* Indicates student co-author
Poo, Cindi, Gautam Agarwal, Niccolò Bonacci, and Zachary F. Mainen. “Spatial Maps in Piriform Cortex During Olfactory Navigation.” Nature, vol. 601, 2022, pp. 595-599.
Abstract: Odours are a fundamental part of the sensory environment used by animals to guide behaviours such as foraging and navigation. Primary olfactory (piriform) cortex is thought to be the main cortical region for encoding odour identity. Here, using neural ensemble recordings in freely moving rats performing an odour-cued spatial choice task, we show that posterior piriform cortex neurons carry a robust spatial representation of the environment. Piriform spatial representations have features of a learned cognitive map, being most prominent near odour ports, stable across behavioural contexts and independent of olfactory drive or reward availability. The accuracy of spatial information carried by individual piriform neurons was predicted by the strength of their functional coupling to the hippocampal theta rhythm. Ensembles of piriform neurons concurrently represented odour identity as well as spatial locations of animals, forming an odour–place map. Our results reveal a function for piriform cortex in spatial cognition and suggest that it is well-suited to form odour–place associations and guide olfactory-cued spatial navigation.
Lakin, Hilary Ann, Hannah Tavalire, Kaori Sakamoto, Peter Buss, Michele Miller, Sarah A. Budischak, Kristina Raum, Vanessa O. Ezenwa, Brianna Beechler, and Anna Jolles. “Bovine Tuberculosis in African buffalo (Syncerus caffer): Progression of Pathology During Infection.” PLOS Neglected Tropical Diseases, vol. 16, no. 11, 2022, e0010906.
Abstract: Background: Bovine tuberculosis (BTB) is a zoonotic disease of global importance endemic in African buffalo (Syncerus caffer) in sub-Saharan Africa. Zoonotic tuberculosis is a disease of global importance, accounting for over 12,000 deaths annually. Cattle affected with BTB have been proposed as a model for the study of human tuberculosis, more closely resembling the localization and progression of lesions in controlled studies than murine models. If disease in African buffalo progresses similarly to experimentally infected cattle, they may serve as a model, both for human tuberculosis and cattle BTB, in a natural environment. Methodology/Principal findings: We utilized a herd of African buffalo that were captured, fitted with radio collars, and tested for BTB twice annually during a 4-year-cohort study. At the end of the project, BTB positive buffalo were culled, and necropsies performed. Here we describe the pathologic progression of BTB over time in African buffalo, utilizing gross and histological methods. We found that BTB in buffalo follows a pattern of infection like that seen in experimental studies of cattle. BTB localizes to the lymph nodes of the respiratory tract first, beginning with the retropharyngeal and tracheobronchial lymph nodes, gradually increasing in lymph nodes affected over time. At 36 months, rate of spread to additional lymph nodes sharply increases. The lung lesions follow a similar pattern, progressing slowly, then accelerating their progression at 36 months post infection. Lastly, a genetic marker that correlated to risk of M. bovis infection in previous studies was marginally associated with BTB progression. Buffalo with at least one risk allele at this locus tended to progress faster, with more lung necrosis. Conclusions/Significance: The progression of disease in the African buffalo mirrors the progression found in experimental cattle models, offering insight into BTB and the interaction with its host in the context of naturally varying environments, host, and pathogen populations.
Warburton, Elizabeth M., Sarah A. Budischak, Anna E. Jolles, and Vanessa O. Ezenwa. “Within-Host and External Environments Differentially Shape β-Diversity Across Parasite Life Stages.” Journal of Animal Ecology, vol. 92, no. 3, 2022, pp. 665-676.
Abstract: 1. Uncovering drivers of community assembly is a key aspect of learning how biological communities function. Drivers of community similarity can be especially useful in this task as they affect assemblage-level changes that lead to differences in species diversity between habitats. Concepts of β-diversity originally developed for use in free-living communities have been widely applied to parasite communities to gain insight into how infection risk changes with local conditions by comparing parasite communities across abiotic and biotic gradients. 2. Factors shaping β-diversity in communities of immature parasites, such as larvae, are largely unknown. This is a key knowledge gap as larvae are frequently the infective life-stage and understanding variation in these larval communities is thus key for disease prevention. Our goal was to uncover links between β-diversity of parasite communities at different life stages; therefore, we used gastrointestinal nematodes infecting African buffalo in Kruger National Park, South Africa, to investigate within-host and extra-host drivers of adult and larval parasite community similarity. 3. We employed a cross-sectional approach using PERMANOVA that examined each worm community at a single time point to assess independent drivers of β-diversity in larvae and adults as well as a longitudinal approach with path analysis where adult and larval communities from the same host were compared to better link drivers of β-diversity between these two life stages. 4. Using the cross-sectional approach, we generally found that intrinsic, within-host traits had significant effects on β-diversity of adult nematode communities, while extrinsic, extra-host variables had significant effects on β-diversity of larval nematode communities. However, the longitudinal approach provided evidence that intrinsic, within-host factors affected the larval community indirectly via the adult community. 5. Our results provide key data for the comparison of community-level processes where adult and immature stages inhabit vastly different habitats (i.e. within-host vs. abiotic environment). In the context of parasitism, this helps elucidate host infection risk via larval stages and the drivers that shape persistence of adult parasite assemblages, both of which are useful for predicting and preventing infectious disease.
