bluuebunny/crossref_metadata_2025 huggingface dataset:
Size-selective mortality fosters evolutionary changes in collective learning across ontogeny and decision-making in zebrafish,Danio rerio
Authors: Roy Tamal , Rohr Tabea , Arlinghaus Robert
Published: March 2022

Size-selective harvesting evolutionary alters the life-history, behavioural and physiological traits in exploited fish populations. Changes in these traits may cause alteration in learning and decision-making abilities, either due to energetic trade-offs with brain investment that may vary across development or via correlations with boldness, sociability or other personality traits. Whether size-selective harvesting evolutionarily alters learning and decision-making abilities in fish remains unexplored, despite the global scale of fisheries. We tested the hypothesis that persistent removal of large-bodied individuals typical of many fisheries reduces learning ability in adults but not in juveniles, increases cognitive flexibility but reduces decision-making ability in adults. We examined associative learning through ontogeny, and reversal learning and collective decision-making in adults in three selection lines of zebrafish (Danio rerio)generated through positive, negative and random size-selective harvesting for five generations. Fish groups of each selection line were tested across ontogeny using a colour-discrimination paradigm with a food reward. The associative reversal task was conducted with a social reward, and the propensity to make group decisions was tested in an associative task. All selection lines showed significant learning ability and improved performance across ontogeny. Consistent with our hypothesis, the large-harvested line fish revealed a significantly reduced learning speed as subadults and adults, while the small-harvested line fish showed slower error rate compared to controls as 4-month old adults. We found no evidence of memory decay, and the selection lines did not vary in associative reversal ability. Decision-making speed did not vary across lines, but the large-harvested line made faster decisions during the probe trial. We conclude that size-selective harvesting typical of many fisheries evolutionarily alters learning and decision making. As this is likely to negatively and persistently affect resource acquisition and survival in exploited populations, we suggest that the cognition-related mechanism we identify may increase natural mortality.
Unleashing alternative polyadenylation analyses with REPAC
Authors: Imada Eddie L , Wilks Christopher , Langmead Ben , Marchionni Luigi
Published: March 2022

Alternative polyadenylation (APA) is an important post-transcriptional mechanism that has major implications in biological processes and diseases. Although specialized sequencing methods for polyadenylation exist, their presence in public repositories is extremely limited when compared to traditional RNA-sequencing. To overcome this, we developed REPAC, a framework for the analysis of APA from RNA-sequencing data. REPAC implements a new method for detection of APA and is designed to take advantage ofrecount3which enables a streamlined way to analyze over 750,000 publicly available samples. Using REPAC, we investigated the landscape of APA caused by activation of B cells. Our analysis revealed that during this process, hundreds of genes are regulated by APA, most notably genes involved in the secretion pathway which is central for the transition to antibody-secreting B-cells. Moreover, we also showed that many genes associated with interferon response are also shortened, suggesting that APA might also play a significant role in the immune response. We also show that REPAC is faster than alternative methods by at least 7-fold and that it scales well to analysis involving hundreds of samples. Overall, the REPAC method offers an accurate, easy, and convenient solution for the exploration of APA across many phenotypes.
Does ankle push-off correct for errors in anterior-posterior foot placement relative to center-of-mass states?
Authors: Jin Jian , van Dieën Jaap H. , Kistemaker Dinant , Daffertshofer Andreas , Bruijn Sjoerd M.
Published: March 2022

I.

Understanding the mechanisms humans use to stabilize walking is vital for predicting falls in elderly. Modeling studies identified two potential mechanisms to stabilize gait in the anterior-posterior direction: foot placement control and ankle push-off control: Foot placement depends on position and velocity of the center-of-mass (CoM) and push-off modulates with deviations between actual and predicted CoM trajectories. While both control mechanisms have been reported in humans, it is unknown whether especially the latter one is employed in unperturbed steady-state walking. On the one hand, the covariance between CoM states and anterior-posterior foot placement served as a measure of foot placement control. On the other hand, we determined variations in ankle push-off as a function of differences between the actual foot placement and the one predicted from CoM states. We estimated the corresponding correlations and consider them indictors for push-off control based on foot placement errors. We found ankle push-off torque to be correlated to the foot placement error in 30 participants when walking at normal and slow speed, with mean correlation values of up to 0.45. Our study suggests that humans use a push-off strategy for correcting foot placement errors in steady-state walking.
Nitrogen and phosphorus deficiencies alter primary and secondary metabolites of soybean roots
Authors: Nezamivand-Chegini Mahnaz , Metzger Sabine , Moghadam Ali , Tahmasebi Ahmad , Koprivova Anna , Eshghi Saeid , Mohammadi-Dehchesmeh Manijeh , Kopriva Stanislav , Niazi Ali , Ebrahimie Esmaeil
Published: March 2022

