bluuebunny/crossref_metadata_2025 huggingface dataset:
Drug dependence in cancer is exploitable by optimally constructed treatment holidays
Authors: Maltas Jeff , Singleton Katherine R. , Wood Kris C. , Wood Kevin B.
Published: July 2022

Recent work in cell culture models, animal models, and human patients indicates that cancers with acquired resistance to a drug can become simultaneously dependent upon the presence of that drug for survival. This drug dependence offers a potential avenue for improving treatments aimed at slowing resistance, yet relatively little is known about the frequency with which drug dependence arises, the mechanisms underlying that dependence, and how drug schedules might be tuned to optimally exploit drug dependence. In this work, we address these open questions using a combination of laboratory evolution, in vitro experiments, and simple mathematical models. First, we used laboratory evolution to select more than 100 resistant BRAF mutant melanoma cell lines with acquired resistance to BRAF, MEK, or ERK inhibitors. We found that nearly half of these lines exhibit drug dependence, and the dependency response is associated with EGFR-driven senescence induction, but not apoptosis, following drug withdrawal. Then, using melanoma populations with evolved resistance to the BRAF inhibitor PLX4720, we showed that drug dependence can be leveraged to dramatically reduce population growth when treatment strategies include optimally chosen drug-free “holidays”. On short timescales, the duration of these holidays depends sensitively on the composition of the population, but for sufficiently long treatments it depends only on a single dimensionless parameter (γ) that describes how the growth rates of each cell type depend on the different treatment environments. Experiments confirm that the optimal holiday duration changes in time–with holidays of different durations leading to optimized treatments on different timescales. Furthermore, we find that the presence of “non-dependent” resistant cells does not change the optimal treatment schedule but leads to a net increase in population size. Finally, we show that even in the absence of detailed information about the composition and growth characteristics of cellular clones within a population, a simple adaptive therapy protocol can produce near-optimal outcomes using only measurements of total population size, at least when these measurements are sufficiently frequent. As a whole, these results may provide a stepping-stone toward the eventual development of evolution-inspired treatment strategies for drug dependent cancers.
Morphological and genetic diversity of maize landraces along an altitudinal gradient in the Southern Andes
Authors: Rivas Juan G. , Gutierrez Angela V. , Defacio Raquel A. , Schimpf Jorge , Vicario Ana L. , Hopp H. Esteban , Paniego Norma B. , Lia Veronica V.
Published: July 2022

Maize (Zea mays ssp. mays) is a major cereal crop worldwide and is traditionally or commercially cultivated almost all over the Americas. The northwestern region of Argentina (NWA) constitutes one of the main diversity hotspots of the Southern Andes, with contrasting landscapes and a large number of landraces. Despite the extensive collections performed by the “Banco Activo de Germoplasma INTA Pergamino, Argentina” (BAP), most of them have not been characterized yet. Here we report the morphological and molecular evaluation of 30 accessions collected from NWA, along an altitudinal gradient between 1120 and 2950 meters above sea level (masl). Assessment of morphological variation in a common garden allowed the discrimination of two groups, which differed mainly in endosperm type and overall plant size. Although the groups retrieved by the molecular analyses were not consistent with morphological clusters, they showed a clear pattern of altitudinal structuring. Affinities among accessions were not in accordance with racial assignments. Overall, our results revealed that there are two maize gene pools co-existing in NWA, probably resulting from various waves of maize introduction in pre-Columbian times as well as from the adoption of modern varieties by local farmers.

In conclusion, the NWA maize landraces preserved at the BAP possess high morphological and molecular variability. Our results highlight their potential as a source of diversity for increasing the genetic basis of breeding programs and provide useful information to guide future sampling and conservation efforts.
The mosquito vectors that sustained malaria transmission during the Magude project despite the combined deployment of indoor residual spraying, insecticide-treated nets and mass-drug administration
Authors: Montoya Lucia Fernandez , Martí-Soler Helena , Máquina Mara , Comiche Kiba , Cuamba Inocencia , Alafo Celso , Koekemoer Lizette L. , Sherrard-Smith Ellie , Bassat Quique , Galatas Beatriz , Aide Pedro , Cuamba Nelson , Jotamo Dulcisaria , Saúte Francisco , Paaijmans Krijn P.
Published: July 2022

