bluuebunny/crossref_metadata_2025 huggingface dataset:
Clock genesperiodandtimelesscontrol synaptogenesis inDrosophilamotor terminals
Authors: Ferreiro María José , Astrada Soledad , Cantera Rafael , Ruiz Santiago
Published: November 2024

Some neurons undergo rhythmic morphological changes that persist in constant darkness and require the expression of clock genes. Flight motoneuron MN5, one of the best studied neurons ofDrosophila melanogasterexhibits several examples of this type of circadian structural plasticity. During the morning, when the fly is active, synaptic boutons are larger than during the night when the fly is resting though more synaptic boutons and synapses are observed. Here, by comparing bouton numbers at different timepoints in normal flies and in flies carrying loss-of-function mutations in clock genestimeless(tim) orperiod(per), we investigate whether the rhythmic changes in numbers of boutons and synapses require the expression of these genes. Absence oftimexpression abolished the rhythm in bouton number whereas absence ofperexpression appeared to increase the rhythm’s amplitude. This indicates that in normal flies TIM protein is necessary to drive the normal rhythm of bouton number and PER probably has a damping effect on it. In addition, it appears thattimandperexpression normally act as inhibitor of synaptogenesis because their loss-of-function mutations caused over-proliferation of synapses. Unexpectedly, TIM and PER were expressed in different cells. TIM was found in the glial sheath wrapping the motoneuron’s axon and PER was predominantly found along the axon, suggesting that the control of the rhythmic change in bouton and synapse numbers requires interactions between different cell types.
Targeted protein evolution in the gut microbiome by diversity-generating retroelements
Authors: Macadangdang Benjamin R. , Wang Yanling , Woodward Cora , Revilla Jessica I. , Shaw Bennett M. , Sasaninia Kayvan , Makanani Sara K. , Berruto Chiara , Ahuja Umesh , Miller Jeff F.
Published: November 2024

Diversity-generating retroelements (DGRs) accelerate evolution by rapidly diversifying variable proteins. The human gastrointestinal microbiota harbors the greatest density of DGRs known in nature, suggesting they play adaptive roles in this environment. We identified >1,100 unique DGRs among human-associatedBacteroidesspecies and discovered a subset that diversify adhesive components of Type V pili and related proteins. We show thatBacteroidesDGRs are horizontally transferred across species, that some are highly active while others are tightly controlled, and that they preferentially alter the functional characteristics of ligand-binding residues on adhesive organelles. Specific variable protein sequences are enriched whenBacteroidesstrains compete with other commensal bacteria in gnotobiotic mice. Analysis of >2,700 DGRs from diverse phyla in mother-infant pairs shows thatBacteroidesDGRs are preferentially transferred to vaginally delivered infants where they actively diversify. Our observations provide a foundation for understanding the roles of stochastic, targeted genome plasticity in shaping host-associated microbial communities.
The conserved aphid saliva chemosensory protein effector Mp10 targets plant AMSH deubiquitinases at cellular membranes to suppress pattern-triggered immunity
Authors: Gravino Matteo , Mugford Sam T. , Kreuter Nathan , Joyce Joshua , Wilson Christine , Kliot Adi , Canham James , Mathers Thomas C. , Drurey Claire , Maqbool Abbas , Martins Carlo , Saalbach Gerhard , Hogenhout Saskia A.
Published: November 2024

Chemosensory proteins (CSPs) are a conserved family present in insects and other arthropods, recognized for their critical roles in both intra- and interspecies communication. However, the functional mechanisms of these proteins remain largely unexplored. In our previous research, we identified a CSP in aphid saliva, Mp10, from the peach-potato aphidMyzus persicae, which functions as an effector protein modulating host plant immunity. Mp10 suppresses pattern recognition receptor (PRR)-triggered immunity (PTI), the first layer of plant defence, while also inducing effector-triggered immunity (ETI). In this study, we elucidate the molecular mechanisms by which Mp10 suppresses PTI. Our findings reveal that Mp10 interacts with AMSH deubiquitinase enzymes in plants, as shown by yeast two-hybrid, co-immunoprecipitation (co-IP), and FRET-FLIM assays, with these interactions predominantly localized to intracellular membranes. Mp10 was found to modulate the dynamics of membrane-bound PRR receptor kinases in plant cells. Co-IP and mass spectrometry analyses demonstrated that Mp10 and AMSH2 associate with a range of PRR kinases, PRR-associated kinases, and proteins involved in the intracellular trafficking of membrane proteins. Mp10 reduces the accumulation of these kinases at the cell surface by promoting their internalization to internal membranes, thereby dampening PTI. Supporting this, a dominant-negative catalytically inactive variant of AMSH2 also inhibits PTI. Interestingly, Mp10 orthologues from other sap-feeding hemipteran insects exhibit similar immune-suppressive activities, and our findings show that their interaction with plant AMSH proteins is conserved, indicating this immune-suppression mechanism is evolutionarily ancient.
Reconstitution of Human Brain Cell Diversity in Organoids via Four Protocols
Authors: Naas Julia , Balmãna Meritxell , Holcik Laurenz , Novatchkova Maria , Dobnikar Lina , Krausgruber Thomas , Ladstätter Sabrina , Bock Christoph , von Haeseler Arndt , Esk Christopher , Knoblich Jürgen A.
Published: November 2024

