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1. Sensory perception plays a larger role in foraging efficiency than does heavy-tailed movement strategies.

   https://doi.org/doi:10.1016/j.ecolmodel.2019.02.015  

   LaScala-Gruenewald, DE; Mehta, RS; Denny, MW (January 2019, Ecological modelling)

   Animals must balance their rates of energetic intake and expenditure while foraging. Several mathematical models have been put forward as energetically optimal foraging strategies when the food environment is sparse (i.e., the distance between food patches in the environment is much larger than the distance from which the forager can perceive food). In particular, Lévy walks with a power law exponent approaching 1 are considered optimal for destructive foragers. However, these models have yet to explore the role of sensory perception in foraging success as the distance between food patches approaches the distance from which the forager can perceive food. Here, we used an agent-based modeling approach to address this question. Our results concur that lower values of the power law exponent (i.e. values approaching 1) result in the most food found, but in contrast to previous studies, we note that, in many cases, lower exponents are not optimal when we consider food found per unit distance traveled. For example, higher values of the exponent resulted in comparable or higher foraging success relative to lower values when the forager's range of sensory perception was restricted to an angle±30° from its current heading. In addition, we find that sensory perception has a larger effect on foraging success than the power law exponent. These results suggest that a deeper examination of how animals perceive food sources from a distance may affect longstanding assumptions regarding the optimality of Lévy walk foraging patterns, and lend support to the developing theoretical shift towards models that place increasing emphasis on how organisms interact with their environments. 

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2. Fascicle dynamics of the tibialis anterior muscle reflect whole-body walking economy

   https://doi.org/10.1038/S41598-023-31501-2  

   Kwak, Samuel T.; Chang, Young-Hui (December 2023, Scientific Reports)

   Humans can inherently adapt their gait pattern in a way that minimizes the metabolic cost of transport, or walking economy, within a few steps, which is faster than any known direct physiological sensor of metabolic energy. Instead, walking economy may be indirectly sensed through mechanoreceptors that correlate with the metabolic cost per step to make such gait adaptations. We tested whether velocity feedback from tibialis anterior (TA) muscle fascicles during the early stance phase of walking could potentially act to indirectly sense walking economy. As participants walked within a range of steady-state speeds and step frequencies, we observed that TA fascicles lengthen on almost every step. Moreover, the average peak fascicle velocity experienced during lengthening reflected the metabolic cost of transport of the given walking condition. We observed that the peak TA muscle activation occurred earlier than could be explained by a short latency reflex response. The activation of the TA muscle just prior to heel strike may serve as a prediction of the magnitude of the ground collision and the associated energy exchange. In this scenario, any unexpected length change experienced by the TA fascicle would serve as an error signal to the nervous system and provide additional information about energy lost per step. Our work helps provide a biomechanical framework to understand the possible neural mechanisms underlying the rapid optimization of walking economy. 

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3. Starvation reduces thermal limits of the widespread copepod Acartia tonsa

   https://doi.org/10.1002/ece3.10586  

   Rueda Moreno, Gaia; Sasaki, Matthew C. (October 2023, Ecology and Evolution)

   Abstract Organismal thermal limits affect a wide range of biogeographical and ecological processes. Copepods are some of the most abundant animals on the planet and play key roles in aquatic habitats. Despite their abundance and ecological importance, there is limited data on the factors that affect copepod thermal limits, impeding our ability to predict how aquatic ecosystems will be affected by anthropogenic climate change. In a warming ocean, one factor that may have particularly important effects on thermal limits is the availability of food. A recently proposed feedback loop known as “metabolic meltdown” suggests that starvation and exposure to high temperatures interact to drastically reduce organismal thermal limits, increasing vulnerability to warming. To investigate one component of this feedback loop, we examined how starvation affects thermal limits (critical thermal maxima: CT_max) ofAcartia tonsa, a widespread estuarine copepod. We found that there was no effect of short‐duration exposure to starvation (up to 2 days). However, after 3 days, there was a significant decrease in the CT_maxof starved copepods relative to the fed controls. Our results provide empirical evidence that extended periods of starvation reduce thermal limits, potentially initiating “metabolic meltdown” in this key species of coastal copepod. This suggests that changes in food availability may increase the vulnerability of copepods to increasing temperatures, amplifying the effects of climate change on coastal systems. 

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4. Metabolic model guided CRISPRi identifies a central role for phosphoglycerate mutase in Chlamydia trachomatis persistence

   https://doi.org/10.1128/msystems.00717-24  

   Chowdhury, Niaz Bahar; Pokorzynski, Nick; Rucks, Elizabeth A; Ouellette, Scot P; Carabeo, Rey A; Saha, Rajib (July 2024, mSystems)

   Imam, Saheed (Ed.)