The “Magude project” aimed but failed to interrupt local malaria transmission in Magude district, southern Mozambique, by using a comprehensive package of interventions, including indoor residual spraying (IRS), pyrethroid-only long-lasting insecticide treated nets (LLINs) and mass-drug administration (MDA). Here we present detailed information on the vector species that sustained malaria transmission, their association with malaria incidence and behaviors, and their amenability to the implemented control interventions. Mosquitoes were collected monthly between May 2015 and October 2017 in six sentinel sites in Magude district, using CDC light traps both indoors and outdoors. Anopheles arabiensis was the main vector during the project, while An. funestus s.s., An. merus, An. parensis and An. squamosus likely played a secondary role. The latter two species have never previously been found positive for Plasmodium falciparum in southern Mozambique. The intervention package successfully reduced vector sporozoite rates in all species throughout the project. IRS was effective in controlling An. funestus s.s. and An. parensis, which virtually disappeared after its first implementation, but less effective at controlling An. arabiensis. Despite suboptimal use, LLINs likely provided significant protection against An. arabiensis and An. merus that sought their host largely indoors when people where in bed. Adding IRS on top of LLINs and MDA likely added value to the control of malaria vectors during the Magude project. Future malaria elimination attempts in the area could benefit from i) increasing the use of LLINs, ii) using longer-lasting IRS products to counteract the increase in vector densities observed towards the end of the high transmission season, and iii) a higher coverage with MDA to reduce the likelihood of human infection. However, additional interventions targeting vectors that survive IRS and LLINs b,y e.g. biting outdoors or indoors before people go to bed, will be likely needed to achieve local malaria elimination.
Retrograde axonal autophagy and endocytic pathways are parallel but separate in neurons
Authors: Kulkarni Vineet Vinay , Stempel Max Henry , Anand Anip , Sidibe David Kader , Maday Sandra
Published: July 2022

Autophagy and endocytic trafficking are two key pathways that regulate the composition and integrity of the neuronal proteome. Alterations in these pathways are sufficient to cause neurodevelopmental and neurodegenerative disorders. Thus, defining how autophagy and endocytic pathways are organized in neurons remains a key area of investigation. These pathways share many features and converge on lysosomes for cargo degradation, but what remains unclear is the degree to which the identity of each pathway is preserved in each compartment of the neuron. Here, we elucidate the degree of intersection between autophagic and endocytic pathways in axons of primary neurons. Using microfluidic chambers, we labeled newly-generated bulk endosomes and signaling endosomes in the distal axon, and systematically tracked their trajectories, molecular composition, and functional characteristics relative to autophagosomes. We find that newly-formed endosomes and autophagosomes both undergo retrograde transport in the axon, but as distinct organelle populations. Moreover, these pathways differ in their degree of acidification and association with molecular determinants of organelle maturation. These results suggest that the identity of autophagic and newly endocytosed organelles is preserved for the length of the axon. Lastly, we find that expression of a pathogenic form of α-synuclein, a protein enriched in presynaptic terminals, increases merging between autophagic and endocytic pathways. Thus, aberrant merging of these pathways may represent a mechanism contributing to neuronal dysfunction in Parkinson’s disease and related α-synucleinopathies.

SIGNIFICANCE STATEMENT

Autophagy and endocytic trafficking are retrograde pathways in neuronal axons that fulfill critical degradative and signaling functions. These pathways share many features and converge on lysosomes for cargo degradation, but the extent to which the identity of each pathway is preserved in axons is unclear. We find that autophagosomes and endosomes formed in the distal axon undergo retrograde transport to the soma in parallel but separate pathways. These pathways also have distinct maturation profiles along the mid-axon, further highlighting differences in the potential fate of transported cargo. Strikingly, expression of a pathogenic variant of α-synuclein increases merging between autophagic and endocytic pathways, suggesting that mis-sorting of axonal cargo may contribute to neuronal dysfunction in Parkinson’s disease and related α-synucleinopathies.
In vivo spatiotemporal dynamics of astrocyte reactivity following neural electrode implantation
Authors: Savya Sajishnu P , Li Fan , Lam Stephanie , Wellman Steven M. , Stieger Kevin C. , Chen Keying , Eles James R. , Kozai Takashi D.Y.
Published: July 2022

Brain computer interfaces (BCIs), including penetrating microelectrode arrays, enable both recording and stimulation of neuronal cells. However, device implantation inevitably causes injury to brain tissue and induces a foreign body response, leading to reduced recording performance and stimulation efficacy. Astrocytes in the healthy brain play multiple roles including regulating energy metabolism, homeostatic balance, transmission of neural signals, and neurovascular coupling. Following an insult to the brain, they are activated and observed to gather around the site of injury. These reactive astrocytes have been regarded as one of the main contributors to the formation of a glial scar which affects the performance of microelectrode arrays. This study investigates the dynamics of astrocytes within the first 2 weeks after implantation of an intracortical microelectrode into the mouse brain using two-photon microscopy. From our observation astrocytes are highly dynamic during this period, exhibiting patterns of process extension, soma migration, morphological activation, and device encapsulation that are spatiotemporally distinct from other glial cells, such as microglia or oligodendrocyte precursor cells. This detailed characterization of astrocyte reactivity will help to better understand the tissue response to intracortical devices and lead to the development of more effective intervention strategies to improve the functional performance neural interfacing technology.
Responses of thein vitroturtle brain to visual and auditory stimuli during severe hypoxia
Authors: Ariel Michael , Ahuja Shivika , Warren Daniel E.
Published: July 2022

