bluuebunny/crossref_metadata_2025 huggingface dataset:
High-Activity Enhancer Generation based on Feedback GAN with Domain Constraint and Curriculum Learning
Authors: Li Jiahao , Xiao Liwei , Luo Jiawei , Liu Xianliang , Chen Junjie
Published: December 2023

Enhancers are important cis-regulatory elements, enhancing the transcription of target genes. De novo design of high-activity enhancers is one of long-standing goals in generated biology for both clinical purpose and artificial life, because of their vital roles on regulation of cell development, differentiation, and apoptosis. But designing the enhancers with specific properties remains challenging, primarily due to the unclear understanding of enhancer regulatory codes. Here, we propose an AI-driven enhancer design method, named Enhancer-GAN, to generate high-activity enhancer sequences. Enhancer-GAN is firstly pre-trained on a large enhancer dataset that contains both low-activity and high-activity enhancers, and then is optimized to generate high-activity enhancers with feedback-loop mechanism. Domain constraint and curriculum learning were introduced into Enhancer-GAN to alleviate the noise from feedback loop and accelerate the training convergence. Experimental results on benchmark datasets demonstrate that the activity of generated enhancers is significantly higher than ones in benchmark dataset. Besides, we find 10 new motifs from generated high-activity enhancers. These results demonstrate Enhancer-GAN is promising to generate and optimize bio-sequences with desired properties.
Single-cell measurement of microbial growth rate with Raman microspectroscopy
Authors: Caro Tristan A. , Kashyap Srishti , Brown George , Chen Claudia , Kopf Sebastian H. , Templeton Alexis S.
Published: December 2023

Rates of microbial activity and growth are fundamental to understanding environmental geochemistry and ecology. However, measuring the heterogeneity of microbial activity at the single-cell level, especially within complex populations and environmental matrices, remains a forefront challenge. Stable Isotope Probing (SIP) is a standard method for assessing microbial activity and involves measuring the incorporation of an isotopically labeled compound into microbial biomass. Here, we assess the utility of Raman microspectroscopy as a SIP technique, specifically focusing on the measurement of deuterium (2H), a tracer of microbial biomass production. We generate calibrations of microbial biomass2H values and find that Raman microspectroscopy reliably quantifies2H incorporation ranging between 0 and 40 at. %. Applying the results of this calibration to a SIP model, we explicitly parameterize the factors controlling microbial growth quantification, demonstrating how Raman-SIP can measure the growth of microorganisms with doubling times ranging from hours to years. Furthermore, we correlatively compare our Raman-derived measurements with those of nanoscale secondary ion mass spectrometry (nanoSIMS) to compare the relative strengths of nanoSIMS- and Raman-based SIP approaches. We find that Raman microspectroscopy is a robust, accessible methodology that can readily differentiate and quantify the growth of individual microbial cells in complex samples.

Importance

Growth rate, the rate at which organisms grow and reproduce, is a key metric with which to evaluate microbial physiology and contributions to system-level processes. The heterogeneity of microbial growth across space, time, and populations is often difficult to capture with bulk-scale techniques. Single-cell methods hold promise for measuring the heterogeneity of microbial growth rates and responses to changing conditionsin situ, without the need for cultivation of microbial isolates. In this study, we evaluated the ability of Raman microspectroscopy, a non-destructive and rapid technique, to measure the assimilation of isotopically labeled water into individual microbial cells and thereby calculate their rates of growth. We explicitly parameterize the factors controlling the quantification of microbial growth rate and compare this technique to standard methods. The framework we report allows researchers to couple single-cell and aggregate rate measurements to functional or system-level properties, a forefront challenge in microbiology.
A Mechanistic Model for the Release of Ceramide from the CERT START Domain
Authors: Moqadam Mahmoud , Gartan Parveen , Talandashti Reza , Chiapparino Antonella , Titeca Kevin , Gavin Anne-Claude , Reuter Nathalie
Published: December 2023

Ceramide transfer protein CERT is the mediator of non-vesicular transfer of ceramide from ER to Golgi. In CERT, START is the domain responsible for the binding and transport of ceramide. A wealth of structural data has revealed a helix-grip fold surrounding a large hydrophobic holding the ceramide. Yet little is known about the mechanisms by which START releases the ceramide through the polar region and into the packed environment of cellular membranes. As such events do not lend themselves easily to experimental investigations we used multiple unbiased microsecond-long molecular simulations. We propose a membrane-assisted mechanism in which the passage of the ceramide acyl chains is facilitated by the intercalation of a single phosphatidylcholine lipid in the cavity, practically greasing the ceramide way out. We verify using experimental lipidomics data that CERT forms stable complexes with phosphatidylcholine lipids, in addition to ceramide, thus providing a validation for the proposed computational model.
Delta-Rhythmic Activity in the Medulla Develops Coincident with Cortical Delta in Sleeping Infant Rats
Authors: Ahmad Midha , Kim Jangjin , Dwyer Brett , Sokoloff Greta , Blumberg Mark S.
Published: December 2023