   ABSTRACT Upon nutrient starvation,Chlamydia trachomatisserovar L2 (CTL) shifts from its normal growth to a non-replicating form, termed persistence. It is unclear if persistence reflects an adaptive response or a lack thereof. To understand this, transcriptomics data were collected for CTL grown under nutrient-replete and nutrient-starved conditions. Applying K-means clustering on transcriptomics data revealed a global transcriptomic rewiring of CTL under stress conditions in the absence of any canonical global stress regulator. This is consistent with previous data that suggested that CTL’s stress response is due to a lack of an adaptive response mechanism. To investigate the impact of this on CTL metabolism, we reconstructed a genome-scale metabolic model of CTL (iCTL278) and contextualized it with the collected transcriptomics data. Using the metabolic bottleneck analysis on contextualized iCTL278, we observed that phosphoglycerate mutase (pgm) regulates the entry of CTL to the persistence state. Our data indicate thatpgmhas the highest thermodynamics driving force and lowest enzymatic cost. Furthermore, CRISPRi-driven knockdown ofpgmin the presence or absence of tryptophan revealed the importance of this gene in modulating persistence. Hence, this work, for the first time, introduces thermodynamics and enzyme cost as tools to gain a deeper understanding on CTL persistence. IMPORTANCEThis study uses a metabolic model to investigate factors that contribute to the persistence ofChlamydia trachomatisserovar L2 (CTL) under tryptophan and iron starvation conditions. As CTL lacks many canonical transcriptional regulators, the model was used to assess two prevailing hypotheses on persistence—that the chlamydial response to nutrient starvation represents a passive response due to the lack of regulators or that it is an active response by the bacterium. K-means clustering of stress-induced transcriptomics data revealed striking evidence in favor of the lack of adaptive (i.e., a passive) response. To find the metabolic signature of this, metabolic modeling pin-pointed pgm as a potential regulator of persistence. Thermodynamic driving force, enzyme cost, and CRISPRi knockdown of pgm supported this finding. Overall, this work introduces thermodynamic driving force and enzyme cost as a tool to understand chlamydial persistence, demonstrating how systems biology-guided CRISPRi can unravel complex bacterial phenomena. 

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5. mRNA Degradation Rates Are Coupled to Metabolic Status in Mycobacterium smegmatis

   https://doi.org/10.1128/mBio.00957-19  

   Vargas-Blanco, Diego A.; Zhou, Ying; Zamalloa, L. Gregory; Antonelli, Tim; Shell, Scarlet S.; Barkan, Daniel (August 2019, mBio)

   ABSTRACT The success of Mycobacterium tuberculosis as a human pathogen is due in part to its ability to survive stress conditions, such as hypoxia or nutrient deprivation, by entering nongrowing states. In these low-metabolism states, M. tuberculosis can tolerate antibiotics and develop genetically encoded antibiotic resistance, making its metabolic adaptation to stress crucial for survival. Numerous bacteria, including M. tuberculosis , have been shown to reduce their rates of mRNA degradation under growth limitation and stress. While the existence of this response appears to be conserved across species, the underlying bacterial mRNA stabilization mechanisms remain unknown. To better understand the biology of nongrowing mycobacteria, we sought to identify the mechanistic basis of mRNA stabilization in the nonpathogenic model Mycobacterium smegmatis . We found that mRNA half-life was responsive to energy stress, with carbon starvation and hypoxia causing global mRNA stabilization. This global stabilization was rapidly reversed when hypoxia-adapted cultures were reexposed to oxygen, even in the absence of new transcription. The stringent response and RNase levels did not explain mRNA stabilization, nor did transcript abundance. This led us to hypothesize that metabolic changes during growth cessation impact the activities of degradation proteins, increasing mRNA stability. Indeed, bedaquiline and isoniazid, two drugs with opposing effects on cellular energy status, had opposite effects on mRNA half-lives in growth-arrested cells. Taken together, our results indicate that mRNA stability in mycobacteria is not directly regulated by growth status but rather is dependent on the status of energy metabolism. IMPORTANCE The logistics of tuberculosis therapy are difficult, requiring multiple drugs for many months. Mycobacterium tuberculosis survives in part by entering nongrowing states in which it is metabolically less active and thus less susceptible to antibiotics. Basic knowledge on how M. tuberculosis survives during these low-metabolism states is incomplete, and we hypothesize that optimized energy resource management is important. Here, we report that slowed mRNA turnover is a common feature of mycobacteria under energy stress but is not dependent on the mechanisms that have generally been postulated in the literature. Finally, we found that mRNA stability and growth status can be decoupled by a drug that causes growth arrest but increases metabolic activity, indicating that mRNA stability responds to metabolic status rather than to growth rate per se . Our findings suggest a need to reorient studies of global mRNA stabilization to identify novel mechanisms that are presumably responsible. 

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