North American pond turtles (Emydidae) are renowned for their ability to survive extreme hypoxia and anoxia, which enables several species to overwinter in ice-locked, anoxic freshwater ponds and bogs for months. Centrally important for surviving these conditions is a profound metabolic suppression, which enables ATP demands to be met entirely with glycolysis. Despite this, turtles have occasionally been observed exploring their natural and laboratory environments while anoxic and can still respond to sensory stimuli. To better understand whether anoxia limits a special sensory function, we recorded evoked potentials in a reduced brain preparation,in vitro,that was perfused with severely hypoxic artificial cerebral spinal fluid (aCSF). For recordings of visual responses, an LED light was flashed onto retinal eyecups while evoked potentials were recorded from the retina or the optic tectum. For recordings of auditory responses, a piezo motor-controlled glass actuator vibrated the tympanic membrane while evoked potentials were recorded from the cochlear nuclei. We found that visual responses decreased even with moderately hypoxic perfusate (aCSF PO2= 30-60 torr) and completely abolished under severe hypoxia. In contrast, the evoked response within the cochlear nuclei was unattenuated with severe hypoxia (aCSF PO2< 20 torr). These data provide further support that pond turtles have a limited ability to sense visual information in their environment even while moderately hypoxic, but that auditory input may become a principal avenue of sensory perception during extreme diving in this species.

Summary Statement

Severe hypoxia attenuates the visual, but not auditory responses in a reduced brain preparation from a pond turtle.
A biophysical minimal model to investigate age-related changes in CA1 pyramidal cell electrical activity
Authors: McKiernan Erin C. , Herrera-Valdez Marco A. , Marrone Diano F.
Published: July 2022

Aging is a physiological process that is still poorly understood, especially with respect to effects on the brain. There are open questions about aging that are difficult to answer with an experimental approach. Underlying challenges include the difficulty of recordingin vivosingle cell and network activity simultaneously with submillisecond resolution, and brain compensatory mechanisms triggered by genetic, pharmacologic, or behavioral manipulations. Mathematical modeling can help address some of these questions by allowing us to fix parameters that cannot be controlled experimentally and investigate neural activity under different conditions. We present a biophysical minimal model of CA1 pyramidal cells (PCs) based on general expressions for transmembrane ion transport derived from basic thermodynamical principles. The model allows directly varying the contribution of ion channels by changing their number. By analyzing the dynamics of the model, we find parameter ranges that reproduce the variability in electrical activity seen in PCs. In addition, increasing the L-type Ca2+channel expression in the model reproduces age-related changes in excitability that are qualitatively and quantitatively similar to those observed in PCs from aged animals.
Recombination rate inference via deep learning is limited by sequence diversity
Authors: Johnson Mackenzie M. , Wilke Claus O.
Published: July 2022

A common inference task in population genetics is to estimate recombination rate from multiple sequence alignments. Traditionally, recombination rate estimators have been developed from biologically-informed, statistical models, but more recently deep learning models have been employed for this task. While deep learning approaches offer unique advantages, their performance is inconsistent across the range of potential recombination rates. Here, we generate and characterize data sets (genotype alignments with known recombination rates) for use by deep learning estimators and assess how their features limit estimator performance. We find that certain input parameter regimes produce genotype alignments with low sequence diversity, which are inherently information-limited. We next test how estimator performance is impacted by training and evaluating neural networks on data sets with varying degrees of diversity. The inclusion of genotype alignments with low diversity at high frequency results in considerable performance declines across two different network architectures. In aggregate, our results suggest that genotype alignments have inherent information limits when sequence diversity is low, and these limitations need to be considered both when training deep learning recombination rate estimators and when using them in inference applications.
Quantifying trade-offs in the choice of ribosomal barcoding markers for fungal amplicon sequencing: a case study on the grapevine trunk mycobiome
Authors: Monod Vinciane , Hofstetter Valérie , Zufferey Vivian , Viret Olivier , Gindro Katia , Croll Daniel
Published: July 2022

The evolution of sequencing technology and multiplexing has rapidly expanded our ability to characterize fungal diversity in the environment. However, obtaining an unbiased assessment of the fungal community using ribosomal markers remains challenging. Longer amplicons were shown to improve taxonomic resolution and resolve ambiguities by reducing the risk of spurious operational taxonomic units. We examined the implications of barcoding strategies by amplifying and sequencing two ribosomal DNA fragments. We analyzed the performance of the full internal transcribed spacer (ITS) and a longer fragment including also a part of the 28S replicated on 60 grapevine trunk core samples. Grapevine trunks harbor highly diverse fungal communities with implications for disease development. Using identical handling, amplification and sequencing procedures, we obtained higher sequencing depths for the shorter ITS amplicon. Despite the more limited access to polymorphism, the overall diversity in amplified sequence variants was higher for the shorter ITS amplicon. We detected no meaningful bias in the phylogenetic composition due to the amplicon choice across analyzed samples. Despite the increased resolution of the longer ITS-28S amplicon, the higher and more consistent yields of the shorter amplicons produced a clearer resolution of the fungal community of grapevine stem samples. Our study highlights that the choice of ribosomal amplicons should be carefully evaluated and adjusted according to specific goals.
Two notorious nodes: a critical examination of MCMCTree relaxed molecular clock estimates of the bilaterian animals and placental mammals
Authors: Budd Graham E. , Mann Richard P.
Published: July 2022

