area than other oil crops, is often economically viable in sites unsuitable for most other crops, and generates considerable wealth for at least some actors. Global demand for vegetable oils is projected to increase by 46% by 20509. Meeting this demand through additional expansion of oil palm versus other vegetable oil crops will lead to substantial differential effects on biodiversity, food security, climate change, land degradation, and livelihoods. Our review highlights that, although substantial gaps remain in our understanding of the relationship between the environmental, socio-cultural and economic impacts of oil palm, and the scope, stringency and effectiveness of initiatives to address these, there has been little research into the impacts and trade-offs of other vegetable oil crops. 65 Greater research attention needs to be given to investigating the impacts of palm oil production 66 compared to alternatives for the trade-offs to be assessed at a global scale

Influence of integrated soil fertility management in wheat and tef productivity and soil chemical properties in the highland tropical environment

Soil fertility depletion and soil quality decline have been threatening the ecological and economic sustainability of crop production. In order to improve soil fertility and nutrient management approaches, on-farm integrated soil fertility management (ISFM) trials were conducted to evaluate the effects of organic and inorganic fertilizers on wheat (Triticum estivum L.) and tef (Eragrostis tef) yield and soil fertility in the highland Nitisol area of Ethiopia during 2010 and 2011 cropping seasons. The treatments were five selected combinations of N and P, manure and compost. These included control, farmers' practice (23/10 kg NP ha^-1), recommended NP rate (60/20 kg NP ha^-1), 50% of recommended NP rate (30/10 NP kg ha^-1) + 50% manure and compost as inorganic N equivalence (3.25 tons ha^-1). and 50% manure + 50% compost as N equivalence. Results revealed that yields of wheat and tef, and some soil chemical properties significantly responded to the different soil fertility management treatments. The application of 60/20 kg NP ha^-1 and 30/10 kg NP ha^-1 with 50% manure and compost as N equivalence increased mean grain yield of wheat by 151 and 129% respectively compared to the control, and by 85 and 68% respectively compared to the farmers' treatment (23/10 kg NP ha^-1). Similarly, the same treatments increased tef grain yield by 141 and 122% compared to the control, and by 44 and 33% compared to the farmers' treatment. The application of compost or manure with half the recommended NP fertilizer rate resulted in a comparable yield as that of full NP dose, which could beconsidered as an alternative option for sustainable soil health and crop productivity. In conclusion, the two year result showed that the application of ISFM may optimize yield of wheat and tef as well as improve the fertility status of the soil

DEVELOPMENT OF A TECHNIQUE TO MEASURE ARM MOVEMENT DURING PHYSICAL ACTIVITY: IMPLICATIONS FOR STERNAL PRECAUTIONS

C. Gatlin, G. Vanbeek, J. Aguilera, J. Sattgast, T. LaPier Eastern Washington University, Cheney, WA Median sternotomy is frequently used during cardiac surgery. Patients are commonly prescribed Sternal Precautions (SP) during recovery to minimize post-surgical complications, but resumption of physical activity and arm movement are important for recovery. PURPOSE: To develop an objective methodology to distinguish between specific, purposeful arm movements and total, whole-body arm movements using 3 accelerometers. METHODS: ActiGraph GT9X Link, a validated 3-axis accelerometer (3AA), was used to measure movement. Subjects wore 3 activity monitors (3xAM), one on each wrist and at the waist for 4 consecutive days. The sum of acceleration measured in 3 axes was calculated and divided by 1000, resulting in a vector magnitude kilocount (VMC) expressed per day. Raw data from the wrist 3AA were filtered by a low-frequency extension filter. Data obtained from the waist monitor was used to determine periods of ambulation. Data was broken up into 15 second epochs during which arm movement was assumed to be arm swing and therefore non-purposeful when 5 or greater steps were taken. This allowed determination of both total arm movement and specific arm movement not associated with gait. Cross-sectional 3xAM data from adults \u3e 65 years old (n = 17) were compared to data obtained with established activity measurements. Next, we analyzed the ability of the 3xAM technique to discriminate between whole body and arm specific activity. Statistical analyses included correlations, ANOVA, and t-tests with Bonferroni correction (P \u3c 0.05). Currently, we have initiated 3xAM longitudinal data collection before, during, and after simulated sternal precautions. RESULTS: We found significant correlations (r = 0.4 – 0.7) between the 3xAM data and activity measures. When comparing the raw, filtered, and gait removed data, the raw data (15,000 VMC) was significantly greater than the modified data (6,000 VMC). Pilot data demonstrated a trend showing decreased activity during and immediately after SP that did not return to prior activity levels. CONCLUSIONS: The 3xAM technique described shows concurrent validity and successfully differentiates arm movement from whole body activity. Longitudinal pilot data suggests 3xAM VMC reflect arm movement patterns before, during, and after SP, indicating utility for measuring return to function

Applying Behavioral and Physiological Measures to Assess the Relative Impact of the Prolonged COVID-19 Pandemic Closure on Two Mammal Species at the Oregon Zoo: Cheetah (A. jubatus) and Giraffe (G. c. reticulata and G. c. tippelskirchii)

The effect of visitor presence on zoo animals has been explored in numerous studies over the past two decades. However, the opportunities for observations without visitors have been very limited at most institutions. In 2020, the Oregon Zoo was closed, in response to the global SARSCoV-2 (COVID-19) pandemic, from 15 March 2020 to 12 July 2020, resulting in approximately four consecutive months without visitor presence. This study aimed to quantify potential behavioral and hormonal changes expressed during two transition periods in zoo visitor attendance: the initial time period before and after closure in March 2020 and time before and after reopening in July 2020. Fecal glucocorticoid metabolite (fGM) concentrations of resident giraffes (n = 2) and cheetahs (n = 2) were tracked using enzyme immunoassay (EIA) analyses. Average fGM concentrations during the two transition periods were compared using a two-way mixed ANOVA. Additionally, twice-weekly scan sampling was used to quantify behavioral observations across the transitions, which were analyzed as individual behavior proportions. Individual behavior proportions were compared across the Zoo’s opening status and time of day using Kruskal–Wallis (H) tests. The results of our analyses showed the following outcomes: (1) significant increases in fGM concentrations for cheetahs and giraffes between the transition periods but not within them; (2) a significant increase in time spent ‘not visible’ in the cheetahs in the second transition period; and (3) increased vigilance behaviors in the giraffes