Human brain organoids are powerfulin vitromodels for brain development and disease. However, their variability can complicate use in biomedical research and drug discovery. Both the specific protocol as well as the pluripotent starting cell line influence organoid variability and can result in incomplete representation of brain cell types in an organoid experiment. Here, we systematically analyze the cellular and transcriptional landscape of brain organoids grown from multiple cell lines using four different protocols recapitulating dorsal and ventral forebrain, midbrain, and striatum. We establish the NEST-Score as a quantitative readout for cell line-driven and protocol-driven differentiation propensities by comparing cellular states across multiple cell lines and toin vivoreference data sets. Thereby, we establish a set of organoid protocols that together recreate the vast majority of cell types in the developing human brain and provide a reference for how well cell types are recapitulated across cell lines in each protocol. Additionally, we survey factors contributing to variability during organoid development and identify early gene expression signatures predicting protocol-driven organoid generation at later stages. We provide easy online access to our data through a web-based analysis tool, creating a reference for brain organoid research that allows rapid, straightforward validation of protocol and cell line performance.
Diverse quorum sensing systems regulate microbial communication and biogeochemical processes in deep-sea cold seeps
Authors: Peng Jiaxue , Liu Xinyue , Wang Jieni , Meng Nan , Cai Runlin , Peng Yongyi , Han Yingchun , Liao Jing , Li Chengcheng , Rubin-Blum Maxim , Ma Qiao , Dong Xiyang
Published: November 2024

Quorum sensing is a fundamental chemical communication mechanism that enables microorganisms to coordinate behavior and adapt to environmental conditions. In deep-sea cold seep ecosystems, where diverse microbial communities thrive, quorum sensing is likely a key mechanism driving microbial interactions. However, the distribution, mechanisms, and ecological roles of quorum sensing in cold seeps remain poorly understood. To address this, we analyzed 173 metagenomes, 33 metatranscriptomes, and 18 metabolomes from 17 global cold seep sites. We identified 299,355 quorum sensing genes from the seep non-redundant gene catalog, representing 34 gene types across six quorum sensing systems, with distribution patterns influenced by sediment depth and seep type. These quorum sensing genes were present in 3,576 metagenome-assembled genomes from 12 archaeal and 108 bacterial phyla, revealing a complex network of intraspecies and interspecies communication. Microbial groups involved in key metabolic processes, such as sulfate-reducing bacteria, anaerobic methanotrophic archaea, diazotrophs and organohalide reducers, were extensively regulated by quorum sensing, influencing biogeochemical cycles of carbon, nitrogen, and sulfur. Phylogenetic analysis and protein domain identification highlighted the functional roles of key quorum sensing-related proteins (e.g., PDEs, CahR, RpfC/G and LuxR) in modulating microbial behaviors, such as motility and chemotaxis. Heterologous expression and metabolomic profiling further confirmed the activity of representative LuxI-R pairs and identified inhibitors of quorum sensing in cold seep sediments. Overall, these findings highlight complexity and significance of quorum sensing in microbial interactions, ecological adaptation, and biogeochemical cycling within cold seep ecosystems, advancing our understanding of microbial communication in the deep biosphere.
Unbiased profiling of multipotency landscapes reveals spatial modulators of clonal fate biases
Authors: Erickson Alek G , Isaev Sergey , Artemov Artem , He Jingyan , Semsch Bettina , Murtazina Aliia , Sun Jia , Mangold Katrin , Chalou Anthi , Frisen Jonas , Ratz Michael , Andersson Emma , Kharchenko Peter V. , Adameyko Igor
Published: November 2024

Embryogenesis is commonly viewed through a tree model of cell differentiation, which does not adequately represent the spatiotemporal modulation of cell multipotency underlying morphogenesis. Here we develop an integrated approach, combiningin vivosingle-cell high-throughput clonal lineage tracing with machine learning, to systematically decompose continuous spectra of clonal fate biases in mouse embryos traced from neurulation until mid-gestation. The reconstructed patterns of clonal variation uncovered gene programs driving dynamic positional biasing of clonal composition during axial skeletogenesis and peripheral neurogenesis. Mosaic combinatorial perturbations targeting multiple receptors, including the Hedgehog pathway, led to novel clone types, which has implications for engineering custom cell type assemblages from well-defined progenitorsin vivo. Altogether, our work demonstrates an effective practical approach for interrogating programs guiding lineage specification.
Chromosomal Instability in Human Trophoblast Stem Cells and Placentas
Authors: Wang Danyang , Cearlock Andrew , Lane Katherine , Jan Ian , McCoy Rajiv , Yang Min
Published: November 2024