Nitrogen (N) and phosphorus (P) are two essential plant macronutrients that can limit plant growth by different mechanisms. We aimed to shed light on how soybean respond to low nitrogen (LN), low phosphorus (LP) and their combined deficiency (LNP). Generally, these conditions triggered changes in gene expression of the same processes, including cell wall organization, defense response, response to oxidative stress, and photosynthesis, however, response was different in each condition. A typical primary response to LN and LP was detected also in soybean, i.e., the enhanced uptake of N and P, respectively, by upregulation of genes for the corresponding transporters. The regulation of genes involved in cell wall organization showed that in LP roots tended to produce more casparian strip, in LN more secondary wall biosynthesis occurred, and in LNP reduction in expression of genes involved in secondary wall production accompanied by cell wall loosening was observed. Flavonoid biosynthesis also showed distinct pattern of regulation in different conditions: more anthocyanin production in LP, and more isoflavonoid production in LN and LNP, which we confirmed also on the metabolite level. Interestingly, in soybean the nutrient deficiencies reduced defense response by lowering expression of genes involved in defense response, suggesting a role of N and P nutrition in plant disease resistance. In conclusion, we provide detailed information on how LN, LP, and LNP affect different processes in soybean roots on the molecular and physiological levels.
Coevolution of Patch Selection in Stochastic Environments
Authors: Schreiber Sebastian J. , Hening Alexandru , Nguyen Dang H.
Published: March 2022

Abstract

Species interact in landscapes where environmental conditions vary in time and space. This variability impacts how species select habitat patches. Under equilibrium conditions, coevolution of this patch selection can result in ideal-free distributions where per-capita growth rates are zero in occupied patches and negative in unoccupied patches. These ideal-free distributions, however, don’t explain why species occupy sink patches, competitors have overlapping spatial ranges, or why predators avoid highly productive patches. To understand these patterns, we analyze multi-species Lotka-Volterra models accounting for spatial heterogeneity and environmental stochasticity. In occupied patches at the coESS, we show that the differences between the local contributions to the mean and the variance of the long-term population growth rate are equalized. Applying this characterization to models of antagonistic interactions reveals that environmental stochasticity can partially exorcize the ghost of competition past, select for new forms of enemy-free and victimless space, and generate Hydra effects over evolutionary time scales. Viewing our results through the economic lens of Modern Portfolio Theory highlights why the coESS for patch selection is often a bet-hedging strategy coupling stochastic sink populations. Our results highlight how environmental stochasticity can reverse or amplify evolutionary outcomes due to species interactions or spatial heterogeneity.
minute: A MINUTE-ChIP data analysis workflow
Authors: Navarro Carmen , Martin Marcel , Elsässer Simon
Published: March 2022

Quantitative ChIP-seq methods are essential for accurately characterizing and comparing genome-wide DNA-protein interactions across samples. Procedures that enable such quantitative comparisons involve addition of spike-in chromatin or recombinant nucleosome material, or a multiplexed process using barcoding of chromatin fragments. ChIP-seq analysis workflows typically require a number of computational steps involving multiple tools in order to reach interpretable results, and quantitative analyses require additional steps that ensure scaling of the processed output according to the quantitative measurements. Crucially, the different quantitative approaches have unique analysis requirements reflecting the disparate experimental workflows, hence no universal analysis pipeline exists for quantitative ChIP-seq. Here, we developed minute, a user-friendly computational workflow to easily process multiplexed ChIP data that handles the specific needs of quantitative ChIP. minute enables transformation of raw, multiplexed FASTQ files into a set of normalized, scaled bigWig files that can serve as a basis for a quantitative, comparative downstream analysis. minute is implemented in Python and Snakemake and paired with a Conda environment, to facilitate usability and reproducibility in different platforms.

Source code of minute is available on GitHub: https://github.com/NBISweden/minute
Mixture of Learning Strategies Underlies Rodent Behavior in Dynamic Foraging
Authors: Le Nhat Minh , Yildirim Murat , Wang Yizhi , Sugihara Hiroki , Jazayeri Mehrdad , Sur Mriganka
Published: March 2022

In volatile foraging environments, animals need to adapt their learning in accordance with the uncertainty of the environment and knowledge of the hidden structure of the world. In these contexts, previous studies have distinguished between two types of strategies, model-free learning, where reward values are updated locally based on external feedback signals, and inference-based learning, where an internal model of the world is used to make optimal inferences about the current state of the environment. Distinguishing between these strategies during the dynamic foraging behavioral paradigm has been a challenging problem for studies of reward-guided decisions, due to the diversity in behavior of model-free and inference-based agents, as well as the complexities that arise when animals mix between these types of strategies. Here, we developed two solutions that jointly tackle these problems. First, we identified four key behavioral features that together benchmark the switching dynamics of agents in response to a change in reward contingency. We performed computational simulations to systematically measure these features for a large ensemble of model-free and inference-based agents, uncovering an organized structure of behavioral choices where observed behavior can be reliably classified into one of six distinct regimes in the two respective parameter spaces. Second, to address the challenge that arises when animals use multiple strategies within single sessions, we developed a novel state-space method, block Hidden Markov Model (blockHMM), to infer switches in discrete latent states that govern the choice sequences across blocks of trials. Our results revealed a remarkable degree of mixing between different strategies even in expert animals, such that model-free and inference-based learning modes often co-existed within single sessions. Together, these results invite a re-evaluation of the stationarity of behavior during dynamic foraging, provide a comprehensive set of tools to characterize the evolution of learning strategies, and form the basis of understanding neural circuits involved in different modes of behavior within this domain.
Induction of promoter methylation and transcriptional gene silencing upon high pressure spraying of 24-nt small RNAs in Nicotiana benthamiana
Authors: Walz Melanie , Hohenwarter Linus , Krczal Gabi , Wassenegger Michael , Uslu Veli Vural
Published: March 2022