Deol*, Reina, Ashweetha Louis*, Harper Lee Glazer*, Warren Hosseinion*, Anna Bagley*, and Pete Chandrangsu. “Poly-Gamma Glutamic Acid Secretion Protects Bacillus Subtilis from Zinc and Copper Intoxication.” Microbiology Spectrum, vol. 10, issue 2, 2022, e0132921.
Abstract: Zinc and copper are essential micronutrients that serve as a cofactors for numerous enzymes. However, when present at elevated concentrations, zinc and copper are highly toxic to bacteria. To combat the effects of zinc and copper excess, bacteria have evolved a wide array of defense mechanisms. Here, we show that the Gram-positive soil bacterium, Bacillus subtilis, produces the extracellular polymeric substance, poly-gamma-glutamate (γ-PGA) as a protective mechanism in response to zinc and copper excess. Furthermore, we provide evidence that zinc and copper dependent γ-PGA production is independent of the DegS-DegQ two-component regulatory system and likely occurs at a posttranscriptional level through the small protein, PgsE. These data provide new insight into bacterial metal resistance mechanisms and contribute to our understanding of the regulation of bacterial γ-PGA biosynthesis.
Chen, Audrey, Eric Tarapore, Allisen G. To*, Davis M. Catolico*, Kelly C. Nguyen, Melissa J. Coleman, and Rory D. Spence. “Introducing Immunohistochemistry to the Molecular Biology Laboratory.” Biochemistry and Molecular Biology Education, vol. 50, issue 2, 2022, pp. 229-236.
Abstract: Widely used in research laboratories, immunohistochemistry (IHC) is a transferable skill that prepares undergraduate students for a variety of careers in the biomedical field. We have developed an inquiry-based learning IHC laboratory exercise, which introduces students to the theory, procedure, and data interpretation of antibody staining. Students are tasked with performing IHC using an “unknown” antibody and then asked to identify the cells or molecular structures within the nervous systems specific for that unknown antibody. In two lab sessions, students are exposed to handling of delicate brain slices, fluorescent microscopy, and data analysis using the Allen Brain Atlas (ABA), an online freely accessible database of mRNA transcript expression patterns in the brain. Here, we present guidelines for easy implementation in the classroom and assess learning gains achieved by the students upon completion of the IHC laboratory module. Students clearly displayed an increase in knowledge in data interpretation, procedural knowledge, and theory surrounding IHC. Thus, this module works as an inquiry-based learning based method to introduce IHC principles to undergraduate students.
Chen, Audrey, Eric Tarapore, Allisen G. To*, Davis M. Catolico*, Kelly C. Nguyen, Melissa J. Coleman, and Rory D. Spence. “Introducing Immunohistochemistry to the Molecular Biology Laboratory.” Biochemistry and Molecular Biology Education, vol. 50, issue 2, 2022, pp. 229-236.
Abstract: Widely used in research laboratories, immunohistochemistry (IHC) is a transferable skill that prepares undergraduate students for a variety of careers in the biomedical field. We have developed an inquiry-based learning IHC laboratory exercise, which introduces students to the theory, procedure, and data interpretation of antibody staining. Students are tasked with performing IHC using an “unknown” antibody and then asked to identify the cells or molecular structures within the nervous systems specific for that unknown antibody. In two lab sessions, students are exposed to handling of delicate brain slices, fluorescent microscopy, and data analysis using the Allen Brain Atlas (ABA), an online freely accessible database of mRNA transcript expression patterns in the brain. Here, we present guidelines for easy implementation in the classroom and assess learning gains achieved by the students upon completion of the IHC laboratory module. Students clearly displayed an increase in knowledge in data interpretation, procedural knowledge, and theory surrounding IHC. Thus, this module works as an inquiry-based learning based method to introduce IHC principles to undergraduate students.
Finseth, Findley, Keely Brown, Andrew Demaree, and Lila Fishman. “Supergene Potential of a Selfish Centromere.” Philosophical Transactions of the Royal Society B, vol. 377, issue 1856, 2022, 20210208.
Abstract: Selfishly evolving centromeres bias their transmission by exploiting the asymmetry of female meiosis and preferentially segregating to the egg. Such female meiotic drive systems have the potential to be supergenes, with multiple linked loci contributing to drive costs or enhancement. Here, we explore the supergene potential of a selfish centromere (D) in Mimulus guttatus, which was discovered in the Iron Mountain (IM) Oregon population. In the nearby Cone Peak population, D is still a large, non-recombining and costly haplotype that recently swept, but shorter haplotypes and mutational variation suggest a distinct population history. We detected D in five additional populations spanning more than 200 km; together, these findings suggest that selfish centromere dynamics are widespread in M. guttatus. Transcriptome comparisons reveal elevated differences in expression between driving and non-driving haplotypes within, but not outside, the drive region, suggesting large-scale cis effects of D's spread on gene expression. We use the expression data to refine linked candidates that may interact with drive, including Nuclear Autoantigenic Sperm Protein (NASPSIM3), which chaperones the centromere-defining histone CenH3 known to modify Mimulus drive. Together, our results show that selfishly evolving centromeres may exhibit supergene behaviour and lay the foundation for future genetic dissection of drive and its costs.