The human placenta, a unique tumor-like organ, is typically thought to exhibit rare aneuploidy associated with adverse pregnancy outcomes. Discrepancies in reported aneuploidy prevalence in placenta likely stem from limitations in modeling and the resolution of detection methods. Here, we used isogenic trophoblast stem cells (TSCs) derived from both naive and primed human pluripotent stem cells (hPSCs) to reveal the spontaneous occurrence of aneuploidy, suggesting chromosomal instability (CIN) as an inherent feature of the trophoblast lineage. We identified potential pathways contributing to the occurrence and tolerance of CIN. These findings were further validated using single cell multiome data from human placentas, where we observed a high prevalence of heterogeneous aneuploidy across trophoblast cells. Despite extensive chromosomal abnormalities, TSCs maintained their proliferative and differentiation capacities, suggesting that CIN is a typical aspect of placental development. Our study challenges the traditional view of aneuploidy in the placenta and provides new insights into the role of CIN in normal placental function.
Pathway Specific Unbinding Free Energy Profiles of Ritonavir Dissociation From HIV-1 Protease
Authors: Vig Emily , Sun Jianan , Chang Chia-en A.
Published: November 2024

Investigation of protein-drug recognition is key in understanding drug selectivity and binding affinity. In combination, binding/unbinding free energy landscape and intermolecular interactions can be used to understand the drug binding/unbinding mechanisms. This information is vital for the development of drugs with improved efficacy and explanation of mutation effects. This study investigated the dissociation processes of ritonavir unbinding from HIV protease (HIVp). Analyzing unbinding trajectories modeled by accelerated molecular dynamics (MD) simulations, three distinct pathways, Pathways A, B, and C, were characterized. Using reduced dimensionality strategy with the principal component analysis, we carried out short classical MD runs with explicit water to sample local fluctuation during ritonavir dissociation and applied the milestoning theory to construct unbinding free energy landscape. We found that each pathway showed similar values of binding free energy, albeit Pathway A accounts for over 50 percent of dissociation trajectories. Interesting, residue-residue correlation network analysis showed that in Pathway A, a broad correlation network outside the flap region governs protein motions during ritonavir unbinding which includes residues with reported mutation effects. However, the other two pathways showed limited correlation networks where no reported mutated residues were involved, explaining the favorability of Pathway A. Guided by the free energy profile, we investigated how and why of an energy barrier and minimum and demonstrated that hydrogen bonding governed the movement of the flap regions, directly impacting the calculated energy. Our study provided a new strategy to estimate ligand binding free energy and demonstrated the importance of the transient interactions during ligand-protein dissociation pathways in understanding drug unbinding.
Encapsulation of Select Violacein Pathway Enzymes in the 1,2-Propanediol Utilization Bacterial Microcompartment to Divert Pathway Flux
Authors: Palmero Brett Jeffrey , Gamero Emily , Mangan Niall M. , Tullman-Ercek Danielle
Published: November 2024

A continual goal in metabolic engineering is directing pathway flux to desired products and avoiding loss of pathway intermediates to competing pathways. Encapsulation of the pathway is a possible solution, as it creates a diffusion barrier between pathway intermediates and competing enzymes. It is hypothesized that bacteria use organelles known as bacterial microcompartments - proteinaceous shells encapsulating a metabolic pathway - for this purpose. We aim to determine to what degree this hypothesized benefit is conferred to encapsulated pathways. To this end, we used bacterial microcompartments to encapsulate select enzymes from the violacein pathway, which is composed of five enzymes that produce violacein as the main product and deoxyviolacein as a side product. Importantly, we studied the pathway in a cell-free context, allowing us to hold constant the concentration of unencapsulated and encapsulated enzymes and increase our control over reaction conditions. The VioE enzyme is a branch point in that it makes the precursor for both violacein and deoxyviolacein, the VioC enzyme is required for production of deoxyviolacein, and the VioD enzyme is required for violacein production. When we encapsulated VioE and VioC and left VioD unencapsulated, the product profile shifted toward deoxyviolacein and away from violacein compared to when VioC and VioD were both unencapsulated. This work provides the first fully quantitative evidence that microcompartment-based encapsulation can be used to divert pathway flux to the encapsulated pathway. It provides insight into why certain pathways are encapsulated natively and could be leveraged for metabolic engineering applications.
Symbiosis collapses during development of asexual offspring in the absence of heterotrophic feeding in a model cnidarian-algal symbiosis
Authors: Bedgood Samuel A. , Plichon Keyla , Weis Virginia M.
Published: November 2024

A stable symbiosis between corals and dinoflagellate algae is crucial for coral reef health, and it is driven by nutrient exchange and environmental interactions. Our understanding of the homeostasis between host cnidarian and algal symbiont during the host adult stage is a longtime area of focus, but little is known about the balance of partners during development and regeneration. We investigated the role of symbiotic algae and heterotrophic feeding on development in the sea anemone model organism commonly called Aiptasia. We focused on asexually-produced offspring (G1), examining the effects of autotrophic and heterotrophic nutrition on developmental rates. We found that the presence of symbionts enhanced growth in fed conditions but impeded development and survival under starvation. The effect of symbiont presence on starved offspring was dose-dependent where those offspring with more symbionts at an earlier stage lost tentacles and mass faster than those with fewer symbionts. Our data demonstrate the importance of heterotrophic nutrition during early development and establishment of symbiosis. We propose that suppression of immunity during development may account for the observed patterns, although further research is required to validate this hypothesis. Our results provide insight into the metabolic costs and benefits of symbiosis under different nutritional conditions during development and regeneration of symbiotic cnidarians.
Unexpected levels of antibiotic resistance in marine bacterial communities not solely explained by urban river discharge
Authors: Chan Brandon , Xue Carolyn , Lozano-Huntelman Natalie , Jimenez Karina , Jay Jennifer , Yeh Pamela , Kremer Colin
Published: November 2024