The popularity of MCMCTree for Bayesian inference of clade origin timings has generated several recent publications with focal results considerably older than the fossils of the clades in question. Here we critically examine two such clades; the animals (with focus on the bilaterians) and the mammals (with focus on the placentals). Each example displays a set of characteristic pathologies which, although much commented on, are rarely corrected for. We conclude that in neither case does the molecular clock analysis provide any evidence for an origin of the clade deeper than what the fossil record might suggest. In addition, both these clades have other features (including, in the case of the placental mammals, proximity to a large mass extinction) that allow us to generate precise expectations of the timings of their origins. Thus, in these instances the fossil record can provide a powerful test of molecular clock methodology, and why it goes astray.
Differential stage-specific mortality as a mechanism for diversification
Authors: Chaparro-Pedraza P. Catalina
Published: July 2022

Individual variability in mortality is widespread in nature. The general rule is that larger organisms have a greater chance of survival than smaller conspecifics. There is growing evidence that differential mortality between developmental stages has important consequences for the ecology and evolution of populations and communities. However, we know little about how it can influence diversification. Using an eco-evolutionary model of diversification that considers individual variability in mortality, we show that commonly observed differences in mortality between juveniles and adults facilitate ecological diversification. We find that juvenile-biased mortality reduces the threshold of minimum resource productivity required for diversification. Diversification is hence less restricted when mortality is more biased towards juveniles than when all individuals experience the same mortality rate. This is because, by altering the population composition, juvenile-biased mortality increases the strength of intraspecific competition. Strong intraspecific competition in turn induces frequency-dependent selection, which drives ecological diversification. Our results demonstrate the strong influence that differential mortality between developmental stages has on diversification, and highlight the need for integrating developmental processes into the theoretical framework of diversification.
Single-component multilayered self-assembling protein nanoparticles presenting glycan-trimmed uncleaved prefusion optimized envelope trimers as HIV-1 vaccine candidates
Authors: Zhang Yi-Nan , Paynter Jennifer , Antanasijevic Aleksandar , Allen Joel D. , Eldad Mor , Lee Yi-Zong , Copps Jeffrey , Newby Maddy , He Linling , Chavez Deborah , Frost Pat , Goodroe Anna , Dutton John , Lanford Robert , Chen Christopher , Wilson Ian A. , Crispin Max , Ward Andrew B. , Zhu Jiang
Published: July 2022

Uncleaved prefusion-optimized (UFO) design can stabilize diverse HIV-1 envelope glycoproteins (Envs). Single-component, self-assembling protein nanoparticles (1c-SApNP) can display 8 or 20 trimeric antigens as multivalent vaccines. Here, we characterized the biophysical, structural, and antigenic properties of 1c-SApNPs that present the BG505 UFO trimer with wildtype and modified glycans. Trimming the glycan shield improved Env recognition by broadly neutralizing antibodies (bNAbs) to the CD4 binding site and other major glycan-containing epitopes. In mice, rabbits, and nonhuman primates, glycan trimming increased the frequency of vaccine responders (FVR) and steered antibody responses away from immunodominant glycan holes and glycan epitopes. The mechanism of vaccine-induced immunity was examined in mice. Compared with the soluble trimer, two large 1c-SApNPs showed 420 times longer retention, 20-32 times greater presentation on follicular dendritic cell dendrites, and up-to-4 times stronger germinal center reactions in lymph node follicles. These findings will inform the next phase of HIV-1 vaccine development.

ONE-SENTENCE SUMMARY

Glycan trimming of HIV-1 Env immunogens improves the vaccine-induced neutralizing antibody responses in small animals and primates
Stress-induced plasticity of a novel CRHGABA projection disrupts reward behaviors
Authors: Birnie Matthew T. , Short Annabel K. , de Carvalho Gregory B. , Gunn Benjamin G. , Pham Aidan L. , Itoga Christy A. , Xu Xiangmin , Chen Lulu Y. , Mahler Stephen V. , Chen Yuncai , Baram Tallie Z.
Published: July 2022

Disrupted operations of the reward circuit are thought to underlie major emotional disorders including depression and drug abuse1–3. These disorders commonly arise following early life stress4,5; however, how stress early in life enduringly impacts reward circuit functions to promote disease remains unclear. Here, we discover and characterize a novel stress-sensitive reward-circuit projection connecting the basolateral amygdala (BLA) and nucleus accumbens (NAc) that co-expresses GABA and the stress-reactive neuropeptide corticotropin-releasing hormone (CRH). We then identify a crucial role for this projection in executing the disrupted reward behaviors provoked by early-life adversity (ELA): Chemogenetic and optogenetic stimulations of the CRHGABA BLA→NAc projection in typically reared mice suppressed several reward seeking behaviors, recapitulating deficits resulting from ELA and demonstrating a key contribution of this pathway in the normal operations of the reward circuit. Next, inhibition of the CRHGABA BLA→NAc projection in adult mice that experienced ELA restored typical reward behaviors in these mice, and, in contrast, had little effect in typically reared mice, indicating a selective ELA-induced maladaptive plasticity of this reward-circuit projection. We discover a novel, stress-sensitive, reward inhibiting projection from the BLA→NAc with unique molecular features, which may provide targets for intervention in disabling mental illnesses.
Anatomical and biophysical characterization of intergeneric graft-incompatibility within the Solanoideae
Authors: Thomas Hannah R , Gevorgyan Alice , Frank Margaret H
Published: July 2022