Friedman, Eric J., and Adam S. Landsberg. “Winning Strategies: The Emergence of Base 2 in the Game of Nim.” The Mathematical Gazette, vol. 106, issue 566, 2022, pp. 212-219.
Abstract: Many players know that the secret of winning the game of nim (and other “impartial” combinatorial games) is to write the sizes of the game’s piles in base 2 and then add them together without carry. The proof of this well-known procedure (described below) is both straightforward and convincing. Nonetheless, the procedure still appears magical, as though a rabbit has been pulled out of a hat. Astute students (and frustrated professors) often ask why the winning strategy for such games involves base 2, and not some other base. After all, nothing about the game of nim itself – the game rules, the configuration of the tokens, etc. – provides any hints about the origin of base 2 in this setting. Minimal insight is offered by most published proofs, which themselves tend to either appear almost wizardly in nature (i.e. assume the base-2 method and show that it miraculously solves the problem) or employ combinatorial arguments that supply little abstract intuition (at least to the authors of this article).
Christensen*, Trevor A., Kristi Y. Lee*, Simone Z.P. Gottlieb*, Mikayla B. Carrier*, and Aaron M. Leconte. “Mutant Polymerases Capable of 2’ Fluoro-Modified Nucleic Acid Synthesis and Amplification with Improved Accuracy.” RSC Chemical Biology, vol. 3, issue 8, 2022, pp. 1044-1051.
Abstract: Nonnatural nucleic acids (xeno nucleic acids, XNA) can possess several useful properties such as expanded reactivity and nuclease resistance, which can enhance the utility of DNA as a biotechnological tool. Native DNA polymerases are unable to synthesize XNA, so, in recent years mutant XNA polymerases have been engineered with sufficient activity for use in processes such as PCR. While substantial improvements have been made, accuracy still needs to be increased by orders of magnitude to approach natural error rates and make XNA polymerases useful for applications that require high fidelity. Here, we systematically evaluate leading Taq DNA polymerase mutants for their fidelity during synthesis of 2′F XNA. To further improve their accuracy, we add mutations that have been shown to increase the fidelity of wild-type Taq polymerases, to some of the best current XNA polymerases (SFM4–3, SFM4–6, and SFP1). The resulting polymerases show significant improvements in synthesis accuracy. In addition to generating more accurate XNA polymerases, this study also informs future polymerase engineering efforts by demonstrating that mutations that improve the accuracy of DNA synthesis may also have utility in improving the accuracy of XNA synthesis.
Lamberti, Martina, Michael Hess*, Inês Dias, Michael van Putten, Joost le Feber, and Sarah Marzen. “Maximum Entropy Models Provide Functional Connectivity Estimates in Neural Networks.” Scientific Reports, vol. 12, 2022, 9656.
Abstract: Tools to estimate brain connectivity offer the potential to enhance our understanding of brain functioning. The behavior of neuronal networks, including functional connectivity and induced connectivity changes by external stimuli, can be studied using models of cultured neurons. Cultured neurons tend to be active in groups, and pairs of neurons are said to be functionally connected when their firing patterns show significant synchronicity. Methods to infer functional connections are often based on pair-wise cross-correlation between activity patterns of (small groups of) neurons. However, these methods are not very sensitive to detect inhibitory connections, and they were not designed for use during stimulation. Maximum Entropy (MaxEnt) models may provide a conceptually different method to infer functional connectivity. They have the potential benefit to estimate functional connectivity during stimulation, and to infer excitatory as well as inhibitory connections. MaxEnt models do not involve pairwise comparison, but aim to capture probability distributions of sets of neurons that are synchronously active in discrete time bins. We used electrophysiological recordings from in vitro neuronal cultures on micro electrode arrays to investigate the ability of MaxEnt models to infer functional connectivity. Connectivity estimates provided by MaxEnt models correlated well with those obtained by conditional firing probabilities (CFP), an established cross-correlation based method. In addition, stimulus-induced connectivity changes were detected by MaxEnt models, and were of the same magnitude as those detected by CFP. Thus, MaxEnt models provide a potentially powerful new tool to study functional connectivity in neuronal networks.
Marzen, Sarah E. and James P. Crutchfield. “Interference, Prediction, and Entropy-Rate Estimation of Continuous-Time, Discrete Event Processes.” Entropy, vol. 24, issue 11, 2022, 1675.
Abstract: Inferring models, predicting the future, and estimating the entropy rate of discrete-time, discrete-event processes is well-worn ground. However, a much broader class of discrete-event processes operates in continuous-time. Here, we provide new methods for inferring, predicting, and estimating them. The methods rely on an extension of Bayesian structural inference that takes advantage of neural network’s universal approximation power. Based on experiments with complex synthetic data, the methods are competitive with the state-of-the-art for prediction and entropy-rate estimation.
Marzen, Sarah E. and James P. Crutchfield. “Probabilistic Deterministic Finite Automata and Recurrent Networks, Revisited.” Entropy, vol. 24, issue 1, 2022, 90.