Exogenous RNA application is a promising transgene-free approach for crop protection and improvement. In almost all applications reported so far, exogenous RNA molecules (double stranded RNAs or small RNAs) are applied to plants in order to trigger degradation of a given mRNA (of plant, pest or pathogen origin), in a process termed post-transcriptional gene silencing (PTGS). However, whether exogenous RNAs can also trigger epigenetic modifications to plants such as RNA-directed DNA methylation (RdDM) and transcriptional gene silencing (TGS) remains largely unaddressed. Here, we provide evidence that high pressure spraying of a 24-nt short interfering RNA (siRNA) designed to target the CaMV 35S promoter that drives the expression of a GFP transgene, resulted in promoter RdDM in N. benthamiana. Moreover, the methylation at the target site spreads both up and downstream neighboring sites. Importantly, GFP expression was reduced in the sprayed leaf tissues. Small RNA sequencing excluded the presence siRNAs mapping to the GFP gene body and documented substantial amount of secondary RNAs in the promoter, suggesting that the GFP silencing was transcriptional rather than post-transcriptional. Our study provides a proof of principle for spray induced epigenetic modification (SPIEM) that could be used in modern crop breeding platforms.
Model-guided design of the diversity of a synthetic human gut community
Authors: Connors Bryce M. , Ertmer Sarah , Clark Ryan L. , Thompson Jaron , Pfleger Brian F. , Venturelli Ophelia S.
Published: March 2022

Microbial communities have tremendous potential as therapeutics. However, a major bottleneck is manufacturing high-diversity microbial communities with desired species compositions. We develop a two-stage, model-guided framework to produce microbial communities with target species compositions. We apply this method to optimize the diversity of a synthetic human gut community. The first stage exploits media components to enable uniform growth responses of individual species and the second stage uses a design-test-learn cycle with initial species abundance as a control point to manipulate community composition. Our designed culture conditions yield 91% of the maximum possible diversity. Leveraging these data, we construct a dynamic ecological model to guide the design of lower-order communities with desired temporal properties over a longer timescale. In sum, a deeper understanding of how microbial community assembly responds to changes in environmental factors, initial species abundances, and inter-species interactions can enable the predictable design of community dynamics.
Transmission blocking activity of low dose tafenoquine in healthy volunteers experimentally infected with Plasmodium falciparum
Authors: Webster Rebecca , Mitchell Hayley , Peters Jenny M. , Heunis Juanita , O’Neill Brighid , Gower Jeremy , Lynch Sean , Jennings Helen , Amante Fiona H. , Llewellyn Stacey , Marquart Louise , Potter Adam J. , Birrell Geoffrey W. , Edstein Michael D. , Shanks G. Dennis , McCarthy James S. , Barber Bridget E.
Published: March 2022

Background

Blocking the transmission of parasites from humans to mosquitoes is a key component of malaria control. Tafenoquine exhibits activity against all stages of the malaria parasite and may have utility as a transmission blocking agent. We aimed to characterize the transmission blocking activity of low dose tafenoquine.

Methods

Healthy adults were inoculated with P. falciparum 3D7-infected erythrocytes on day 0. Piperaquine was administered on days 9 and 11 to clear asexual parasitemia while allowing gametocyte development. A single 50 mg oral dose of tafenoquine was administered on day 25. Transmission was determined by enriched membrane feeding assays pre-dose and at 1, 4 and 7 days post-dose. Artemether-lumefantrine was administered following the final assay. Outcomes were the reduction in mosquito infection and gametocytemia post-tafenoquine, and safety parameters.

Results

Six participants were enrolled, and all were infective to mosquitoes pre-tafenoquine, with a median 86% (range: 22–98) of mosquitoes positive for oocysts and 57% (range: 4–92) positive for sporozoites. By day 4 post-tafenoquine, the oocyst and sporozoite positivity rate had reduced by a median 35% (IQR: 16–46) and 52% (IQR: 40–62), respectively, and by day 7, 81% (IQR 36–92) and 77% (IQR 52–98), respectively. The decline in gametocyte density post-tafenoquine was not significant. No significant participant safety concerns were identified.

Conclusion

Low dose tafenoquine reduces P. falciparum transmission to mosquitoes, with a delay in effect.

Trial registration

Australian New Zealand Clinical Trials Registry (ACTRN12620000995976).