In early development, active sleep is the predominant sleep state before it is supplanted by quiet sleep. In rats, the developmental increase in quiet sleep is accompanied by the sudden emergence of the cortical delta rhythm (0.5-4 Hz) around postnatal day 12 (P12). We sought to explain the emergence of cortical delta by assessing developmental changes in the activity of the parafacial zone (PZ), a medullary structure thought to regulate quiet sleep in adults. We recorded from PZ in P10 and P12 rats and predicted an age-related increase in neural activity during increasing periods of delta-rich cortical activity. Instead, during quiet sleep we discovered sleep-dependent rhythmic spiking activity—with intervening periods of total silence—phase-locked to a local delta rhythm. Moreover, PZ and cortical delta were coherent at P12, but not at P10. PZ delta was also phase-locked to respiration, suggesting sleep-dependent modulation of PZ activity by respiratory pacemakers in the ventral medulla. Disconnecting the main olfactory bulbs from the cortex did not diminish cortical delta, indicating that the influence of respiration on delta at this age is not mediated indirectly through nasal breathing. Finally, we observed an increase in parvalbumin-expressing terminals in PZ across these ages, supporting a role for GABAergic inhibition in PZ’s rhythmicity. The discovery of delta-rhythmic neural activity in the medulla—when cortical delta is also emerging—opens a new path to understanding the brainstem’s role in regulating sleep and synchronizing rhythmic activity throughout the brain.
Chemotactile perception and associative learning of amino acids in yellowjacket workers
Authors: Mattiacci Analía , Pietrantuono Ana Laura , Masciocchi Maité , Corley Juan C.
Published: December 2023

Learning and memory are essential for animal survival, influencing preferences, decision-making, and foraging behaviour. In this study, we explore the perceptual and learning abilities ofVespula germanica(yellowjacket wasps) to various amino acids. We hypothesize thatV. germanicacan qualitatively evaluate various amino acid solutions, given their scavenging habits and the possibility of metabolizing amino acids to fuel energy. Through chemo-tactile differential conditioning, we studied worker wasp’ maxilla labium extension response (MaLER) to essential (Lysine, Tryptophan, Arginine) and non-essential amino acids (Ornithine, Aspartic acid, Glycine). Conditioning sessions included individual amino acids against water and comparisons between different amino acids. Additionally, we tested retention, discrimination, and generalization abilities, 30 minutes later with conditioned and novel stimuli. Our results show that wasps exhibit the ability to learn and discriminate various amino acids. The discrimination capacity extended to differentiating between pairs of amino acids. Memory retention was generally robust, but certain associations observed during conditioning did not persist after a 30-minute interval. Moreover, when wasps were trained with essential amino acids, the acquired learning did not generally extend to other non-essential amino acids, except for Arginine, which exhibited generalization when tested with its precursor, Ornithine. Conversely, when trained with non-essential amino acids, the acquired learning generalized to other essential amino acids. These results suggest that, unlike other hymenopterans, wasps can detect, discriminate, and generalize free amino acids, crucial for their foraging decisions. This knowledge contributes to understanding the cognitive dimensions ofV. germanicaand their implications for targeted pest management.

Summary statement

This study onVespula germanica’s amino acid perception enhances our understanding of foraging behaviours. The findings contribute to insect cognition studies, with potential implications for pest management.
Unveiling genome plasticity and a novel phage inMycoplasma felis: genomic investigations of four feline isolates
Authors: Klose Sara M. , Legione Alistair R. , Bushell Rhys N. , Browning Glenn F. , Vaz Paola K.
Published: December 2023

Mycoplasma felishas been isolated from diseased cats and horses, but to date only a single fully assembled genome of this species, of an isolate from a horse, has been characterised. This study aimed to characterise and compare the completely assembled genomes of four clinical isolates ofM. felisfrom three domestic cats, assembled with the aid of short and long read sequencing methods. The completed genomes encoded a median of 759 open reading frames (min, 743, max 777) and had a median average nucleotide identity (ANI) of 98.2% with the genome of the available equid origin reference strain. Comparative genomic analysis revealed the occurrence of multiple horizontal gene transfer (HGT) events and significant genome reassortment. This had resulted in the acquisition or loss of numerous genes within the Australian felid isolate genomes, encoding putative proteins involved in DNA transfer, metabolism, DNA replication, host cell interaction, and restriction modification systems. Additionally, a novel mycoplasma phage was detected in one Australian felidM. felisisolate by genomic analysis and visualised using cryo-transmission electron microscopy. This study has highlighted the complex genomic dynamics in different host environments. Furthermore, the sequences obtained in this work will enable the development of new diagnostic tools, and identification of future infection control and treatment options for the respiratory disease complex in cats.

Data summary

All genome data for this study have been deposited in GenBank under BioProject PRJNA906261. Genome assemblies, as well as Illumina and Oxford Nanopore sequence reads for each isolate, can be found under their respective BioSamples:SAMN32182834(isolate 047),SAMN32182835(isolate 219),SAMN32182836(isolate 329 and associated phage), andSAMN32182837(isolate 632). The authors confirm all supporting data and protocols have been provided within the article.