Abstract: Reservoir computers (RCs) and recurrent neural networks (RNNs) can mimic any finite-state automaton in theory, and some workers demonstrated that this can hold in practice. We test the capability of generalized linear models, RCs, and Long Short-Term Memory (LSTM) RNN architectures to predict the stochastic processes generated by a large suite of probabilistic deterministic finite-state automata (PDFA) in the small-data limit according to two metrics: predictive accuracy and distance to a predictive rate-distortion curve. The latter provides a sense of whether or not the RNN is a lossy predictive feature extractor in the information-theoretic sense. PDFAs provide an excellent performance benchmark in that they can be systematically enumerated, the randomness and correlation structure of their generated processes are exactly known, and their optimal memory-limited predictors are easily computed. With less data than is needed to make a good prediction, LSTMs surprisingly lose at predictive accuracy, but win at lossy predictive feature extraction. These results highlight the utility of causal states in understanding the capabilities of RNNs to predict.
Tyler*, Conrad, Sarah Marzen, and Jenna Monroy. “Mathematically Modeling Prey-Catching Behavior of the Tomato Frog.” Spora, vol. 8, 2022, article 1.
Abstract: Many microhylid frog species, such as the tomato frog, Dyscophus sp., have demonstrated the ability to aim their tongues independently of head and jaw movements. However, a trade-off between tongue-aiming and head-only aiming exists in which the former allows for crypsis but lacks speed whereas the latter is faster but less accurate and more noticeable to prey. For frogs that can move their tongues independently of their heads, under what circumstances will they utilize each strategy, and why? We derive a model, dependent on factors relevant for prey-catching, for the probability the frog will turn its head (and not tongue) given the prey angle. Our model behaves as expected when altering prey-catching factors, but underestimates head turning behavior with increasing prey angle. We later allow for variance in perceived prey location to be a function of prey angle. We find such variance must generally increase with prey angle.
External grant: Marzen, Sarah. Scialog Fellow for Molecular Basis of Recognition. Research Corporation for Science Advancement, 2022.
External grant: Marzen, Sarah. “Sensory Prediction: Engineered and Evolved.” National Science Foundation, 2022, $48,280.
Lundberg, Joyce, Donald A. McFarlane, and Guy Van Rentergem. “The Nitrogen Dynamics of Deer Cave, Sarawak, and the Role of Bat Caves as Biogeochemical Sinks in Tropical Moist Forests.” International Journal of Speleology, vol. 51, no. 3, 2022, pp. 205-221.
Abstract: A better understanding of the role of bat caves as nitrogen sinks in tropical moist forest ecosystems can be expected to shed light on regional and spatial variability in nutrient recycling studies. We measured the nitrogen flux (in air and water) associated with a very large Chaerephon plicata bat colony in Deer Cave, Borneo, in the process generating a new, quantitative, estimate of the total bat population (774,828±48,320), and the first detailed modelling of an ammonia plume in a cave. Long-term storage of N does not occur in this wet cave. Our final budget numbers indicate that, of the daily input of N (ie, ecologically-useful fixed-N in guano) to this cave, ammonia production is minor (and most of it is exported in water rather than air). The conclusion is that the export budget is dominated (perhaps as large as 94.4%) by microbial denitrification of fixed-N to diatomic N exported in air. Deer Cave thus acts as a nitrogen sink, potentially removing up to 39% of the ecologically-useful fixed-N from the total forest nitrogen budget over an area of hundreds of square kilometers.
McFarlane Donald, A. and Joyce Lundberg. "Potrential Cosmogenic 10Be /36 Cl Dating of Fossil Guano Deposits." Proceedings of the 18th International Congress of Speleology, Savioe Mont Blanc, vol. 5, 2022, pp. 105-107.
Norman, John, Justin Wheaton, and Donald and McFarlane. "Blasting for Rescue Applications." Journal of Explosives Engineering, vol. 39, no. 4, 2022, pp. 28-35.
Churilov, Alexander N. and John G. Milton. “Modeling Pulsativity in the Hypothalamic-Pituitary-Adrenal Hormonal Axis.” Scientific Reports, vol. 12, 2022, 8480.
Abstract: A new mathematical model for biology rhythms in the hypothalamic-pituitary-adrenal (HPA) axis is proposed. This model takes the form of a system of impulsive time-delay differential equations which include pulsatile release of adrenocorticotropin (ACTH) by the pituitary gland and a time delay for the release of glucocorticoid hormones by the adrenal gland. Numerical simulations demonstrate that the model’s response to period and circadian inputs from the hypothalamus are consistent with those generated by recent models which do not include a pulsatile pituitary. In contrast the oscillatory phenomena generated by the impulsive delay equation mode occur even if the time delay is zero. The observation that the time delay merely introduces a small phase shift suggesting that the effects of the adrenal gland are “downstream” to the origin of pulsativity. In addition, the model accounts for the occurrence of ultradian oscillations in an isolated pituitary gland. These observations suggest that principles of pulse modulated control, familiar to control engineers, may have an increasing role to play in understanding the HPA axis.
Hurley*, Kathryn L., Jordan R. Bassett*, and Jenna A. Monroy. “Active Muscle Stiffness is Reduced During Rapid Unloading in Muscles from TtnΔ112-158 Mice with a Large Deletion to PEVK Titin.” Journal of Experimental Biology, vol. 225, issue 16, 2022, jeb243584.