Driven by anthropogenic pressures, antibiotic resistance has become more prevalent within urban bacterial communities over recent decades. In general, resistance is expected to spread from highly impacted areas into surrounding environments as the spatial patterns of resistance reflect the balance between the ability of dispersal and horizontal gene transfer to spread resistance, and the effects of dilution or selection driven by other environmental or ecological factors that change along these gradients. However, the strength and scale of this effect is less clear, especially in coastal environments. We investigated antibiotic resistance of bacterial communities along a transect from a freshwater site in the Los Angeles River (surrounded by high-density urban development) out into the San Pedro Basin in the Pacific Ocean. We determined the minimum concentration of twelve different antibiotics needed to inhibit the growth of bacterial communities across eight sites. We also examined community composition and the prevalence of known genes related to antibiotic resistance from anthropogenic sources in each sample using 16S rRNA sequencing and qPCR. In contrast to our expectations, marine bacteria communities displayed higher resistance than the freshwater LA River community. Rather than the presence of known resistance genes or proximity to urban impacts, patterns of resistance were more strongly associated with the higher species diversity found in marine communities. These unexpected results open new opportunities to determine why marine bacterial communities possess high resistance and the repercussions for potentially pathogenic bacteria and their impacts on the health of humans and wildlife.
Neural correlates of unconscious and conscious visual processing
Authors: Menétrey Maëlan Q. , Herzog Michael H. , Pascucci David
Published: November 2024

Postdictive effects, where later events influence the perception of earlier ones, suggest that conscious perception is not a continuous stream but occurs at discrete moments, preceded by extended periods of unconscious processing. This is evident in the Sequential Metacontrast Paradigm (SQM), where a stream of lines and vernier offsets is unconsciously integrated over several hundred milliseconds before conscious perception emerges: regardless of whether one or multiple verniers are shown, only a single offset is perceived from the first to the last line. Postdictive phenomena offer a unique opportunity to study the neural correlates of unconscious and conscious stages of perception because unconscious and conscious processing are well separated in time. Using EEG recordings during the SQM, we identified two distinct stages of neural activity. Early occipital EEG activity patterns (∼200 ms after the initial vernier presentation) capture unconscious processing, while later centro-parietal EEG patterns (∼400-600 ms after the onset of the stimulus stream) are associated with conscious perception, aligning closely with behavioral reports. We propose that the transition between these distinct neural topographies reflects the discrete moments when conscious perception emerges.
Discovery of antibiotics in the archaeome using deep learning
Authors: Torres Marcelo D. T. , Wan Fangping , de la Fuente-Nunez Cesar
Published: November 2024

Antimicrobial resistance (AMR) is one of the greatest threats facing humanity, making the need for new antibiotics more critical than ever. While most antibiotics have traditionally been derived from bacteria and fungi, archaea—a distinct and underexplored domain of life—offer a largely untapped reservoir for antibiotic discovery. In this study, we leveraged deep learning to systematically explore the archaeome, uncovering promising new candidates for combating AMR. By mining 233 archaeal proteomes, we identified 12,623 molecules with potential antimicrobial activity. These newly discovered peptide compounds, termed archaeasins, exhibit unique compositional features that differentiate them from traditional antimicrobial peptides, including a distinct amino acid profile. We synthesized 80 archaeasins, 93% of which demonstrated antimicrobial activityin vitro. Notably,in vivovalidation identified archaeasin-73 as a lead candidate, significantly reducing bacterial loads in mouse infection models, with effectiveness comparable to established antibiotics like polymyxin B. Our findings highlight the immense potential of archaea as a resource for developing next-generation antibiotics.
Rarely categorical, always high-dimensional: how the neural code changes along the cortical hierarchy
Authors: Posani Lorenzo , Wang Shuqi , Muscinelli Samuel , Paninski Liam , Fusi Stefano
Published: November 2024

A long-standing debate in neuroscience concerns whether individual neurons are organized into functionally distinct populations that encode information differently ("categorical" representations) and the implications for neural computation. Here, we systematically analyzed how cortical neurons encode cognitive, sensory, and movement variables across 43 cortical regions during a complex task (14,000+ units from the International Brain Laboratory public Brainwide Map data set) and studied how these properties change across the sensory-cognitive cortical hierarchy. We found that the structure of the neural code was scale-dependent: on a whole-cortex scale, neural selectivity was categorical and organized across regions in a way that reflected their anatomical connectivity. However, within individual regions, categorical representations were rare and limited to primary sensory areas. Remarkably, the degree of categorical clustering of neural selectivity was inversely correlated to the dimensionality of neural representations, suggesting a link between single-neuron selectivity and computational properties of population codes that we explained in a mathematical model. Finally, we found that the fraction of linearly separable combinations of experimental conditions ("Shattering Dimensionality") was near maximal across all areas, indicating a robust and uniform ability for flexible information encoding throughout the cortex. In conclusion, our results provide systematic evidence for a non-categorical, high-dimensional neural code in all but the lower levels of the cortical hierarchy.
Heat Shock Factor 1 Governs Sleep-Wake Cycles Across Species
Authors: Yamazaki Shintaro , Valekunja Utham K. , Chen-Roetling Jing , Reddy Akhilesh B.
Published: November 2024