Funding

QIMR Berghofer Medical Research Institute.
Hibernation shows no apparent effect on germline mutation rates in grizzly bears
Authors: Wang Richard J. , Peña-Garcia Yadira , Bibby Madeleine , Raveendran Muthuswamy , Harris R. Alan , Jansen Heiko T. , Robbins Charles T. , Rogers Jeffrey , Kelley Joanna L. , Hahn Matthew W.
Published: March 2022

A male mutation bias is observed across vertebrates, and, where data are available, this bias is accompanied by increased per-generation mutation rates with parental age. While continuing mitotic cell division in the male germline post-puberty has been proposed as the major cellular mechanism underlying both patterns, little direct evidence for this role has been found. Understanding the evolution of the per-generation mutation rate among species requires that we identify the molecular mechanisms that change between species. Here, we study the per-generation mutation rate in an extended pedigree of the brown (grizzly) bear, Ursus arctos horribilis. Brown bears hibernate for one-third of the year, a period during which spermatogenesis slows or stops altogether. The cessation of spermatogenesis is predicted to lessen the male mutation bias and to lower the per-generation mutation rate in this species. However, using whole-genome sequencing, we find that both male bias and per-generation mutation rates are the same as expected for a non-hibernating species. We also carry out a phylogenetic comparison of substitution rates along the lineage leading to brown bear and panda (a non-hibernating species) and find no slowing of the substitution rate in the hibernator. Our results contribute to accumulating evidence that suggests that male germline cell division is not the major determinant of mutation rates and mutation biases. The results also provide a quantitative basis for improved estimates of the timing of carnivore evolution.
Inbreeding depression in an outbred nine-spined stickleback (Pungitius pungitius) population
Authors: Fraimout Antoine , Rastas Pasi , Lv Lei , Merilä Juha
Published: March 2022

Inbreeding depression refers to the reduced fitness of offspring produced by related individuals and is expected to be rare in large outbred populations. When it occurs, marked fitness loss is possible as large populations can carry large loads of recessive harmful mutations which are normally sheltered at the heterozygous state. Using experimental cross data and genome-wide identity-by-descent (IBD) relationships from an outbred marine nine-spined stickleback (Pungitius pungitius) population, we documented a significant decrease in offspring survival probability with increasing parental IBD sharing associated with an average inbreeding load (B) of 15.896. Interestingly, we found that this relationship was also underlined by a positive effect of paternal inbreeding coefficient on offspring survival, suggesting that certain combinations of parental inbreeding and genetic relatedness among mates may promote offspring survival. Apart from demonstrating substantial inbreeding load in an outbred population, the results also highlight the potential caveat associated with artificial establishment of families in experimental studies: wild founder individuals are often - and perhaps mistakenly - assumed to be unrelated.
Hybrid-derived weedy rice maintains adaptive combinations of alleles associated with seed dormancy
Authors: Imaizumi Toshiyuki , Kawahara Yoshihiro , Auge Gabriela
Published: March 2022

Hybridization is a widespread phenomenon in plants and is a pathway for the evolution of adaptive traits. However, this process may also affect the persistence of combinations of adaptive alleles evolved through natural selection when hybridization occurs between adapted and non-adapted populations. Hybridization between weedy and cultivated rice has been confirmed with an adaptive introgression of deep seed dormancy alleles from cultivated rice. In this study, we explored the influence of hybridization on the conservation of combinations of adaptive alleles by evaluating the natural variation in and the genetic structure of genomic regions associated with seed dormancy. Based on sequence variation in the genomic regions associated with seed dormancy, we revealed that hybrid-derived weedy rice strains maintained most of the adaptive combinations for this trait that were observed in the parental weedy rice, despite equal representation of the parental weedy and cultivated rice in the whole genome sequence. Moreover, the hybrid-derived weedy rice strains had deeper seed dormancy than their parental weedy rice strains. This study suggests that hybridization between weedy rice (having adaptive allelic combinations for seed dormancy) and cultivated rice (having non-adaptive combinations) generates weedy rice strains that express deep seed dormancy caused by genome stabilization through the removal of alleles derived from cultivated rice, in addition to the adaptive introgression of deep seed dormancy alleles derived from cultivated rice. Thus, hybridization between adapted and non-adapted populations seems to be reinforcing the trajectory towards the evolution of adaptive traits.
Targeting Cblb-Notch1 axis as a novel immunotherapeutic strategy to boost CD8+ T-cells responses
Authors: Monticone Giulia , Csibi Fred , Leit Silvana , Ciccone David , Champhekar Ameya S. , Austin Jermaine E. , Ucar Deniz A. , Hossain Fokhrul , Huang Zhi , Ibba Salome V. , Boulares A. Hamid , Carpino Nicholas , Majumder Samarpan , Xu Keli , Osborne Barbara A. , Loh Christine , Miele Lucio
Published: March 2022

A critical feature of cancer is the ability to induce immunosuppression and evade immune responses. Tumor-induced immunosuppression diminishes the efficacy of endogenous immune responses and decreases the efficacy of cancer immunotherapy. In this study, we describe a new immunosuppressive pathway in which adenosine promotes Cbl-b-mediated Notch1 degradation, causing suppression of CD8+ T-cells effector functions. Genetic KO and pharmacological inhibition of Cbl-b prevents Notch1 degradation in response to adenosine and reactivates its signaling. Reactivation of Notch1 results in enhanced CD8+ T-cell effector functions, anti-cancer response and resistance to immunosuppression. Our work demonstrates that targeting Cbl-b-Notch1 axis is a novel promising strategy for cancer immunotherapy.
Limited effects of age on the use of the ankle and counter-rotation mechanism in the sagittal plane
Authors: van den Bogaart Maud , Bruijn Sjoerd M. , Spildooren Joke , van Dieën Jaap H. , Meyns Pieter
Published: March 2022