Abstract: Evidence suggests that the giant muscle protein titin functions as a tunable spring in active muscle. However, the mechanisms for increasing titin stiffness with activation are not well understood. Previous studies have suggested that during muscle activation, titin binds to actin, which engages the PEVK region of titin, thereby increasing titin stiffness. In this study, we investigated the role of PEVK titin in active muscle stiffness during rapid unloading. We measured elastic recoil of active and passive soleus muscles from TtnΔ112-158 mice characterized by a 75% deletion of PEVK titin and increased passive stiffness. We hypothesized that activated TtnΔ112-158 muscles are stiffer than wild-type muscles as a result of the increased stiffness of PEVK titin. Using a servomotor force lever, we compared the stress–strain relationships of elastic elements in active and passive muscles during rapid unloading and quantified the change in stiffness upon activation. The results show that the elastic modulus of TtnΔ112-158 muscles increased with activation. However, elastic elements developed force at 7% longer lengths and exhibited 50% lower active stiffness in TtnΔ112-158 soleus muscles than in wild-type muscles. Thus, despite having a shorter, stiffer PEVK segment, during rapid unloading, TtnΔ112-158 soleus muscles exhibited reduced active stiffness compared with wild-type soleus muscles. These results are consistent with the idea that PEVK titin contributes to active muscle stiffness; however, the reduction in active stiffness of TtnΔ112-158 muscles suggests that other mechanisms compensate for the increased PEVK stiffness.
Tyler*, Conrad, Sarah Marzen, and Jenna Monroy. “Mathematically Modeling Prey-Catching Behavior of the Tomato Frog.” Spora, vol. 8, 2022, article 1.
Abstract: Many microhylid frog species, such as the tomato frog, Dyscophus sp., have demonstrated the ability to aim their tongues independently of head and jaw movements. However, a trade-off between tongue-aiming and head-only aiming exists in which the former allows for crypsis but lacks speed whereas the latter is faster but less accurate and more noticeable to prey. For frogs that can move their tongues independently of their heads, under what circumstances will they utilize each strategy, and why? We derive a model, dependent on factors relevant for prey-catching, for the probability the frog will turn its head (and not tongue) given the prey angle. Our model behaves as expected when altering prey-catching factors, but underestimates head turning behavior with increasing prey angle. We later allow for variance in perceived prey location to be a function of prey angle. We find such variance must generally increase with prey angle.
Ahmad Affandi, Nurfarhana Alyssa, Norasikin Ahmad Ludin, Mirratul Mukminah Junedi, and Kathleen Purvis-Roberts. “The Resiliency of Photovoltaic Applied Fuelling Station in Malaysia: A Dynamic Urban Emission Displacement Assessment.”Cleaner Engineering and Technology, vol. 11, 2022, 100584.
Abstract: The number of fuelling stations continue to increase with the growing population and demand. Low carbon building for the cities and communities concept has led to a reassessment of service provision and fuel station urbanisation using a safe and matured renewable system; solar photovoltaics. This study uses a dynamic urban emission displacement assessment considering spatial and temporal variables of a fuel retail building in Malaysia. The result shows that the carbon emission potency is not concentrated within the fuelling area; instead, it's redirected through vehicle emission, operation and maintenance. The annual emission displaced by the installed solar photovoltaic system is about 18,022 metric tonnes of CO2/year. The solar-integrated building has its monthly electricity cost reduced by 20% with only 70% of its roof space usage. The life cycle cost of a 50kW photovoltaic system refurbishment translates to around RM22,000 of savings per year. However, the return on investment may take about eight years. In reality, fossil fuel divestment is impossible due to its reliability, but renewable technology can improve the built environment and air quality management in the city.
Derome, Daniel, Halim Razali, Ahmad Fazlizan, Alias Jedi, and Katie Purvis-Roberts. “Determination of Optimal Time-Average Wind Speed Data in the Southern Part of Malaysia.” Baghdad Science Journal, vol. 19, issue 5, 2022, pp. 1111-1122.
Abstract: Mersing is one of the places that have the potential for wind power development in Malaysia. Researchers often suggest it as an ideal place for generating electricity from wind power. However, before a location is chosen, several factors need to be considered. By analyzing the location ahead of time, resource waste can be avoided and maximum profitability to various parties can be realized. For this study, the focus is to identify the distribution of the wind speed of Mersing and to determine the optimal average of wind speed. This study is critical because the wind speed data for any region has its distribution. It changes daily and by season. Moreover, no determination has been made regarding selecting the average wind speed used for wind studies. The wind speed data is averaged to 1, 10, 30, and 60 minutes and used to find the optimal wind speed average. This study used Kolmogorov-Smirnov and Chi-Square as the goodness of fit. The finding shows that the wind speed distribution in Mersing varies according to the time average used and the best fit distribution is Gen. Gamma. In contrast, the optimal average wind speed is 10 minutes due to the highest similarity results with 1-minute data. These affect the reliability of the finding, accuracy of the estimation and decisions made. Therefore, the implementation of this study is significant so that the wind distribution in a particular area is more accurate.