Interspecies grafting is a technique that allows beneficial shoot and root combinations from separate species to be combined into a single organism. Despite its relevance to agricultural production, little is known about the determinants of graft compatibility. One hypothesis for compatibility revolves around the taxonomic degree of relatedness between the two plants. To test how phylogenetic distance affects interspecific graft compatibility within the economically important Solanaceae sub-family, Solanoideae, we characterized the anatomical and biophysical integrity of graft junctions for graft combinations made between four species: tomato (Solanum lycopersicum), eggplant (Solanum melongena), pepper (Capsicum annuum), and groundcherry (Physalis pubescens). We analyzed the survival, growth, and junction integrity via bend tests, and imaged the cellular composition of the graft junctions in order to deduce the status of vascular connectivity across the junction. Utilizing these techniques, we were able to quantitatively assess the degree to which each interspecific combination exhibits compatibility. Despite the fact that most of our graft combinations exhibited high survival rates, we show that only tomato and eggplant heterografts are truly compatible. Unlike incompatible grafts, the formation of reconnected vascular tissue within the tomato and eggplant heterografts contributed to biophysically stable grafts that were resistant to snapping. Furthermore, we identified 10 graft combinations that show delayed incompatibility, providing a useful, economically relevant system to pursue deeper work into genetic and genomic determinants of graft compatibility. This work provides new evidence indicating that graft compatibility may be limited to intrageneric combinations within the Solanoideae subfamily. Further research using more extensive graft combinations amongst Solanaceous species can be used to test whether our hypothesis broadly applies to this family.
Exploring Taxonomic and Functional Microbiome of Hawaiian Stream and Spring Irrigation Water Systems Using Illumina and Oxford Nanopore Sequencing Platforms
Authors: Klair Diksha , Dobhal Shefali , Ahmed Amjad , Hassan Zohaib Ul , Uyeda Jensen , Silva Joshua , Wang Koon-Hui , Kim Seil , Alvarez Anne M. , Arif Mohammad
Published: July 2022

Irrigation water is a potential source of contamination that carries plant and foodborne human pathogens and provides a niche for survival and proliferation of microbes in agricultural settings. This project investigated bacterial communities and their functions in the irrigation water from wetland taro farms on Oahu, Hawai’i using different DNA sequencing platforms. Irrigation water samples (stream, spring, and tank stored water) were collected from North, East, and West sides of Oahu and subjected to high quality DNA isolation, library preparation and sequencing of the V3-V4 region, full length 16S rRNA, and shotgun metagenome sequencing using Illumina iSeq100, Oxford Nanopore MinION and Illumina NovaSeq, respectively. Illumina reads provided the most comprehensive taxonomic classification at the phylum level where Proteobacteria was identified as the most abundant phyla in river stream source and associated wet taro field water samples. Cyanobacteria was also a dominant phylum from tank and spring water, whereas Bacteroidetes were most abundant in wetland taro fields irrigated with spring water. However, over 50% of the valid short amplicon reads remained unclassified and inconclusive at the species level. Whereas samples sequenced for full length 16S rRNA and shotgun metagenome, clearly illustrated that Oxford Nanopore MinION is a better choice to classify the microbes to the genus and species levels. In terms of functional analyses, only 12% of the genes were shared by two consortia. Total 95 antibiotic resistant genes (ARGs) were detected with variable relative abundance. Description of microbial communities and their functions are essential for the development of better water management strategies to produce safer fresh produce and to protect plant, animal, human and environmental health. This project identified analytical tools to study microbiome of irrigation water.
Complex functional phenotypes of NMDA receptor disease variants
Authors: Iacobucci Gary J , Liu Beiying , Wen Han , Sincox Brittany , Zheng Wenjun , Popescu Gabriela K.
Published: July 2022

NMDA receptors have essential roles in the physiology of central excitatory synapses and their dysfunction causes severe neuropsychiatric symptoms. Recently, a series of genetic variants have been identified in patients, however, functional information about these variants is sparse and their role in pathogenesis insufficiently known. Here we investigate the mechanism by which two GluN2A variants may be pathogenic. We use molecular dynamics simulation and single-molecule electrophysiology to examine the contribution of GluN2A subunit-residues, P552 and F652, and their pathogenic substitutions, P552R and F652V, affect receptor functions. We found that P552 and F652 interact during the receptors’ normal activity cycle; the interaction stabilizes receptors in open conformations and is required for a normal electrical response. Engineering shorter side-chains at these positions (P552A and/or F652V) caused a loss of interaction energy and produced receptors with severe gating, conductance, and permeability deficits. In contrast, the P552R sidechain resulted in stronger interaction and produced a distinct, yet still drastically abnormal electrical response. These results identify the dynamic contact between P552 and F652 as a critical step in the NMDA receptor activation, and show that both increased and reduced communication through this interaction cause dysfunction. Results show that subtle differences in NMDA receptor primary structure can generate complex phenotypic alterations whose binary classification is too simplistic to serve as a therapeutic guide.

Main findings

Two NMDA receptor residues whose substitution results in encephalopathies, were found to form new interactions during activation, and the energy provided by this interaction is required for normal receptor gating.