Heat Shock Factor 1 (HSF1) is a critical transcription factor for cellular proteostasis, but its role in sleep regulation remains unexplored. We demonstrate that nuclear HSF1 levels in the mouse brain fluctuate with sleep-wake cycles, increasing during extended wakefulness and decreasing during sleep. Using CUT&RUN and RNA-seq, we identified HSF1-regulated transcriptional changes involved in synaptic organization, expanding its known functions beyond traditional heat shock responses. Both systemic and brain-specificHsf1knockout mice exhibit altered sleep homeostasis, including increased delta power after sleep deprivation and upregulation of sleep-related genes. However, these knockouts struggle to maintain sleep due to disrupted synaptic organization. InDrosophila, knockout of HSF1’s ortholog results in fragmented sleep patterns, suggesting a conserved role for HSF1 in sleep regulation across species. Our findings reveal a novel molecular mechanism underlying sleep regulation and offer potential therapeutic targets for sleep disturbances.
Upregulating ANKHD1 in PS19 mice reduces Tau phosphorylation and mitigates Tau-toxicity-induced cognitive deficits
Authors: Tian Xiaolin , Le Nathan , Zhao Yuhai , Alawamleh Dina , Schwartz Andrew , Meyer Lauren , Helm Elizabeth , Wu Chunlai
Published: November 2024

Abnormal accumulation of Tau protein in the brain disrupts normal cellular function and leads to neuronal death linked with many neurodegenerative disorders such as Alzheimer’s disease. An attractive approach to mitigate Tau-induced neurodegeneration is to enhance the clearance of toxic Tau aggregates. We previously showed that upregulation of the fly genemaskprotects against FUS- and Tau-induced photoreceptor degeneration in fly disease models. Here we have generated a transgenic mouse line carrying Cre-inducible ANKHD1, the mouse homolog ofmask, to determine whether the protective role ofmaskis conserved from flies to mammals. Utilizing the TauP301S-PS19 mouse model for Tau-related dementia, we observed that ANKHD1 significantly reduced hyperphosphorylated human Tau in 6-month-old mice. Additionally, there was a notable trend towards reduced gliosis levels in these mice, suggesting a protective role of ANKHD1 against TauP301S-linked degeneration. Further analysis of 9-month- old mice revealed a similar trend of effects. Moreover, we found that ANKHD1 also suppresses the cognitive defect of 9-month-old PS19 female mice in novel object recognition (NOR) behavioral assay. Unlike previous therapeutic strategies that primarily focus on inhibiting Tau phosphorylation or directly clearing aggregates, this study highlights the novel role of ANKHD1 in promoting autophagy as a means to mitigate Tau pathology. This novel mechanism not only underscores ANKHD1’s potential as a unique therapeutic target for tauopathies but also provides new insights into autophagy-based interventions for neurodegenerative diseases.
Mapping Pesticide-Induced Metabolic Alterations in Human Gut Bacteria
Authors: Chen Li , Yan Hong , Di Shanshan , Guo Chao , Zhang Huan , Zhang Shiqi , Gold Andrew , Wang Yu , Hu Ming , Wu Dayong , Johnson Caroline H. , Wang Xinquan , Zhu Jiangjiang
Published: November 2024

Pesticides can modulate gut microbiota (GM) composition, but their specific effects on GM remain largely elusive. Our study demonstrated that pesticides inhibit or promote growth in various GM species, even at low concentrations, and can accumulate in GM to prolong their presence in the host. Meanwhile, the pesticide induced changes in GM composition are associated with significant alterations in gut bacterial metabolism that reflected by the changes of hundreds of metabolites. We generated a pesticide-GM-metabolites (PMM) network that not only reveals pesticide-sensitive gut bacteria species but also report specific metabolic changes in 306 pesticide-GM pairs (PGPs). Using anin vivomice model, we further demonstrated a PGP’s interactions and verified the inflammation-inducing effects of pesticides on the host through dysregulated lipid metabolism of microbes. Taken together, our findings generate a PMM interactions atlas, and shed light on the molecular level of how pesticides impact host health by modulating GM metabolism.