Junedi, Mirratul Mukminah, Norasikin Ahmad Ludin, N.H. Hamid, Kathleen Purvis-Roberts, Hasila Jarimi, Nurfarhana Alyssa Ahmad Affandi. “Environmental and Economic Performance Assessment of Integrated Conventional Solar Photovoltaic and Agrophotovoltaic Systems.” Renewable and Sustainable Energy Reviews, vol. 168, 2022, 112799.
Abstract: Land utilisation by the solar energy industry and other sectors, such as residential and agriculture, has become increasingly competitive in recent years. Therefore, space optimisation is essential to reduce greenhouse gas (GHG) emissions while optimising electricity generation and profiting from the solar power plant. This article aims to discuss the different configurations of integrated photovoltaic (PV) systems, which combine the requirement features of a ground-mounted photovoltaic farm (GMPV) grouped into three systems: PV-wind, building integrated- or applied- PV (BIPV/BAPV) and agrophotovoltaic (agroPV). These systems generate electricity but differ because PV–wind systems generate electricity from two energy sources, whilst BIPV/BAPV systems utilise existing building space. Improving these systems, the agroPV system combines the benefits of producing power and using the vacant ground beneath the PV panels by cultivating crops. As a result, the BIPV system possesses the lowest emission rate with a range of −0.906–0.071 kgCO2eq/kWh. The manufacturing PV system's emission rate for these systems is highly affected. Meanwhile, the longest energy payback time (EPBT) is 6.3 years (BAPV), and the shortest is 0.5 years (GMPV). GMPV has the lowest EPBT due to the high electricity production of the plant, which allows the immediate repayment of the primary energy consumed. GMPV system has the lowest levelised cost of energy (LCOE) with the range of $0.04–$0.13/kWh. Meanwhile, the agroPV system has a good performance with an emission rate of 0.02 kgCO2eq/kWh, comparable to GMPV systems and lower than other integrated systems in terms of emission. The system has the LCOE of ∼$0.1/kWh, which is slightly higher than GMPV systems due to the system's higher cost but still provides monetary benefit.
Schlau, Benjamin Marcus. “Wildfire Disturbance Affects Species Interactions of a Harmful Invasive Annual in Second Year of Post-Fire Vegetative Recovery.” Biological Invasions, vol. 24, 2022, pp. 373-383.
Abstract: The increasing frequency of wildfires in Southern California’s Mediterranean-type habitats has been facilitating the displacement of native plants by invasive annuals. Black mustard (Brassica nigra) is an abundant, allelopathically harmful, invasive forb, which readily colonizes soil niches following most disturbances. Wildfires, however, are unlike other forms of disturbance because they can fundamentally alter plant–soil interactions through both physical and chemical changes in the soil. Here, a comparative field study of burned and unburned sites suggests that the Woolsey Fire—the largest wildfire ever recorded in California’s Santa Monica Mountains—inhibited dispersal of B. nigra and changed how it interacts with other plant species in the second year of post-fire recovery. More surprisingly, native plants were more likely to replace B. nigra than non-native plants in burned sites. These results indicate the possibility of post-fire seeding with specific “fire follower” native plant species may allow native flora to occupy soil niche space until longer-lived, competitive native shrubs establish.
Higham, Timothy E., Lars Schmitz, and Karl J. Niklas. “The Evolution of Mechanical Properties of Conifer and Angiosperm Woods.” Integrative and Comparative Biology, vol. 62, issue 3, 2022, pp. 668-682.
Abstract: The material properties of the cells and tissues of an organism dictate, to a very large degree, the ability of the organism to cope with the mechanical stresses induced by externally applied forces. It is, therefore, critical to understand how these properties differ across diverse species and how they have evolved. Herein, a large data base (N = 84 species) for the mechanical properties of wood samples measured at biologically natural moisture contents (i.e., “green wood”) was analyzed to determine the extent to which these properties are correlated across phylogenetically diverse tree species, to determine if a phylogenetic pattern of trait values exists, and, if so, to assess whether the rate of trait evolution varies across the phylogeny. The phylogenetic comparative analyses presented here confirm previous results that critical material properties are significantly correlated with one another and with wood density. Although the rates of trait evolution of angiosperms and gymnosperms (i.e., conifers) are similar, the material properties of both clades evolved in distinct selective regimes that are phenotypically manifested in lower values across all material properties in gymnosperms. This observation may be related to the structural differences between gymnosperm and angiosperm wood such as the presence of vessels in angiosperms. Explorations of rate heterogeneity indicate high rates of trait evolution in wood density in clades within both conifers and angiosperms (e.g., Pinus and Shorea). Future analyses are warranted using additional data given these preliminary results, especially because there is ample evidence of convergent evolution in the material properties of conifers and angiosperm wood that appear to experience similar ecological conditions.
Sheung, Janet Y., Jonathan Garamella, Stella K. Kahl, Brian Y. Lee, Ryan J. McGorty and Rae M. Robertson-Anderson. “Motor-Driven Advection Competes with Crowding to Drive Spatiotemporally Heterogeneous Transport in Cytoskeleton Composites.” Frontiers in Physics, vol. 10, 2022.