Experimental substitutions of these residues that change the strength of their interaction reduce the receptor open probability, unitary conductance, and calcium permeability.

Receptors with variations at these positions identified in patients display a broad range of both gain- and loss-of-function changes depending on the stimulation protocol.
Aggressive interactions between smooth-coated otters and water monitor lizards in Singapore
Authors: Bungum Haaken Zhong , Johns Philip
Published: July 2022

Smooth-coated otters (Lutrogale perspicillata) and Malayan water monitor lizards (Varanus salvator) occupy similar habitats and and interact regularly in Singapore’s waterways. These interactions have a range of potential outcomes and are sometimes lethal. Few formal behavioral studies exist for either species. We analyzed interactions between otters and monitor lizards by gleaning data from publicly available videos from citizen scientists to examine what factors influence aggressive and defensive behaviors, and what influences vigilance in otters. Behavioral sequence analysis revealed no obvious monitor lizard behavior that predicted otter aggression towards monitors. We found that the presence and number of otter pups is positively associated with otter aggression. Otters also tended to be more vigilant in groups with more pups, and more vigilant on land than water. Monitor lizards displayed aggressive and defensive behaviors more frequently than did otters, regardless of whether the otters were aggressive towards lizards. These observations suggests that otters vary their aggression and vigilance levels depending on the context of each interaction.
Comparative study of bacterial SPOR domains identifies functionally important differences in glycan binding affinity
Authors: Yahashiri Atsushi , Kaus Gabriela M. , Popham David L. , Houtman Jon C.D. , Weiss David S.
Published: July 2022

Bacterial SPOR domains target proteins to the divisome by binding septal peptidoglycan (PG) at sites where cell wall amidases have removed stem peptides. These PG structures are referred to as denuded glycans. Although all characterized SPOR domains bind denuded glycans, whether there are differences in affinity is not known. Here we use isothermal titration calorimetry (ITC) to determine the relative PG glycan binding affinity (Kd) of four Escherichia coli SPOR domains and one Cytophaga hutchinsonii SPOR domain. We found that the Kd values ranged from approximately 1 µM for E. coli DamXSPOR and C. hutchinsonii CHU2221SPOR to about 10 µM for E. coli FtsNSPOR. To ask whether these differences in PG binding affinity are important for SPOR domain protein function, we constructed and characterized a set of DamX and FtsN “swap” proteins. As expected, all SPOR domain swap proteins localized to the division site, and in the case of FtsN all of the heterologous SPOR domains supported cell division. But for DamX only the high-affinity SPOR domain from CHU2221 supported normal function in cell division. In summary, different SPOR domains bind denuded PG glycans with different affinity, which appears to be very important for the function of some SPOR domain proteins (e.g., DamX) but not others (e.g., FtsN).

Importance

SPOR domain proteins are prominent components of the cell division apparatus in a wide variety of bacteria. The primary function of SPOR domains is to target proteins to the division site, which they accomplish by binding to septal peptidoglycan. But whether SPOR domains have any functions beyond septal targeting is unknown. Here we show that SPOR domains vary in their PG binding affinities and, at least in the case of the E. coli cell division protein DamX, having a high-affinity SPOR domain contributes to proper function.
Reconstruction and analysis of thermodynamically-constrained models reveal metabolic responses of a deep-sea bacterium to temperature perturbations
Authors: Dufault-Thompson Keith , Nie Chang , Jian Huahua , Wang Fengping , Zhang Ying
Published: July 2022

Microbial acclimation to different temperature conditions can involve broad changes in cell composition and metabolic efficiency. A systems-level view of these metabolic responses in non-mesophilic organisms, however, is currently missing. In this study, thermodynamically-constrained genome-scale models were applied to simulate the metabolic responses of a deep-sea psychrophilic bacterium, Shewanella psychrophila WP2, under suboptimal (4°C), optimal (15°C), and supraoptimal (20°C) growth temperatures. The models were calibrated with experimentally determined growth rates of WP2. Gibbs free energy change of reactions (ΔrG’), metabolic fluxes, and metabolite concentrations were predicted using random simulations to characterize temperature-dependent changes in the metabolism. The modeling revealed the highest metabolic efficiency at the optimal temperature, and it suggested distinct patterns of ATP production and consumption that could lead to the lower metabolic efficiency under suboptimal or supraoptimal temperatures. The modeling also predicted rearrangement of fluxes through multiple metabolic pathways, including the glycolysis pathway, Entner-Doudoroff pathway, tricarboxylic acid (TCA) cycle, and the electron transport system, and these predictions were corroborated through comparisons to WP2 transcriptomes. Furthermore, predictions of metabolite concentrations revealed the potential conservation of reducing equivalents and ATP in the suboptimal temperature, consistent with experimental observations from other psychrophiles. Taken together, the WP2 models provided mechanistic insights into the metabolism of a psychrophile in response to different temperatures.