Graphical Abstract
Primed bovine embryonic stem cell lines can be derived at diverse stages of blastocyst development with similar efficiency and molecular characteristics
Authors: Guiltinan Carly , Botigelli Ramon C. , Candelaria Juliana I. , Smith Justin M. , Arcanjo Rachel B. , Denicol Anna C.
Published: November 2024

In this study, we established bovine embryonic stem cell (bESC) lines from early (eBL) and full (BL) blastocysts to determine the efficiency of bESC derivation from an earlier embryonic stage and compare the characteristics of the resulting lines. Using established medium and protocols for derivation of primed bESCs from expanded blastocysts, we derived bESC lines from eBLs and BLs with the same efficiency (4/12 each, 33%). Regardless of original blastocyst stage, bESC lines had a similar phenotype, including differentiation capacity, stable karyotype, and pluripotency marker expression over feeder-free transition and long-term culture. Transcriptome and functional analyses indicated that eBL– and BL-derived lines were in primed pluripotency. We additionally compared RNA-sequencing data from our lines to bovine embryos and stem cells from other recent reports, finding that base medium was the predominant source of variation among cell lines. In conclusion, our results show that indistinguishable bESC lines can be readily derived from eBL and BL, widening the pool of embryos available for bESC establishment. Finally, our investigation points to sources of variation in cell phenotype among recently reported bESC conditions, opening the door to future studies investigating the impact of factors aside from signaling molecules on ESC derivation, maintenance, and performance.

SUMMARY STATEMENT

Primed bovine embryonic stem cell lines can be readily established from early blastocysts and are indistinguishable from full blastocyst-derived lines, widening the pool of embryos available for stem cell derivation.
Corticotropin-releasing factor neurons of the bed nucleus of the stria terminalis demonstrate sex- and estrous phase-dependent differences in synaptic activity and in their role in anxiety-potentiated startle
Authors: Chudoba Rachel , Dabrowska Joanna
Published: November 2024

Background

The prevalence of post-traumatic stress disorder (PTSD) and anxiety disorders is higher in women than men. The severity of hallmark symptoms including hypervigilance and fear reactivity to unpredictable threats varies with sex and reproductive cycle, but the underlying mechanisms remain unclear. Here, we investigated corticotropin-releasing factor (CRF) neurons in the dorsolateral bed nucleus of the stria terminalis (BNSTDL) as a potential nexus for the influence of biological sex and reproductive cycle on fear- and anxiety-related behaviors.

Methods

103 male and 132 cycle-monitored female CRF-Cre rats were used. BNSTDL-CRF neuron excitability and synaptic activity was recorded with slice electrophysiology. Chemogenetic inhibition of BNSTDL-CRF neurons was performed before elevated-plus maze, predator odor exposure, shock-induced startle sensitization, and anxiety-potentiated startle (APS) following unpredictable fear conditioning.

Results

BNSTDL-CRF neurons in females exhibit higher excitability (cycle-independent) and lower sensitivity to excitatory synaptic inputs (proestrus and diestrus) compared to males. BNSTDL-CRF neuron inhibition reduces open-arm time in estrous females but not males, suggesting that BNSTDL-CRF neurons reduce anxiety during sexual receptivity. In the APS, BNSTDL-CRF neuron inhibition attenuates short-term startle potentiation in males, whereas it causes persistent APS in diestrous females.

Conclusions

Unpredictable fear conditioning elicits sex- and estrous phase-specific APS, differentially regulated by BNSTDL-CRF neurons. Persistent APS in females align with hormonal phases marked by low reproductive hormones, mirroring human PTSD findings. Our findings underscore the sex- and hormone-specific role of BNSTDL-CRF neurons in APS. Widely used in human studies, APS may bridge animal and human research, supporting biomarker development and more effective pharmacotherapies.
Design of facilitated dissociation enables control over cytokine signaling duration
Authors: Broerman Adam J. , Pollmann Christoph , Lichtenstein Mauriz A. , Jackson Mark D. , Tessmer Maxx H. , Ryu Won Hee , Abedi Mohamad H. , Sahtoe Danny D. , Allen Aza , Kang Alex , De La Cruz Joshmyn , Brackenbrough Evans , Sankaran Banumathi , Bera Asim K. , Zuckerman Daniel M. , Stoll Stefan , Praetorius Florian , Piehler Jacob , Baker David
Published: November 2024

Protein design has focused primarily on the design of ground states, ensuring they are sufficiently low energy to be highly populated. Designing the kinetics and dynamics of a system requires, in addition, the design of excited states that are traversed in transitions from one low-lying state to another. This is a challenging task as such states must be sufficiently strained to be poorly populated, but not so strained that they are not populated at all, and because protein design methods have generally focused on creating near-ideal structures. Here we describe a general approach for designing systems which use an induced-fit power stroke to generate a structurally frustrated and strained excited state, allosterically driving protein complex dissociation. X-ray crystallography, double electron-electron resonance spectroscopy, and kinetic binding measurements demonstrate that incorporating excited states enables design of effector-induced increases in dissociation rates as high as 6000-fold. We highlight the power of this approach by designing cytokine mimics which can be dissociated within seconds from their receptors.
ASAP: An automatic sustained attention prediction method for infants and toddlers using wearable device signals
Authors: Zhang Yisi , Martinez-Cedillo A. Priscilla , Mason Harry T. , Vuong Quoc C. , Garcia-de-Soria M. Carmen , Mullineaux David , Knight Marina , Geangu Elena
Published: November 2024