Impact statement

Mycoplasma felisis commonly associated with clinical cases of conjunctivitis and feline respiratory disease complex in cats, the leading cause of euthanasia in animal shelters. In the absence of vaccines, infection control is currently limited to the prolonged treatment with antimicrobials. Prior to this study there was only one complete genome assembly of an isolate ofM. felis, which had been obtained from a horse. This study has provided the first high quality hybrid assembled genomes ofM. felisisolates from cats. This work adds four new genomes from clinical cases, as well as the identification and validation of the presence of a novel phage that utilises the mycoplasma translation code. The genomic data presented here can assist future projects investigating improved diagnostics and development of new treatment options for this significant feline pathogen.
Hyperosmolality tolerance of freshwater largemouth bass (Micropterus salmoides) to brackish at early ontogenetic stages: Eggs, embryos and yolk-sac larvae
Authors: Luo Du , Yang Dingtian
Published: December 2023

Salinity is recognized as a pivotal factor limiting the migration of freshwater fish to brackish environments. The largemouth bass (LMB,Micropterus salmoides), a globally translocated freshwater fish, exhibits estuarine distribution, yet its hyperosmoregulatory capacity during early ontogenetic stages remains inadequately understood. To investigate the impact of freshwater salinization, a series of experiments were conducted in the Pearl River Delta, China. The study aimed to elucidate the osmoregulatory abilities of LMB eggs and embryos, assess the salinity toxicity on hatching, and explore the acute effects of hyperosmolality on yolk-sac larvae. Our results revealed that freshwater-activated mature eggs and naturally fertilized oocytes maintained nearly identical osmotic homeostasis, with diameters of 1.38 ± 0.068 mm and 1.37 ± 0.054 mm, respectively. Furthermore, both exhibited peak water excretion at a salinity of 15.0 ppt. Remarkably, a reduction in water permeability was observed in hyperosmotic environments. Spontaneous hatching rates increased from 27.5 ± 14.4% in the 1.0 ppt group to 75.1 ± 12.0% in the 6.0 ppt group under fluctuating temperature conditions. Yolk-sac LMB larvae consistently reduced survival time from 12.5 d at 1.0 ppt to 50.7 ± 2.1 min at 35.0 ppt. Similarly, more developed larvae also experienced a decrease in survival time. Logistic regression models fitting lethal time with salinity indicated a sharp decrease between 10.0 ppt and 20.0 ppt. These findings offer practical insights for predicting distribution patterns and enhancing aquaculture technology for LMB. Moreover, they may contribute theoretically to the broader understanding of the osmoregulatory mechanisms of freshwater fish.
Benchmarking Reverse Docking through AlphaFold2 Human Proteome
Authors: Luo Qing , Wang Sheng , Li Hoi Yeung , Zheng Liangzhen , Mu Yuguang , Guo Jingjing
Published: December 2023

Predicting binding of a small molecule to the human proteome by reverse docking methods, we can predict the target interactions of drug compounds in the human body, as well as further evaluate their potential off-target effects or toxic side effects. In this study, we constructed 11 pipelines to evaluate and benchmark thoroughly the predictive capabilities of these reverse docking pipelines. The pipelines were built using site prediction tools (PointSite and SiteMap) based on the AF2 human proteome, docking programs (Glide and AutoDock Vina), and scoring functions (Glide, Autodock Vina, RTMScore, DeepRMSD, OnionNet-SFCT). The results show that pipeline glide_sfct (PS) exhibited the best target prediction ability and successfully predicted the similar proteins of native targets. This finding provides important clues for understanding the promiscuity between the drug ligand and the whole human proteome. In general, our study has the potential to increase the success rate and reduce the development timeline of drug discovery, thereby saving costs.
Action history and target uncertainty co-determine human reaching direction under time pressure
Authors: Keane B , Smith L , Carroll TJ
Published: December 2023

Given the inaccuracies that are inherent in biological sensory and motor functions, animal sensorimotor control should be probabilistic. Effective neural control systems for movement must estimate the most likely true state of the world on the basis of uncertain sensory information, and to select and execute movements that are most likely to be successful given motor variability. Bayesian inference dictates that if sensory information is ambiguous (e.g. low light conditions), animals should rely more on their past experience of target locations to guide motor planning, and less on their current sensory information about target location. Here we investigated how time pressure affects degree to which the precision of sensory information about a target influences movement direction bias towards previous target locations. We used a paradigm developed by Dekleva et al. (2016) that involved uncertain cues to the location of a hidden target for reaching with movement preparation time strictly controlled. One group of participants (n=10) were required to initiate their reaches within 150-300ms of target presentation, and a second group (n=10) were required to initiate their reaches with 1150-1300ms of target presentation. We found that participants relied more on prior target location information when target precision was reduced under time pressure, which suggests that integration of target uncertainty information according to Bayesian principles is an inherent component of sensorimotor transformation and does not require time-consuming cognitive processes.
In situstructural determination of cyanobacterial phycobilisome-PSII supercomplex by STAgSPA strategy
Authors: Zhang Xing , Xiao Yanan , You Xin , Sun Shan , Sui Sen-Fang
Published: December 2023