Two mechanisms can be used to accelerate the center of mass (CoM) to control the CoM in relation to the base of support during standing. The first is applying ankle moments to shift the center of pressure (CoP), which has been coined the “CoP mechanism”. The second is changing the angular momentum around the CoM to change the direction of the ground reaction force, i.e., the “counter-rotation mechanism”. At both the beginning and the end of the lifespan, problems with postural control are common. In this study, we asessed anteroposterior balance performance and the related use of these postural control mechanisms in children, younger adults, and older adults. Sixteen pre-pubertal children (6-9y), 17 younger adults (18-24y) and eight older adults (65-80y) performed bipedal upright standing trials of 16 seconds on a rigid surface and on three balance boards that could freely move in the sagittal plane, varying in height (15-19 cm) of the board above the point of contact with the floor. Full body kinematics were measured. Performance related outcome measures, i.e., the number of trials with balance loss and the Root Mean Square (RMS) of the time series of the CoM acceleration were calculated. Additionally, the RMS of the time series of the CoM acceleration due to the CoP and counter-rotation mechanism and the contributions of the CoP and the counter-rotation mechanism to the CoM acceleration (in %) in the sagittal plane were calculated. Furthermore, selected kinematic measures, i.e., the orientation of the board and the head and the Mean Power Frequency of balance board orientation and of CoM acceleration were calculated. Compared to younger adults, children and older adults showed a poorer balance performance, reflected by a greater RMS of CoM accelerations and more balance loss in older adults. Across age groups and conditions, the contribution of the CoP mechanism to the total CoM acceleration was dominant, i.e., 95%-108%. The contribution of the counter-rotation mechanism ranged between 19%-31% (with totals higher than 100% indicating opposite effects of both mechanisms). We suggest that the contribution of the counter-rotation mechanism is limited, since the counter-rotation mechanism would conflict with stabilizing the orientation of the head in space. Furthermore, children did use the counter-rotation mechanism relatively more to accelerate the CoM compared to younger adults. Possibly this reflects that they are still learning to limit the contribution of the counter-rotation mechanism to the same extent as adults.
Noninvasive stimulation of the ventromedial prefrontal cortex modulates rationality of human decision-making
Authors: Kroker Thomas , Wyczesany Miroslaw , Rehbein Maimu Alissa , Roesmann Kati , Wessing Ida , Junghöfer Markus
Published: March 2022

The framing-effect is a bias that affects decision-making depending on whether the available options are presented with positive or negative connotations. Even when the outcome of two choices is equivalent, people have a strong tendency to avoid the negatively framed option because losses are perceived about twice as salient as gains of the same amount (i.e. loss-aversion). The ventromedial prefrontal cortex (vmPFC) is crucial for rational decision-making, and dysfunctions in this region have been linked to cognitive biases, impulsive behavior and gambling addiction. Using a financial decision-making task in combination with magnetoencephalographic neuroimaging, we show that excitatory compared to inhibitory non-invasive transcranial direct current stimulation (tDCS) of the vmPFC reduces framing-effects while improving the assessment of loss-probabilities, ultimately leading to increased overall gains. Behavioral and neural data consistently suggest that this improvement in rational decision-making is predominately a consequence of reduced loss-aversion. These findings recommend further research towards clinical applications of vmPFC-tDCS in addictive disorders.
Predictable and stable epimutations induced during clonal propagation with embryonic transcription factors
Authors: Wibowo Anjar Tri , Antunez-Sanchez Javier , Dawson Alexander , Price Jonathan , Meehan Cathal , Wrightsman Travis , Collenberg Maximillian , Bezrukov Ilja , Becker Claude , Benhamed Moussa , Weigel Detlef , Gutierrez-Marcos Jose
Published: March 2022

Although clonal propagation is frequently used in commercial plant breeding and plant biotechnology programs because it minimizes genetic variation, it is not uncommon to observe clonal plants with stable phenotypic changes, a phenomenon known as somaclonal variation. Several studies have shown that epigenetic modifications induced during regeneration are associated with this newly acquired phenotypic variation. However, the factors that determine the extent of somaclonal variation and the molecular changes associated with it remain poorly understood. To address this gap in our knowledge, we compared clonally propagatedArabidopsis thalianaplants derived from somatic embryogenesis using two different embryonic transcription factors-RWP-RK DOMAIN-CONTAINING 4 (RKD4)orLEAFY COTYLEDON2 (LEC2)and from two epigenetically distinct tissues. We found that both the epi(genetic) status of explant and the regeneration protocol employed play critical roles in shaping the molecular and phenotypic state of clonal plants. Phenotypic variation of regenerated plants can be largely explained by the inheritance of tissue-specific DNA methylation imprints, which are associated with specific transcriptional and metabolic changes in sexual progeny of clonal plants. Moreover, regenerants from roots were particularly affected by the inheritance of epigenetic imprints, which resulted in increased accumulation of salicylic acid in leaves and accelerated plant senescence. Collectively, our data reveal pathways for targeted manipulation of phenotypic variation in clonal plants.
Fluximplied: A novel approach integrates rate limiting steps and differential expression for pathway analysis
Authors: Sportiello Mike , Geber Adam , Palli Rohith , Embong A Karim , Laniewski Nathan G. , Reilly Emma C. , Emo Kris Lambert , Topham David J.
Published: March 2022