Sustained attention (SA) is a critical cognitive ability that emerges in infancy. The recent development of wearable technology for infants enables the collection of large-scale multimodal data in the natural environment, including physiological signals. To capitalize on these new technologies, psychologists need methods to efficiently extract valid and robust SA measures from large datasets. In this study, we present an innovative automatic sustained attention prediction (ASAP) method that harnesses electrocardiogram (ECG) and accelerometer (Acc) signals recorded with wearable sensors from 75 infants (6-, 9-, 12-, 24- and 36-months). Infants undertook various naturalistic tasks similar to those encountered in their natural environment, including free play with their caregivers. Annotated SA was validated by fixation signals from eye-tracking. ASAP was trained on temporal and spectral features derived from the ECG and Acc signals to detect attention periods, and tested against human-coded SA. ASAP’s performance is similar across all age groups, demonstrating its suitability for studying development. We also investigated the relationship between attention periods and low-level perceptual features (visual saliency, visual clutter) extracted from the egocentric videos recorded during caregiver-infant free play. Saliency increased during attention vs inattention periods and decreased with age for attention (but not inattention) periods. Crucially, there was no observable difference in results from ASAP attention detection relative to the human-coded attention. Our results demonstrate that ASAP is a powerful tool for detecting infant SA elicited in natural environments. Alongside the available wearable sensors, ASAP provides unprecedented opportunities for studying infant development in the ‘wild’.
Social and Contextual Memory Impairments Induced by Amyloid-β Oligomers are Rescued by Sigma-1 Receptor Activation
Authors: Djebari Souhail , Jiménez-Herrera Raquel , Iborra-Lázaro Guillermo , Jiménez-Díaz Lydia , Navarro-López Juan D.
Published: November 2024

Sigma-1 receptors (S1Rs) are widely expressed throughout the central nervous system and modulate neuron intracellular calcium levels, leading to changes in neurotransmitter release and neuronal activity. They also interact with various proteins and signaling pathways, playing a key role in regulating synaptic plasticity in brain areas such as the hippocampus, thereby influencing learning and memory processes. This opens a research avenue to explore S1R modulation as a potential therapeutic target in diseases involving hippocampal synaptic alterations and compromised cognitive processes, such as Alzheimer’s disease (AD). Here, we hypothesize that pharmacological activation of S1R could counteract synaptic plasticity deficits and hippocampal-dependent cognitive alterations in an early-stage amyloidosis model of Alzheimer’s disease, induced by intracerebroventricular (icv) administration of Aβ1-42oligomers (oAβ1-42). For that purpose, we investigateex vivoCA3-CA1 synaptic plasticity, whilein vivo, we performed open field habituation and social recognition tasks to assess contextual and social memory, respectively. Our data show that pharmacological activation of S1Rs with the selective agonist PRE-084 counteract oAβ1-42deleterious effects on CA3-CA1 long-term synaptic plasticity (LTP), and hippocampal-dependent contextual and social memory, without alterations of spontaneous behaviors. Together, these results provide evidence for the role of S1Rs in ameliorating hippocampal synaptic and contextual memory dysfunctions and, for the first time, in early amyloid-induced social memory deficits, highlighting their potential in the development of comprehensive treatments for early AD. Also, the absence of adverse behavioral outcomes associated with PRE-084 treatment accentuates its safety profile, underscoring its potential as a therapeutic agent.
Metabolomic Analysis of Murine Tissues Infected withBrucella melitensis
Authors: Ponzilacqua-Silva Bárbara , Dadelahi Alexis S. , Moley Charles R. , Abushahba Mostafa F.N. , Skyberg Jerod A.
Published: November 2024

Brucellais a gram negative, facultative, intracellular bacterial pathogen that constitutes a substantial threat to human and animal health.Brucellacan replicate in a variety of tissues and can induce immune responses that alter host metabolite availability. Here, mice were infected withB. melitensisand murine spleens, livers, and female reproductive tracts were analyzed by GC-MS to determine tissue-specific metabolic changes at one-, two- and four-weeks post infection. The most remarkable changes were observed at two-weeks post-infection when relative to uninfected tissues, 42 of 329 detected metabolites in reproductive tracts were significantly altered byBrucellainfection, while in spleens and livers, 68/205 and 139/330 metabolites were significantly changed, respectively. Several of the altered metabolites in host tissues were linked to the GABA shunt and glutaminolysis. Treatment of macrophages with GABA did not alter control ofB. melitensisinfection, and deletion of the putative GABA transporter BMEI0265 did not alterB. melitensisvirulence. While glutaminolysis inhibition did not affect control ofB. melitensisin macrophages, glutaminolysis was required for macrophage IL-1β production in response toB. melitensis. In sum, these results indicate thatBrucellainfection alters host tissue metabolism and that these changes could have effects on inflammation and the outcome of infection.
Lactobacillus paracaseiCNCM I-5220-derived postbiotic counteracts skin inflammation and protects skin barrier integrity
Authors: Pimazzoni Silvia , Algieri Francesca , Tanaskovic Nina , Braga Daniele , Penna Giuseppe , Rescigno Maria
Published: November 2024

Introduction

Skin inflammation and damage of skin barrier integrity contribute to the pathogenesis of inflammatory skin diseases such as psoriasis and atopic dermatitis. Nowadays, there is a growing interest in alternative and complementary strategies to counteract skin inflammation and treat dermatologic conditions.