Photosynthesis converting solar energy to chemical energy is one of the most important chemical reactions on earth1. In cyanobacteria, light energy is captured by antenna system phycobilisomes (PBSs) and transferred to photosynthetic reaction centers of photosystem II (PSII) and photosystem I (PSI)2. While most of the protein complexes involved in photosynthesis have been characterized byin vitrostructural analyses, how these protein complexes function togetherin vivois not well understood. Here we developed anin situstructural analysis strategy “STAgSPA” to successfully solve thein situstructure of PBS-PSII supercomplex from the cyanobacteriaSpirulina platensisFACHB-439 at resolution of ∼3.5Å. The structure reveals the unprecedented coupling details among adjacent PBSs and PSII dimers, and the collaborative energy transfer mechanism mediated by multiple “super-PBS” in cyanobacteria. Our results not only provide the insights for understanding the diversity of photosynthesis-related systems between prokaryotic cyanobacteria and eukaryotic red algae, but also a valuable methodological demonstration forin situhigh-resolution structural analysis in cellular or tissue samples.
Incorporation of the HIV-1 envelope glycoprotein into viral particles is regulated by the tubular recycling endosome in a cell type-specific manner
Authors: Lerner Grigoriy , Ding Lingmei , Candor Kathleen , Spearman Paul
Published: December 2023

The HIV-1 envelope glycoprotein (Env) is incorporated into particles during assembly on the plasma membrane (PM). Env initially reaches the PM through the secretory pathway, after which it is rapidly endocytosed via an AP-2- and clathrin-dependent mechanism. Here we show that endocytosed cell surface Env enters the tubular recycling endosome compartment (TRE). Trafficking to the TRE was dependent upon motifs within the CT previously implicated in Env recycling and particle incorporation. Depletion of TRE components MICAL-L1 or EHD1 led to defects in Env incorporation, particle infectivity, and viral replication. Remarkably, defects were limited to cell types defined as nonpermissive for incorporation of CT-deleted Env, including monocyte-derived macrophages, and not observed in 293T, HeLa, or MT-4 cells. This work identifies the TRE as an essential component of Env trafficking and particle incorporation, and provides evidence that the cell type-dependent incorporation of Env is defined by interactions with components of the TRE.
Activation of plant immunity through conversion of a helper NLR homodimer into a resistosome
Authors: Selvaraj Muniyandi , Toghani AmirAli , Pai Hsuan , Sugihara Yu , Kourelis Jiorgos , Yuen Enoch Lok Him , Ibrahim Tarhan , Zhao He , Xie Rongrong , Maqbool Abbas , Concepcion Juan Carlos De la , Banfield Mark J. , Derevnina Lida , Petre Benjamin , Lawson David M. , Bozkurt Tolga O. , Wu Chih-Hang , Kamoun Sophien , Contreras Mauricio P.
Published: December 2023

Nucleotide-binding domain and leucine-rich repeat (NLR) proteins can engage in complex interactions to detect pathogens and execute a robust immune response via downstream helper NLRs. However, the biochemical mechanisms of helper NLR activation by upstream sensor NLRs remain poorly understood. Here, we show that the coiled-coil helper NLR NRC2 accumulatesin vivoas a homodimer that converts into a higher order oligomer upon activation by its upstream virus disease resistance protein Rx. The Cryo-EM structure of NRC2 in its resting state revealed intermolecular interactions that mediate homodimer formation. These dimerization interfaces have diverged between paralogous NRC proteins to insulate critical network nodes and enable redundant immune pathways. Our results expand the molecular mechanisms of NLR activation pointing to transition from homodimers to higher-order oligomeric resistosomes.
Interleukin-1α links peripheral CaV2.2 channel activation to rapid adaptive increases in heat sensitivity in skin
Authors: Salib Anne-Mary N , Crane Meredith J , Lee Sang Hun , Wainger Brian J , Jamieson Amanda M , Lipscombe Diane
Published: December 2023

Neurons have the unique capacity to adapt output in response to changes in their environment. Within seconds, sensory nerve endings can become hypersensitive to stimuli in response to potentially damaging events. The underlying behavioral response is well studied, but several of the key signaling molecules that mediate sensory hypersensitivity remain unknown. We previously discovered that peripheral voltage-gated CaV2.2 channels in nerve endings in skin are essential for the rapid, transient increase in sensitivity to heat, but not to mechanical stimuli, that accompanies intradermal capsaicin. Here we report that the cytokine interleukin-1α (IL-1α), an alarmin, is necessary and sufficient to trigger rapid heat and mechanical hypersensitivity in skin. Of 20 cytokines screened, only IL-1α was consistently detected in hind paw interstitial fluid in response to intradermal capsaicin and, similar to behavioral sensitivity to heat, IL-1α levels were also dependent on peripheral CaV2.2 channel activity. Neutralizing IL-1α in skin significantly reduced capsaicin-induced changes in hind paw sensitivity to radiant heat and mechanical stimulation. Intradermal IL-1α enhances behavioral responses to stimuli and, in culture, IL-1α enhances the responsiveness ofTrpv1-expressing sensory neurons. Together, our data suggest that IL-1α is the key cytokine that underlies rapid and reversible neuroinflammatory responses in skin.
Dynamically adjusted cell fate decisions and resilience to mutant invasion during steady state hematopoiesis revealed by an experimentally parameterized mathematical model
Authors: Komarova Natalia L. , Rignot Chiara , Fleischman Angela G. , Wodarz Dominik
Published: December 2023