Background

Many tools exist to perform a rigorous pathway analysis, though traditional gene set enrichment analysis remains among the most common. While useful for many applications, one common situation where it is less so is the metabolic profiling of bulk omics datasets. Rate limiting steps in more linear pathways are the main determinant of flux through these pathways, but differential expression of the enzymes that catalyze these steps is usually not differentially weighted in pathway analysis. Fluximplied was built to perform pathway analysis with rate limiting steps in mind to assess the implied flux through a number of well validated metabolic pathways.

Results

A database of rate limiting steps and their associated pathway was constructed. Using publicly available human RNA sequencing data from liver, putamen, and adipose tissue, fluximplied generally corroborated the pathway analysis. When comparing two CD8 T cell subsets from mouse lung, our algorithm confirmed previous findings that were not found previously.

Conclusion

Fluximplied is an accessible tool for pathway analysis which is intended to assist the user with hypothesis generation. Unlike traditional approaches to pathway analysis, it specifically queries a database of rate limiting steps in order to infer flux through canonical metabolic pathways.
Allosteric binders of ACE2 are promising anti-SARS-CoV-2 agents
Authors: Hochuli Joshua E. , Jain Sankalp , Melo-Filho Cleber , Sessions Zoe L. , Bobrowski Tesia , Choe Jun , Zheng Johnny , Eastman Richard , Talley Daniel C. , Rai Ganesha , Simeonov Anton , Tropsha Alexander , Muratov Eugene N. , Baljinnyam Bolormaa , Zakharov Alexey V.
Published: March 2022

The COVID-19 pandemic has had enormous health, economic, and social consequences. Vaccines have been successful in reducing rates of infection and hospitalization, but there is still a need for an acute treatment for the disease. We investigate whether compounds that bind the human ACE2 protein can interrupt SARS-CoV-2 replication without damaging ACE2’s natural enzymatic function. Initial compounds were screened for binding to ACE2 but little interruption of ACE2 enzymatic activity. This set of compounds was extended by application of quantitative structure-activity analysis, which resulted in 512 virtual hits for further confirmatory screening. A subsequent SARS-CoV-2 replication assay revealed that five of these compounds inhibit SARS-CoV-2 replication in human cells. Further effort is required to completely determine the antiviral mechanism of these compounds, but they serve as a strong starting point for both development of acute treatments for COVID-19 and research into the mechanism of infection.

Abstract Figure

TOC Graphic: Overall study design.
Omicron BA.1 and BA.2 neutralizing activity elicited by a comprehensive panel of human vaccines
Authors: Bowen John E. , Sprouse Kaitlin R. , Walls Alexandra C. , Mazzitelli Ignacio G. , Logue Jennifer K. , Franko Nicholas M. , Ahmed Kumail , Shariq Asefa , Cameroni Elisabetta , Gori Andrea , Bandera Alessandra , Posavad Christine M. , Dan Jennifer M. , Zhang Zeli , Weiskopf Daniela , Sette Alessandro , Crotty Shane , Iqbal Najeeha Talat , Corti Davide , Geffner Jorge , Grifantini Renata , Chu Helen Y. , Veesler David
Published: March 2022

The SARS-CoV-2 Omicron variant of concern comprises three sublineages designated BA.1, BA.2, and BA.3, with BA.2 steadily replacing the globally dominant BA.1. We show that the large number of BA.1 and BA.2 spike mutations severely dampen plasma neutralizing activity elicited by infection or seven clinical vaccines, with cross-neutralization of BA.2 being consistently more potent than that of BA.1, independent of the vaccine platform and number of doses. Although mRNA vaccines induced the greatest magnitude of Omicron BA.1 and BA.2 plasma neutralizing activity, administration of a booster based on the Wuhan-Hu-1 spike sequence markedly increased neutralizing antibody titers and breadth against BA.1 and BA.2 across all vaccines evaluated. Our data suggest that although BA.1 and BA.2 evade polyclonal neutralizing antibody responses, current vaccine boosting regimens may provide sufficient protection against Omicron-induced disease.
Quorum sensing as a mechanism to harness the wisdom of the crowds
Authors: Moreno-Gámez Stefany , Hochberg Michael E. , van Doorn G. S.
Published: March 2022