Abstract: The cytoskeleton–a composite network of biopolymers, molecular motors, and associated binding proteins–is a paradigmatic example of active matter. Particle transport through the cytoskeleton can range from anomalous and heterogeneous subdiffusion to superdiffusion and advection. Yet, recapitulating and understanding these properties–ubiquitous to the cytoskeleton and other out-of-equilibrium soft matter systems–remains challenging. Here, we combine light sheet microscopy with differential dynamic microscopy and single-particle tracking to elucidate anomalous and advective transport in actomyosin-microtubule composites. We show that particles exhibit multi-mode transport that transitions from pronounced subdiffusion to superdiffusion at tunable crossover timescales. Surprisingly, while higher actomyosin content increases the range of timescales over which transport is superdiffusive, it also markedly increases the degree of subdiffusion at short timescales and generally slows transport. Corresponding displacement distributions display unique combinations of non-Gaussianity, asymmetry, and non-zero modes, indicative of directed advection coupled with caged diffusion and hopping. At larger spatiotemporal scales, particles in active composites exhibit superdiffusive dynamics with scaling exponents that are robust to changing actomyosin fractions, in contrast to normal, yet faster, diffusion in networks without actomyosin. Our specific results shed important new light on the interplay between non-equilibrium processes, crowding and heterogeneity in active cytoskeletal systems. More generally, our approach is broadly applicable to active matter systems to elucidate transport and dynamics across scales.
Solomon-Lane, Tessa K., Rebecca M. Butler, Hans A. Hofmann. “Vasopressin Mediates Nonapeptide and Glucocorticoid Signaling and Social Dynamics in Juvenile Dominance Hierarchies of a Highly Social Cichlid Fish.” Hormones and Behavior, vol. 145, 2022, 105238.
Abstract: Early-life social experience can strongly affect adult behavior, yet the behavioral mechanisms underlying developmental trajectories are poorly understood. Here, we use the highly social cichlid, Burton's Mouthbrooder (Astatotilapia burtoni) to investigate juvenile social status and behavior, as well as the underlying neuroendocrine mechanisms. We placed juveniles in pairs or triads and found that they readily establish social status hierarchies, with some group structural variation depending on group size, as well as the relative body size of the group members. Next, we used intracerebroventricular injections to test the hypothesis that arginine vasopressin (AVP) regulates juvenile social behavior and status, similar to adult A. burtoni. While we found no direct behavioral effects of experimentally increasing (via vasotocin) or decreasing (via antagonist Manning Compound) AVP signaling, social interactions directed at the treated individual were significantly altered. This group-level effect of central AVP manipulation was also reflected in a significant shift in whole brain expression of genes involved in nonapeptide signaling (AVP, oxytocin, and oxytocin receptor) and the neuroendocrine stress axis (corticotropin-releasing factor (CRF), glucocorticoid receptors (GR) 1a and 1b). Further, social status was associated with the expression of genes involved in glucocorticoid signaling (GR1a, GR1b, GR2, mineralocorticoid receptor), social interactions with the dominant fish, and nonapeptide signaling activity (AVP, AVP receptor V1aR2, OTR). Together, our results considerably expand our understanding of the context-specific emergence of social dominance hierarchies in juveniles and demonstrate a role for nonapeptide and stress axis signaling in the regulation of social status and social group dynamics.
Thomson, Diane M., A. Kathryn McEachern, Emily L. Schultz*, Kenneth Niessen, Dieter Wilken, Katherine Chess, Lauren F. Cole*, Ruth Y. Oliver*, Jennifer D. Phillips*, and Acadia Tucker*. “Diverse Native Island Flora Shows Rapid Initial Passive Recovery after Exotic Herbivore Removal on Santa Rosa Island, California.” Biological Invasions, vol. 24, 2022, pp. 1635-1649.
Abstract: Removing exotic vertebrates from islands is an increasingly common and potentially effective strategy for protecting biodiversity. Yet, surprisingly few studies evaluate large-scale effects of island removals on native plants. We surveyed 431 hectares of habitat in 7 canyons on Santa Rosa Island just after exotic herbivore control began (1994–1996), and again after two herbivore species had been eradicated and ~ 90% of herbivores removed (2010–2012). We searched for 68 endemic and/or rare native plant taxa, mapping and recording abundances for the 39 found. Initially most of these 39 species were absent from most canyons (79.9% species-canyon combinations). Nearly 35% of absences changed to presences by 2010–2012, while only 5.5% of presences changed to absences. Thirty-six of these 39 species increased in total area, and 38 increased in total abundance. Graminoids increased more and shrubs less than other life histories, for both apparent colonizations and abundances. Beta diversity and species turnover between canyons was high at both surveys. Although a diversity of the 39 located taxa showed substantial gains, nearly half remained uncommon in 2010–2012. These results reinforce the devastating effects of exotic vertebrate herbivores on island native plants, particularly long-lived, slow-growing species. They also demonstrate significant potential benefits of exotic herbivore removal even without other active restoration, not only for vegetative cover but for a number of rare taxa. Our surveys were more spatially extensive than most post-removal studies; high spatial turnover in these data suggests that larger-scale monitoring may be critical to capture full effects of exotic animal removal.