A major next step in hematopoietic stem cell (HSC) biology is to obtain a thorough quantitative understanding of cellular and evolutionary dynamics involved in undisturbed hematopoiesis. Mathematical models are key in this respect, and are most powerful when parameterized experimentally and containing sufficient biological complexity. Mathematical models of hematopoiesis have either been parameterized experimentally without non-linear dynamics, or they include these complexities but have not been parameterized to the same extent. We bridge this gap using mouse data to parameterize a mathematical model of hematopoiesis that includes homeostatic control mechanisms as well as clonal evolution. We find that non-linear feedback control drastically changes the interpretation of kinetic estimates at homeostasis. This suggests that short-term HSC and multipotent progenitors (MPPs) can dynamically adjust to sustain themselves in the absence of long-term HSCs, even if they differentiate more often than they self-renew in undisturbed homeostasis. Additionally, the presence of feedback control in the model renders the system resilient against mutant invasion. Invasion barriers, however, can be overcome by a combination of age-related changes in stem cell differentiation and a mutant-associated inflammatory environment. This helps us understand the evolution of e.g.TET2, DNMT3A, orJAK2mutants, and how to potentially reduce mutant burden.
Effects of novelty and temporal distance on post-experience reactivation of hippocampal place cells encoding multiple environments
Authors: Yokoi Taiki , Shikano Yu , Yagishita Haruya , Ikegaya Yuji , Sasaki Takuya
Published: December 2023

The hippocampus plays a crucial role in consolidating episodic memories from diverse experiences that encompass spatial, temporal, and novel information. This study analyzed the spike patterns of hippocampal place cells in the CA3 and CA1 areas of rats that sequentially foraged in five rooms, including familiar and novel rooms, followed by a rest period. Across multiple rooms, the generation of place fields by CA1 place cells was coordinated with other place cells. In the subsequent rest period, CA3 place cells that encoded novel environments exhibited stronger and more coordinated reactivation during sharp wave ripples (SWRs) than CA1 place cells. In contrast, CA1 place cells that encoded more recent environments exhibited stronger SWR-associated reactivation, independent of spikes of other cells, with weaker influences from novelty compared to CA3 place cells. These results suggest that post-experience SWR-associated reactivation of CA3 and CA1 neurons primarily processes novelty-related and temporal distance-related aspects of memory, respectively.
Fluvoxamine maleate ameliorates Alzheimer disease pathology by mitigating amyloid-beta load and neuroinflammation in 5XFAD mice
Authors: Kaur Sukhleen , Sharma Kuhu , Sharma Ankita , Sandha Kamalpreet Kaur , Ali Syed Mudassir , Ahmed Riyaz , Ramajayan P. , Singh Parvinder Pal , Ahmed Zabeer , Kumar Ajay
Published: December 2023

Background

Alzheimer pathology (AD) is accompanied by the deposition of amyloid beta (Aβ) and chronic neuroinflammation, where NLRP3 inflammasome is particularly involved. In this study, we found that the OCD drug fluvoxamine maleate (FXN) can potently ameliorate AD pathology in 5XFAD mice by autophagy-mediated clearance of Aβ and inhibition of NLRP3 inflammasome.

Methods

We used mice primary astrocytes to establish the mechanism of action of FXN against NLRP3 inflammasome by using various techniques like ELISA, Western blotting, confocal microscopy, Immunofluorescence, etc. The validation of the anti-AD activity of FXN was done in transgenic 5XFAD mice after two months of treatment followed by behavior analysis and studying inflammatory and autophagy proteins along with immunohistochemistry analysis for Aβ load in the hippocampi.

Results

Our data showed that FXN induces autophagy to inhibit NF-κB and NLRP3 inflammasome at a low concentration of 78 nM apart from directly inhibiting NLRP3 inflammasome in primary astrocytes. FXN activated the PRKAA2 pathway through CAMKK2 signaling, which led to the induction of autophagy in primary astrocytes. FXN inhibited the ATP-mediated NLRP3 inflammasome through autophagic degradation of NF-κB and thus caused the downregulation of pro-IL-1β and NLRP3. The anti-NLRP3 inflammasome effect of FXN was reversed when autophagy was inhibited either by genetic knockdown of the PRKAA2 pathway or by bafilomycin A1.

Furthermore, FXN treatment led to improved AD pathology in 5XFAD mice, which displayed a significant improvement in multiple behavior parameters like working memory and neuromuscular coordination and they behaved more like wild-type animals. We found that FXN improved behavior in 5XFAD mice by clearing the Aβ deposits from the hippocampi along with a significant reduction in multiple inflammatory proteins, including NF-κB, GFAP, IBA1, IL-1β, TNF-α, and IL-6 associated with NF-κB and NLRP3 inflammasome in the brain. Moreover, these changes were accompanied by increased expression of autophagic proteins.