Bacteria release and sense small molecules called autoinducers (AIs) in a process known as ‘quorum sensing’ (QS). The prevailing interpretation of QS is that by sensing AI concentrations, bacteria estimate population density to regulate the expression of functions that are only beneficial when carried out by a sufficiently large number of cells. However, a major challenge to this interpretation is that the concentration of AIs strongly depends on the environment, often rendering AI-based estimates of cell density unreliable. Here we propose an alternative interpretation of QS, where bacteria, by releasing and sensing AIs, harness social interactions to sense the environment as a collective. As shown by a model, this functionality can explain the evolution of QS, and results from individuals improving their estimation accuracy by pooling many imperfect estimates – analogous to the ‘wisdom of the crowds’ in decision theory. Importantly, our model reconciles the observed dependence of QS on both population density and the environment and explains why several QS systems regulate the production of private goods.
Multimodal spatiotemporal phenotyping of human organoid development
Authors: Wahle Philipp , Brancati Giovanna , Harmel Christoph , He Zhisong , Gut Gabriele , Santos Aline , Yu Qianhui , Noser Pascal , Fleck Jonas Simon , Gjeta Bruno , Pavlinić Dinko , Picelli Simone , Hess Maximilian , Schmidt Gregor , Lummen Tom , Hou Yanyan , Galliker Patricia , Renner Magdalena , Pelkmans Lucas , Treutlein Barbara , Camp J. Gray
Published: March 2022

Organoids generated from human pluripotent stem cells (PSCs) provide experimental systems to study development and disease. However, we lack quantitative spatiotemporal descriptions of organoid development that incorporate measurements across different molecular modalities. Here we focus on the retina and use a single-cell multimodal approach to reconstruct human retinal organoid development. We establish an experimental and computational pipeline to generate multiplexed spatial protein maps over a retinal organoid time course and primary adult human retina, registering protein expression features at the population, cellular, and subcellular levels. We develop an analytical toolkit to segment nuclei, identify local and global tissue units, infer morphology trajectories, and analyze cell neighborhoods from multiplexed imaging data. We use this toolkit to visualize progenitor and neuron location, the spatial arrangements of extracellular and subcellular components, and global patterning in each organoid and primary tissue. In addition, we generate a single-cell transcriptome and chromatin accessibility time course dataset and infer a gene regulatory network underlying organoid development. We then integrate genomic data with spatially segmented nuclei into a multi-modal atlas enabling virtual exploration of retinal organoid development. We visualize molecular, cellular, and regulatory dynamics during organoid lamination, and identify regulons associated with neuronal differentiation and maintenance. We use the integrated atlas to explore retinal ganglion cell (RGC) spatial neighborhoods, highlighting pathways involved in RGC cell death. Finally, we show that mosaic CRISPR/Cas genetic perturbations in retinal organoids provide insight into cell fate regulation. Altogether, our work is a major advance toward a virtual human retinal organoid, and provides new directions for how to approach disorders of the visual system. More broadly, our approaches can be adapted to many organoid systems.
Leaf bacterial community structure and variation in wild ruderal plants are shaped by the interaction of host species and defense chemistry with environment
Authors: Mayer Teresa , Reichelt Michael , Gershenzon Jonathan , Agler Matthew
Published: March 2022

Variable phenotypes help plants ensure fitness and survival in the face of unpredictable environmental stresses. Leaf bacteria (bacteriomes) can extend plant phenotypes and are well-known to vary from one plant to the next, but little is known about controls on this variation. Here, we find in 9 populations of Arabidopsis thaliana that core leaf bacteriomes are largely, but not completely, shared with other ground-dwelling ruderal plant species. Strength of differentiation between plant species and between A. thaliana populations shifts from year to year, becoming stronger when plants within populations have more similar leaf bacteriomes (less plant-to-plant variation or stochasticity). Interestingly, across different populations, plants with shared leaf aliphatic glucosinolate chemotypes exhibited similar strong year-to-year stochasticity shifts. Therefore, stochasticity of leaf bacteriomes in plant populations changes in specific ways and might be controlled by plant traits, with important implications for how plants adapt to complex and shifting environments.
Exploring a diverse world of effector domains and amyloid signaling motifs in fungal NLR proteins
Authors: Wojciechowski Jakub W. , Tekoglu Emirhan , Gąsior-Głogowska Marlena , Coustou Virginie , Szulc Natalia , Szefczyk Monika , Kopaczyńska Marta , Saupe Sven J. , Dyrka Witold
Published: March 2022

NLR proteins are intracellular receptors constituting a conserved component of the innate immune system of multicellular organisms. In fungi, NLRs are characterized by high diversity of architectures and presence of amyloid signaling. Here, we explore the diverse world of effector and signaling domains of fungal NLRs using state-of-the-art bioinformatic methods including MMseqs2 for fast clustering, probabilistic context-free grammars for sequence analysis, and AlphaFold2 deep neural networks for structure prediction. In addition to substantially improving the overall annotation, especially in basidiomycetes, the study identifies novel domains and reveals the structural similarity of MLKL-related HeLo- and Goodbye-like domains forming the most abundant superfamily of fungal NLR effectors. Moreover, compared to previous studies, we found several times more amyloid motifs, including novel families, and validated aggregating and prion-forming properties of the most abundant of them in vitro and in vivo. Also, through an extensive in silico search, the NLR-associated amyloid signaling is for the first time identified in basidiomycetes. The emerging picture highlights similarities and differences in the NLR architectures and amyloid signaling in ascomycetes, basidiomycetes and other branches of life.
Long range electromagnetic effects drive protein-protein approaches: an egg of Coulomb
Authors: Niccolai Neri , Morandi Edoardo , Alocci Davide , Toccafondi Alberto , Bernini Andrea
Published: March 2022

Living systems cannot rely on random intermolecular approaches inside cell crowding and hidden mechanisms must be present to favor only those molecular interactions which are specifically required by biological functions. Electromagnetic messaging among proteins is here hypothesized upon the observation that charged amino acids are most commonly located in adjacent sequence positions and/or in spatial close proximity. Molecular Dynamics simulations have been used to explore possible effects arising from concerted motions of charged amino acid side chains in two protein model systems. Protein electrodynamics seems to emerge as the framework for understanding long distance protein-ligand interactions.