Importance

Metabolic flexibility is a central component of any organism’s ability to survive and adapt to changes in environmental conditions. This study represents the first application of thermodynamically-constrained genome-scale models in simulating the metabolic responses of a deep-sea psychrophilic bacterium to varying temperatures. The models predicted differences in metabolic efficiency that were attributed to changes in metabolic pathway utilization and metabolite concentration during growth under optimal and non-optimal temperatures. Experimental growth measurements were used for model calibration, and temperature-dependent transcriptomic changes corroborated the model-predicted rearrangement of metabolic fluxes. Overall, this study highlights the utility of modeling approaches in studying the temperature-driven metabolic responses of an extremophilic organism.
Rapid monitoring for ecological persistence
Authors: Song Chuliang , Simmons Benno I. , Fortin Marie-Josée , Gonzalez Andrew , Kaiser-Bunbury Christopher N. , Saavedra Serguei
Published: July 2022

Effective conservation of ecological communities requires accurate and up-to-date information about whether species are persisting or declining to extinction. The persistence of ecological communities is largely supported by its structured architecture of species interactions, known as an ecological network. While the persistence of the network supporting the whole community is the most relevant scale for conservation, in practice, we can only monitor small subsets of these networks due to logistical sampling constraints. There is therefore an urgent need to establish links between the small snapshots of data conservationists are able to collect, and the ‘big picture’ conclusions about ecosystem health demanded by policy makers, scientists and societies. Here we show that the persistence of small subnetworks in isolation — that is, their persistence when considered separately from the larger network of which they are a part — is a reliable probabilistic indicator of the persistence of the network as a whole. Our results are general across both antagonistic and mutualistic interaction networks. Empirically, we show that our theoretical predictions are supported by data on invaded networks in restored and unrestored areas, even in the presence of environmental variability. Our work suggests that coordinated action to aggregate information from incomplete sampling can provide a means to rapidly assess the persistence of entire ecological networks and the expected success of restoration strategies. This could significantly improve our ability to monitor progress towards achieving policy targets, such as those enshrined in the UN Convention on Biological Diversity.
Aesthetic and physiological effects of naturalistic multimodal music listening
Authors: Czepiel Anna , Fink Lauren K. , Seibert Christoph , Scharinger Mathias , Kotz Sonja A.
Published: July 2022

Compared to audio only (AO) conditions, audiovisual (AV) information can enhance the aesthetic experience of a music performance. However, such beneficial multimodal effects have yet to be studied in naturalistic music performance settings. Further, peripheral physiological correlates of aesthetic experiences are not well-understood. Here, participants were invited to a concert hall for piano performances of Bach, Messiaen, and Beethoven, which were presented in two conditions: AV and AO. They rated their aesthetic experience (AE) after each piece (Experiment 1 and 2), while peripheral signals (cardiorespiratory measures, skin conductance, and facial muscle activity) were continuously measured (Experiment 2). Factor scores of AE were significantly higher in the AV condition in both experiments. LF/HF ratio, a heart rhythm that represents activation of the sympathetic nervous system, was higher in the AO condition, suggesting increased arousal, likely caused by less predictable sound onsets in the AO condition. We present partial evidence that breathing was faster and facial muscle activity was higher in the AV condition, suggesting that observing a performer’s movements likely enhances motor mimicry in these more voluntary peripheral measures. Further, zygomaticus (‘smiling’) muscle activity was a significant predictor of AE. Thus, we suggest physiological measures are related to AE, but at different levels: the more involuntary measures (i.e., heart rhythms) may reflect more sensory aspects, while the more voluntary measures (i.e., muscular control of breathing and facial responses) may reflect the liking aspect of an AE. In summary, we replicate and extend previous findings that AV information enhances AE in a naturalistic music performance setting. We further show that a combination of self-report and peripheral measures benefit a meaningful assessment of AE in naturalistic music performance settings.
GIP receptor reduces osteoclast activity and improves osteoblast survival by activating multiple signaling pathways
Authors: Hansen Morten S. , Søe Kent , Christensen Line L. , Fernandez-Guerra Paula , Hansen Nina W. , Wyatt Rachael A. , Martin Claire , Hardy Rowan S. , Andersen Thomas L. , Olesen Jacob B. , Overgaard Søren , Hartmann Bolette , Rosenkilde Mette M. , Kassem Moustapha , Rauch Alexander , Gorvin Caroline M. , Frost Morten
Published: July 2022

Bone is a dynamic tissue that is remodeled throughout life by bone resorbing osteoclasts and bone forming osteoblasts, to adapt to physiological or mechanical demands. These processes are impaired in osteoporosis, and understanding how bone remodeling is regulated could improve anti-osteoporotic treatments. Clinical investigations show that short-term treatment with glucose-dependent insulinotropic polypeptide (GIP) acutely decreases serum markers of bone resorption and may increase bone formation. However, evidence for direct effects of GIP intracellular signaling and functions in mature human osteoclasts and osteoblasts have not been investigated. We report that the GIP receptor (GIPR) is robustly expressed in mature human osteoclasts. Exposure of osteoclasts to GIP inhibits osteoclastogenesis, delays bone resorption, and increases osteoclast apoptosis by acting upon multiple signaling pathways (cAMP, Src, Akt, calcium, p38) to impair nuclear translocation of nuclear factor of activated T cells 1 (NFATc1) and nuclear factor-κB (NFκB). Human osteoblasts also express GIPR, and GIP improves osteoblast survival via cAMP and Akt-mediated pathways. GIP treatment of co-cultures of osteoclasts and osteoblasts also decreased bone resorption. Antagonizing GIPR with GIP(3-30)NH2 abolished the effects of GIP on osteoclasts and osteoblasts. This study demonstrates that GIP inhibits bone resorption and improves survival of human osteoblasts, which could increase bone mass and strength, supporting clinical investigations of the effect of GIP on bone. Moreover, this study demonstrates that GIPR agonism could be beneficial in the treatment of disorders of bone remodeling, such as osteoporosis.