Conclusion

Our data suggest that to ameliorate AD pathology, FXN simultaneously targets two key pathological features of AD that is Aβ deposits and neuroinflammation. Being an approved drug, FXN can be pushed as a potential drug candidate for human studies against AD.
Diverging roles of TRPV1 and TRPM2 in warm-temperature detection
Authors: Abd El Hay Muad Y. , Kamm Gretel B. , Tlaie Alejandro , Siemens Jan
Published: December 2023

The accurate perception of innocuous temperatures, particularly those experienced as pleasantly warm, is essential for achieving thermal comfort and maintaining thermoregulatory balance. Warm-sensitive neurons (WSN) innervating the skin play a central role in non-painful warmth detection. The TRP ion channels TRPV1 and TRPM2 have been suggested as sensors of warm temperature in WSNs. However, the precise contribution of these channels to the process of warmth detection is not fully understood.

A significant challenge in analysing WSNs lies in their scarcity: fewer than 10 % of sensory neurons in the rodent dorsal root ganglion (DRG) respond to innocuous warm temperatures. In this study, we examined >20,000 cultured mouse DRG neurons using calcium imaging and discovered distinct contributions of TRPV1 and TRPM2 to warm-temperature sensitivity. TRPV1, and to a lesser extent TRPM2, affect the abundance of WSNs, with TRPV1 mediating the rapid, dynamic response to warmth and TRPM2 subtly affecting the population response of WSNs. By carefully tracking animal movement in a whole-body thermal preference paradigm, we observe that these cellular differences correlate with nuanced thermal behaviours. Utilizing a drift-diffusion model to quantitatively analyse the decision-making process of animals exposed to different environmental temperatures, we found that: TRPV1 deletion primarily impairs the precision of evidence accumulation, whereas TRPM2 deletion significantly increases the total duration of exposure to warmer environments that are avoided by wildtype mice.

Our findings provide valuable insights into the distinct molecular responses to warmth stimuli, and underpin the subtle aspects of thermal decision-making when encountering minor temperature variations.
Structure and mechanism of Zorya anti-phage defense system
Authors: Hu Haidai , Hughes Thomas C.D. , Popp Philipp F. , Roa-Eguiara Aritz , Martin Freddie J.O. , Rutbeek Nicole R. , Hendriks Ivo Alexander , Payne Leighton J. , Yan Yumeng , Sousa Victor Klein de , Wang Yong , Nielsen Michael Lund , Berry Richard M. , Erhardt Marc , Jackson Simon A. , Taylor Nicholas M.I.
Published: December 2023

Zorya is a recently identified and widely distributed bacterial immune system, which protects against phage invasion. It consists of a predicted membrane-embedded complex (ZorAB) and soluble components that differ among Zorya subtypes, notably ZorC and ZorD, in type I Zorya systems. Here, we reveal the molecular basis of the Zorya defense system using cryo-electron microscopy, mutagenesis, fluorescence microscopy, proteomics, and functional studies. We demonstrate that ZorAB shares the stoichiometry of other 5:2 inner membrane ion-driven rotary motors. Additionally, ZorA5B2features a dimeric ZorB peptidoglycan binding domain and a pentameric α-helical coiled-coil tail made of ZorA that projects approximately 700 Å into the cytoplasm. We further characterize the structure and function of the soluble Zorya components, ZorC and ZorD, and find that they harbour DNA binding and nuclease activity, respectively. Comprehensive functional and mutational analyses demonstrates that all Zorya components work in concert to protect bacterial cells against invading phages. We present evidence that ZorAB operates as an ion-driven motor that becomes activated and anchors to the cell wall upon sensing of cell envelope perturbations during phage invasion. Subsequently, ZorAB transfers the phage invasion signal through the ZorA cytoplasmic tail to the soluble effectors, which function to prevent phage propagation. In summary, our study elucidates the foundational mechanisms of Zorya function and reveals a novel triggering signal for the rapid activation of an anti-phage defense system.
Modulation of neural gene networks by estradiol in old rhesus macaque females
Authors: Cervera-Juanes Rita , Zimmerman Kip D. , Wilhelm Larry , Zhu Dongqin , Bodie Jessica , Kohama Steven G. , Urbanski Henryk F.
Published: December 2023

The postmenopausal decrease in circulating estradiol (E2) levels has been shown to contribute to several adverse physiological and psychiatric effects. To elucidate the molecular effects of E2 on the brain, we examined differential gene expression and DNA methylation (DNAm) patterns in the nonhuman primate brain following ovariectomy (Ov) and subsequent E2 treatment. We identified several dysregulated molecular networks, including MAPK signaling and dopaminergic synapse response, that are associated with ovariectomy and shared across two different brain areas, the occipital cortex (OC) and prefrontal cortex (PFC). The finding that hypomethylation (p=1.6×10-51) and upregulation (p=3.8×10-3) ofUBE2Macross both brain regions, provide strong evidence for molecular differences in the brain induced by E2 depletion. Additionally, differential expression (p=1.9×10-4; interactionp=3.5×10-2) ofLTBRin the PFC, provides further support for the role E2 plays in the brain, by demonstrating that the regulation of some genes that are altered by ovariectomy may also be modulated by Ov followed by hormone replacement therapy (HRT). These results present real opportunities to understand the specific biological mechanisms that are altered with depleted E2. Given E2’s potential role in cognitive decline and neuroinflammation, our findings could lead to the discovery of novel therapeutics to slow cognitive decline. Together, this work represents a major step towards understanding molecular changes in the brain that are caused by ovariectomy and how E2 treatment may revert or protect against the negative neuro-related consequences caused by a depletion in estrogen as women approach menopause.
Cell surface sculpting using logic-gated protein actuators
Authors: Kofoed Christian , Tay Nicholas E. S. , Ye Xuanjia , Erkalo Girum , Muir Tom W.
Published: December 2023