Highlights

Protein surfaces are often occupied by nearby side chains bearing opposite charges;

Coulomb interactions determine hindered reorientations of charged side chains;

MD simulations suggest time scales and extents of surface charge interactions;

concerted motions of electric charges can yield electromagnetic protein signaling.
Chemical and genetic screens identify new regulators of tetracycline-inducible gene expression system in mammalian cells
Authors: Colicchia Valeria , Häggblad Maria , Sirozh Oleksandra , Porebski Bartlomiej , Balan Mirela , Lidemalm Louise , Carreras-Puigvert Jordi , Hühn Daniela , Fernandez-Capetillo Oscar
Published: March 2022

The tetracycline repressor (tetR)-regulated system is a widely used tool to specifically control gene expression in mammalian cells. Based on this system, we generated a human osteosarcoma cell line which allows for inducible expression of an EGFP-fusion of the TAR DNA-binding protein 43 (TDP-43), which has been linked to neurodegenerative diseases. Consistent with previous findings, TDP-43 overexpression led to the accumulation of aggregates and limited the viability of U2OS. Using this inducible system, we conducted a chemical screen with a library that included FDA-approved drugs. While the primary screen identified several compounds that prevented TDP-43 toxicity, further experiments revealed that these chemicals abrogated doxycyclinedependent TDP-43 expression. This antagonistic effect was observed with both doxycycline and tetracycline, and in several Tet-On cell lines expressing different genes, confirming the general effect of these compounds as inhibitors of the tetR system. Using the same cell line, a genome-wide CRISPR/Cas9 screen identified epigenetic regulators such as the G9a methyltransferase or TRIM28 as potential modifiers of TDP-43 toxicity. Yet again, further experiments revealed that G9a inhibition or TRIM28 loss prevented doxycycline-dependent expression of TDP-43. Together, these results suggest that none of the medically approved drugs significantly mitigates TDP-43 toxicity, identify new chemical and genetic regulators of the tetR system, and raise awareness on the limitations of this approach to conduct chemical or genetic screenings in mammalian cells.
Rapid detection of Staphylococcus aureus and Streptococcus pneumoniae by real-time analysis of volatile metabolites
Authors: Gómez-Mejia Alejandro , Arnold Kim , Bär Julian , Singh Kapil Dev , Scheier Thomas C. , Brugger Silvio D. , Zinkernagel Annelies S. , Sinues Pablo
Published: March 2022

Rapid detection of pathogenic bacteria is needed for rapid diagnostics allowing adequate and timely treatment. In this study, we aimed to evaluate the technical feasibility of Secondary Electro-Spray Ionization-High Resolution Mass Spectrometry (SESI-HRMS) as a diagnostic tool for rapid detection of bacterial infections and compare its performance with the current standard of diagnostics. We compared the time required to confirm growth of the pathogenic bacteria Staphylococcus aureus and Streptococcus pneumoniae by conventional detection by culture and MAL-DI-TOF vs. detection of specific volatile organic compounds (VOCs) produced by these human pathobionts. SESI-HRMS could consistently detect VOCs produced by S. aureus or S. pneumoniae on blood agar plates within minutes, allowing to positively identify bacteria within hours. Unique S. aureus and S. pneumoniae features were detected already at bacterial densities as low as ∼103 colony forming units. Rich mass spectral fingerprints allowed for the distinction of these two bacteria on a species and even strain level. To give an incentive towards clinical application of this technology, further analyzed 17 clinical samples previously diagnosed by conventional methods. We predominantly obtained a separation of samples which showed growth (i.e. presence of living bacteria) compared to samples with no bacterial growth (i.e. presence of dead bacteria). We conclude that SESI-HRMS allows rapid identification of unique bacterial features. Further development of real-time analysis of clinical samples by SESI-HRMS will shorten the time required for microbiological diagnosis with a high level of confidence and sensitivity and should help to improve patient’s tailored treatment.

IMPORTANCE

A timely identification of a pathogenic bacteria causing the infection is of pivotal importance for the initiation of an adequate antimicrobial therapy. In this regard, different technologies have been developed with the aim to achieve a highly reliable, specific, and overall fast identification of pathogenic bacteria. However, conventional diagnostic techniques still require long preprocessing times (hours to days) to acquire enough biological material for an accurate identification of the pathogen. Therefore, in this work, we aimed to further shorten the detection time of current gold standards for microbiological diagnostics by providing a system capable of a fast, sensitive and specific discrimination of different pathogenic bacteria. This system relies on the real-time mass spectrometric detection of volatile organic compounds (VOCs) produced by a given organism during its growth, potentially leading to a significant shortening of the time required to obtain a positive reliable diagnostic.