One-sentence Summary

GIP acts directly on bone cells to regulate bone remodeling
Single-Cell Transcriptome Dynamics of the Autotaxin-Lysophosphatidic Acid Axis During Muscle Regeneration Reveal Proliferative Effects in Mesenchymal Fibro-Adipogenic Progenitors
Authors: Contreras Osvaldo , Harvey Richard P.
Published: July 2022

Lysophosphatidic acid (LPA) is a growth factor-like bioactive phospholipid recognising LPA receptors (LPARs) and mediating signalling pathways that regulate embryonic development, wound healing, carcinogenesis, and fibrosis, via effects on cell migration, proliferation and differentiation. Extracellular LPA is generated from lysophospholipids by the secreted hydrolase - ectonucleotide pyrophosphatase/phosphodiesterase 2 (ENPP2; also, AUTOTAXIN / ATX) and metabolised by different membrane-bound phospholipid phosphatases (PLPPs). Here, we use public bulk and singlecell RNA sequencing datasets to explore the gene expression ofLpar1-6,Enpp2, andPlppgenes under skeletal muscle homeostasis and regeneration conditions. We show that the skeletal muscle system dynamically expresses theEnpp2-Lpar-Plppgene axis, withLpar1being the highest expressed member among LPARs.Lpar1was expressed by mesenchymal fibro-adipogenic progenitors (FAPs) and tenocytes, whereas FAPs mainly expressedEnpp2. Clustering of FAPs identified populations representing distinct cell states with robustLpar1andEnpp2transcriptome signatures in homeostatic cells expressing higher levels of markersDpp4andHsd11b1. However, tissue injury induced transient repression ofLpargenes andEnpp2. The role of LPA in modulating the fate and differentiation of tissue-resident FAPs has not yet been explored. Ex vivo, LPAR1/3 and ENPP2 inhibition significantly decreased the cell-cycle activity of FAPs and impaired fibro-adipogenic differentiation, implicating LPA signalling in the modulation of the proliferative and differentiative fate of FAPs. Together, our results demonstrate the importance of the ENPP2-LPAR-PLPP axis in different muscle cell types and FAP lineage populations in homeostasis and injury, paving the way for further research on the role of this signalling pathway in skeletal muscle homeostasis and regeneration, and that of other organs and tissues, in vivo.

Our reanalysis of single-cell transcriptomics revealed the involvement and temporally dynamic expression of the ENPP2-LPAR-PLPP axis in response to skeletal muscle regeneration.
Electrical spiking of psilocybin fungi
Authors: Gandia Antoni , Adamatzky Andrew
Published: July 2022

Psilocybin fungi, aka “magic” mushrooms, are well known for inducing colourful and visionary states of mind. Such psychoactive properties and the ease of cultivating their basidiocarps within low-tech setups make psilocybin fungi promising pharmacological tools for mental health applications. Understanding of the intrinsic electrical patterns occurring during the mycelial growth can be utilised for better monitoring the physiological states and needs of these species. In this study we aimed to shed light on this matter by characterising the extra-cellular electrical potential of two popular species of psilocybin fungi: Psilo-cybe tampanensis and P. cubensis. As in previous experiments with other common edible mushrooms, the undisturbed fungi have shown to generate electric potential spikes and trains of spiking activity. This short analysis provides a proof of intrinsic electrical communication in psilocybin fungi, and further establishes these fungi as a valuable tool for studying fungal electro-physiology.
Chemical Proteomics Reveals Protein Tyrosination Extends Beyond the Alpha-Tubulins in Human Cells
Authors: Makarov Dmytro , Kielkowski Pavel
Published: July 2022

Tubulin detyrosination-tyrosination cycle regulates the stability of microtubules. Thus far described on α-tubulins, the tyrosination level is maintained by a single tubulin-tyrosine ligase (TTL). However, the precise dynamics and tubulin isoforms which undergo (de)tyrosination in neurons are unknown. Here, we exploit the substrate promiscuity of the TTL to introduce an O-propargyl-L-tyrosine in neuroblastoma cells and neurons. Mass spectrometry-based chemical proteomics in neuroblastoma cells using the O-propargyl-L-tyrosine probe revealed previously discussed tyrosination of TUBA4A, MAPRE1, and other non-tubulin proteins. This finding was further corroborated in differentiating neurons. Together we present the method for tubulin tyrosination profiling in living cells. Our results show that detyrosination-tyrosination is not restricted to α-tubulins with coded C-terminal tyrosine and is thus involved in fine-tuning of the tubulin and non-tubulin proteins during neuronal differentiation.