Hansen, Katherine A., Rose R. Kim, Elisabeth S. Lawton, Janet Tran, Stephanie K. Lewis, Arjan S. Deol, and Ethan B. Van Arnam. “Bacterial Associates of a Desert Specialist Fungus-Growing Ant Antagonize Competitors with a Nocamycin Analog.” ACS Chemical Biology, vol. 17, no. 7, 2022, pp. 1824-1830.
Abstract: Fungus-growing ants are defended by antibiotic-producing bacterial symbionts in the genus Pseudonocardia. Nutrients provisioned by the ants support these symbionts but also invite colonization and competition from other bacteria. As an arena for chemically mediated bacterial competition, this niche offers a window into ecological antibiotic function with well-defined competing organisms. From multiple colonies of the desert specialist ant Trachymyrmex smithi, we isolated Amycolatopsis bacteria that inhibit the growth of Pseudonocardia symbionts under laboratory conditions. Using bioassay-guided fractionation, we discovered a novel analog of the antibiotic nocamycin that is responsible for this antagonism. We identified the biosynthetic gene cluster for this antibiotic, which has a suite of oxidative enzymes consistent with this molecule’s more extensive oxidative tailoring relative to similar tetramic acid antibiotics. High genetic similarity to globally distributed soil Amycolatopsis isolates suggest that this ant-derived Amycolatopsis strain may be an opportunistic soil strain whose antibiotic production allows for competition in this specialized niche. This nocamycin analog adds to the catalog of novel bioactive molecules isolated from bacterial associates of fungus-growing ants, and its activity against ant symbionts represents, to our knowledge, the first putative ecological function for the widely distributed enoyl tetramic acid family of antibiotics.
Westfield, Isaac, John Gunnell, Douglas B. Rasher, Branwen Williams, and Justin B. Ries. “Cessation of Hardground Accretion by the Cold-Water Coralline Algae Clathromorphum Cmopactum and Clathromorphum Nereostratum Predicted Within Two Centuries.” Geochemistry, Geophysics, Geosystems, vol. 23, issue 5, 2022, e2021GC00942.
Abstract: Ocean acidification and warming are expected to disproportionately affect high-latitude calcifying species, such as crustose coralline algae. Clathromorphum nereostratum and Clathromorphum compactum are the primary builders of carbonate-hardgrounds in the Aleutians Islands of Alaska and North Atlantic shelf, respectively, providing habitat and settlement substrates for a large number of species. We exposed wild-collected specimens to 12 pCO2/T treatments (344–3322 μatm; 6.38–12.40°C) for 4 months in a factorially crossed, replicated laboratory experiment. Impacts of pCO2/T on algal calcification were quantified from linear extension and buoyant weight. Here we show that, despite belonging to the same genus, C. nereostratum exhibited greater sensitivity to thermal stress, while C. compactum exhibited greater sensitivity to pH stress. Furthermore, multivariate models of algal calcification derived from the experiment indicate that both C. nereostratum and C. compactum will commence net dissolution as early as 2120 and 2200 AD, respectively. Our results therefore indicate that near-term climate change may lead to substantial degradation of these species and loss of the critical hardground habitats that they form.
External grant: Williams, Branwen. “Geoscience Research Experiences for Post-Baccalaureate Students (GEO-REPS) Supplemental Funding Opportunity.” National Science Foundation, 2022, $39,912.
External grant: Williams, Branwen, senior personnel; Srikandi Bahari, principal investigator. “A Gender-Inclusive Deep-Sea Research Expedition in the Indonesian Seas.” National Geographic, 2022, $150,000.
Liberman-Martin, Allegra L., Mary J. Van Vleet, Tamara Elenberger, Robert J. Cave, and Nancy S.B. Williams. “Geometric Control of Carbon-Carbon Reductive Elimination from a Platinum (IV) Pincer Complex.” Organometallics, vol. 41, 2022, pp. 3104-3108.
Abstract: In five-coordinate transition metal complexes, isomerization between square-pyramidal and trigonal-bipyramidal geometries is generally assumed to be rapid relative to reactions such as reductive elimination. Herein we report a system in which two square-pyramidal isomers of the same compound, [(NCN)Pt(Me)ap(Ph)ba]OTf and [(NCN)Pt(Ph)ap(Me)ba]OTf (ap = apical, ba = basal), undergo reductive elimination to form different products. For [(NCN)Pt(Me)ap(Ph)ba]OTf, methyl migration to the pincer aryl group occurs to form the σ-agostic complex [(N(C–Me)N)Pt(Ph)]OTf. In contrast, reductive elimination from [(NCN)Pt(Ph)ap(Me)ba]OTf affords toluene and (NCN)Pt(OTf). The observation of distinct products from these isomers demonstrates that isomerization between five-coordinate structures is slower than reductive elimination. DFT studies indicate that the barriers to these C–C couplings are dominated by the need for aryl groups to adopt a “face-on” configuration during reductive elimination, the steric requirements of which are kinetically prohibitive for some pathways in this system. Although the calculated barrier to isomerization is low enough for isomerization to be rapid at room temperature as expected, the activation barriers leading to experimentally observed carbon–carbon reductive elimination products are lower still, in agreement with experiment.