Cell differentiation and tissue specialization lead to unique cellular surface landscapes and exacerbated or loss of expression patterns can result in further heterogenicity distinctive of pathological phenotypes1–3. Immunotherapies and emerging protein therapeutics seek to exploit such differences by engaging cell populations selectively based on their surface markers. Since a single surface antigen rarely defines a specific cell type4,5, the development of programmable molecular systems that integrate multiple cell surface features to convert on-target inputs to user-defined outputs is highly desirable. Here, we describe an autonomous decision-making protein device driven by proximity-gated proteintrans-splicing that allows local generation of an active protein from two otherwise inactive fragments. We show that this protein actuator platform can perform various Boolean logic operations on cell surfaces, allowing highly selective recruitment of enzymatic and cytotoxic activities to specific cells within mixed populations. Due to its intrinsic modularity and tunability, this technology is expected to be compatible with different types of inputs, targeting modalities and functional outputs, and as such will have broad application in the synthetic biology and biotechnology areas.
Estimating the frequency of virulence against anStbgene inZymoseptoria triticipopulations by bulk phenotyping on checkerboard microcanopies of wheat NILs
Authors: Suffert Frédéric , Le Prieur Stéphanie , Gélisse Sandrine , Dzialo Emmie , Saintenac Cyrille , Marcel Thierry C.
Published: December 2023

Monitoring virulent strains within fungal pathogen populations is crucial to improve host resistance deployment strategies. Such monitoring increasingly involves field pathogenomics studies of molecular polymorphisms in genomes based on high-throughput screening technologies. However, it is not always straightforward to predict virulence phenotypes from these polymorphisms andin plantaphenotyping remains necessary. We developed a method for ‘bulk phenotyping on checkerboard microcanopies of wheat near-isogenic lines’ (BPC) for estimating the frequency of virulence against anStbgene in populations ofZymoseptoria tritici, the causal agent ofSeptoria triticiblotch in wheat, without the need for strain-by-strain phenotyping. Our method involves the uniform inoculation of a microcanopy of two wheat lines – one with the resistance gene and the other without it – with a multi-strain cocktail representative of the population to be characterized, followed by the differential quantification of infection points (lesions). UsingStb16q, a resistance gene that has recently broken down in Europe, we found a robust correlation between the ratio of the mean number of lesions on each wheat line and the frequency of virulent strains in the inoculum. Using pairs of virulent and avirulent strains, and synthetic populations consisting of 10 virulent strains and 10 avirulent strains mixed in different proportions, we validated the principle of the method and established standard curves at virulence frequencies close to those observed in natural conditions. We discuss the potential of this method for virulence monitoring in combination with recently developed molecular methods.
PUPpy: a primer design pipeline for substrain-level microbial detection and absolute quantification.
Authors: Ghezzi Hans , Fan Michelle Y , Ng Katharine M , Burckhardt Juan C , Pepin Deanna M , Lin Xuan , Ziels Ryan M. , Tropini Carolina
Published: December 2023

Characterizing microbial communities at high-resolution and with absolute quantification is crucial to unravel the complexity and diversity of microbial ecosystems. This can be achieved with PCR assays, which enable highly selective detection and absolute quantification of microbial DNA. However, a major challenge that has hindered PCR applications in microbiome research is the design of highly specific primer sets that exclusively amplify intended targets. Here, we introduce Phylogenetically Unique Primers in python (PUPpy), a fully automated pipeline to design microbe- and group-specific primers within a given microbial community. PUPpy can be executed from a user-friendly GUI, or two simple terminal commands, and it only requires coding sequence files of the community members as input. PUPpy-designed primers enable the detection of individual microbes and quantification of absolute microbial abundance in defined communities below the strain level. We experimentally evaluated the performance of PUPpy-designed primers using two bacterial communities as benchmarks. Each community was comprised of 10 members, exhibiting a range of genetic similarities that spanned from different phyla to substrains. PUPpy-designed primers also enable the detection of groups of bacteria in an undefined community, such as the detection of a gut bacterial family in a complex stool microbiota sample. Taxon-specific primers designed with PUPpy showed 100% specificity to their intended targets, without unintended amplification, in each community tested. Lastly, we show absolute quantification of microbial abundance using PUPpy-designed primers in ddPCR, benchmarked against 16S rRNA and shotgun sequencing. Our data shows that PUPpy-designed microbe-specific primers can be used to quantify substrain-level absolute counts, providing more resolved and accurate quantification in defined communities than short-read 16S rRNA and shotgun sequencing.
Control of three-carbon amino acid homeostasis by promiscuous importers and exporters inBacillus subtilis: Role of the sleeping beauty family of amino acid exporters
Authors: Warneke Robert , Herzberg Christina , Daniel Richard , Hormes Björn , Stülke Jörg
Published: December 2023

The Gram-positive model bacteriumBacillus subtiliscan acquire amino acids by import,de novobiosynthesis, or by degradation of proteins and peptides. The accumulation of several amino acids inhibits growth ofB. subtilis, probably due to misincorporation into cellular macromolecules such as proteins or peptidoglycan or due to interference with other amino acid biosynthetic pathways. Here, we studied the adaptation ofB. subtilisto toxic concentrations of the three-carbon amino acids L-alanine, β-alanine, and 2,3-diaminopropionic acid as well as glycine. Resistance to the non-proteinogenic amino acid β-alanine, which is a precursor for the vitamin B5 and thus for coenzyme A biosynthesis is achieved by mutations that either activate a cryptic amino acid exporter, AexA (previously YdeD), or inactivate the amino acid importers AimA, AimB (previously YbxG), and BcaP. TheaexAgene is very poorly expressed under most conditions studied. However, mutations afecting the transcription factor AerA (previously YdeC), can result in strong constitutiveaexAexpression. AexA is the founding member of a conserved family of amino acid exporters inB. subtilis, which are all very poorly expressed. Therefore, we suggest to call this family “sleeping beauty family of amino acid exporters”. 2,3-Diaminopropionic acid can also be exported by AexA, and this amino acid also seems to be a natural substrate of AerA/ AexA, as it can cause a slight but significant induction ofaexAexpression, and AexA also provides some natural resistance towards 2,3-diaminopropionic acid. Moreover, our work shows how low specificity amino acid transporters contribute to amino acid homeostasis inB. subtilis.

IMPORTANCE

Even thoughB. subtilisis of of the most-studied bacteria, amino acid homeostasis in this organism is not fully understood. We have identified import and export systems for the C2 and C3 amino acids. Our work demonstrates that the responsible amino acid permeases contribute in a rather promiscuitive way to amino acid uptake. In addition, we have discovered AexA, the first member of a family of very poorly expressed amino acid exporters, that we call “sleeping beauty amino acid exporters”. The expression of these transporters is typically triggered by mutations in corresponding regulator genes that are acquired upon exposure to toxic amino acids. These exporters are ubiquitous in all domains of life. It is tempting to speculate that many of them are not expressed until the cells experience a selective pressure by toxic compounds and that the protect the cells from rare but potentially dangerous accounters with such compounds.
Performance analysis of FEC based SR motor drive using fuzzy tuned PI controller
Authors: Damarla Indira , M. Venmathi , V. Krishnakumar , P. Anbarasan
Published: December 2023

Purpose

In this paper, a new front end converter (FEC) topology has been proposed for the switched reluctance (SR) motor drive. This study aims to present the performance analysis of FEC-based SR motor drive using various types of control schemes like conventional proportional integral (PI) controller, fuzzy logic controller (FLC) and fuzzy-tuned proportional integral controller (Fuzzy-PI).

Design/methodology/approach

The proposed FEC-based SR motor drive with various control strategies is derived for the torque ripple minimization and speed control.

Findings

The steady state and the dynamic response of the FEC-based SR motor drive are analyzed using three different controllers under change in speed and loading conditions. The Fuzzy-PI-based control scheme improves the dynamic response of the system when compared with the FLC and the conventional PI controller.

Originality/value

The hardware prototype has been implemented for the FEC-based SR motor drive by using the Xilinx SPARTAN 6 FPGA processor. The experimental verification has been conducted and the results have been measured under steady state and dynamic conditions.
Social media and nonprofit fundraising: the influence of Facebook likes
Authors: Haruvy Ernan E. , Popkowski Leszczyc Peter T.L.
Published: December 2023

Purpose

This paper aims to demonstrate that Facebook likes affect outcomes in nonprofit settings. Specifically, Facebook likes influence affinity to nonprofits, which, in turn, affects fundraising outcomes.

Design/methodology/approach

The authors report three studies that establish that relationship. To examine social contagion, Study 1 – an auction field study – relies on selling artwork created by underprivileged youth. To isolate signaling, Study 2 manipulates the number of total Facebook likes on a page. To isolate commitment escalation, Study 3 manipulates whether a participant clicks a Facebook like.

Findings

The results show that Facebook likes increase willingness to contribute in nonprofit settings and that the process goes through affinity, as well as through Facebook impressions and bidding intensity. The total number of Facebook likes has a direct signaling effect and an indirect social contagion effect.

Research limitations/implications

The effectiveness of the proposed mechanisms is limited to nonprofit settings and only applies to short-term effects.

Practical implications

Facebook likes serve as both a quality signal and a commitment mechanism. The magnitude of commitment escalation is larger, and the relationship is moderated by familiarity with the organization. Managers should target Facebook likes at those less familiar with the organization and should prioritize getting a potential donor to leave a like as a step leading to donation, in essence mapping a donor journey from prospective to active, where Facebook likes play an essential role in the journey. In a charity auction setting, the donor journey involves an additional step of bidder intensity.

Social implications

The approach the authors study is shown effective in nonprofit settings but does not appear to extend to corporate social responsibility more broadly.

Originality/value

To the best of the authors’ knowledge, this study is the first investigation to map Facebook likes to a seller’s journey through signals and commitment, as well as the only investigation to map Facebook likes to charity auctions and show the effectiveness of this in the field.