Objectives

Postbiotics, metabolites released during bacterial fermentation, exert anti-inflammatory proprieties and contribute to the maintenance of epithelial barrier integrity. Therefore, we investigated the effect of LP-PBL, a novelLactobacillus paracaseiCNCM I-5220-derived postbiotic, in controlling skin inflammation and protecting the skin barrier.

Methods

We performed RNA-sequencing on Poly(I:C)-stimulated keratinocytes and investigated LP-PBL efficacy in regulating pro-inflammatory cytokine release. The production of most relevant cytokines was demonstrated by ELISA. Then, we tested postbiotic lenitive efficacy on healthy volunteers’ irritated skin. We compared the effect of a postbiotic-containing cream formulation versus placebo on sodium lauryl sulphate treated skin.

Results

We demonstrate that LP-PBL has anti-inflammatory activity by modulating Poly(I:C)-dependent inflammatory pathways and pro-inflammatory cytokine release in keratinocytes. The postbiotic inhibited the upregulation of interleukin (IL)-23A, which is overexpressed in psoriatic skin, and ofIL-33and thymic stromal lymphopoietin (TSLP) that are upregulated in atopic dermatitis. Moreover, it increased filaggrin and zonula occludens (ZO)-1 expression in Poly(I:C)-stimulated keratinocytes, suggesting beneficial effects on inflamed and damaged skin. Consistently, a clinical test on healthy volunteers showed that topic LP-PBL treatment significantly reduced skin redness upon sodium lauryl sulphate challenge compared to placebo, leading to a rapid recovery of the irritated skin.

Conclusion

Overall, we demonstrated the protective role of LP-PBL on the skin, bothin vitroand in the clinical test, suggesting that postbiotic topical application could represent an innovative and promising strategy to counteract skin inflammation and preserve skin barrier integrity.
Biochemical principles of miRNA targeting in flies
Authors: Vega-Badillo Joel , Zamore Phillip D. , Jouravleva Karina
Published: November 2024

MicroRNAs-direct Argonaute proteins to repress complementary target mRNAs via mRNA degradation or translational inhibition. While mammalian miRNA targeting has been well studied, the principles by whichDrosophilamiRNAs bind their target RNAs remain to be fully characterized. Here, we use RNA Bind-n-Seq to systematically identify binding sites and measure their affinities for four highly expressedDrosophilamiRNAs. Our results reveal a narrower range of binding site diversity in flies compared to mammals, with fly miRNAs favoring canonical seed-matched sites and exhibiting limited tolerance for imperfections within these sites. We also identified non-canonical site types, including nucleation-bulged and 3′-only sites, whose binding affinities are comparable to canonical sites. These findings establish a foundation for future computational models ofDrosophilamiRNA targeting, enabling predictions of regulatory outcomes in response to cellular signals, and advancing our understanding of miRNA- mediated regulation in flies.
A definition of the body of knowledge for real estate: reconceptualizing the discipline and delineating the jurisdictions of its practice
Authors: K'Akumu Owiti A.
Published: November 2024

Purpose

Following calls at different times in the United States for the definition of the body of knowledge (BOK) of real estate discipline, this briefing sets out to define the intellectual boundaries of real estate and applies the definitional concept to map out the scopes of real estate professions and real estate valuation vocation

Design/methodology/approach

The study essentially uses a literature review to draw out definitional issues that have been tackled before. It reviews calls that have been made in the past for a definition of the BOK of the real estate discipline. Further, it reviews past attempts at definition to reveal why they failed at the definition project.

Findings

The study found three key suggestions made in the past: that there is a need to define real estate’s BOK, that there is a need to use a “central structure” to define the BOK of real estate, and that definition of the BOK of real estate should rely on the activity nodes that constitute real estate. The study has relied on these three key ideas to define real estate as the science of value creation, distribution and sustenance in built space.

Practical implications

The definition of the BOK will help in curriculum development for real estate education. It will help faculties and departments to single out what fits into the real estate curriculum and what does not fit in.

Originality/value

A definition of the BOK for real estate: reconceptualizing the discipline and delineating jurisdictional boundaries of its practice.
The emergence of collective moral elevation through multilevel individual and organizational processes
Authors: Marasli Furkan , Golgeci Ismail , Akgun Ali Akber , Müceldili Büşra , Arslan Ahmad
Published: November 2024

Purpose

This paper aims to extend the concept of moral elevation from the individual level to the team/group level by introducing the notion of collective moral elevation (CME) and elucidating its emergence.

Design/methodology/approach

Drawing on social exchange theory and social capital arguments, this paper presents a conceptual framework that outlines the mechanisms through which moral norms, organizational symbols, social cohesion and repeated interactions facilitate the transition from individual internalization of norms to collective aggregation of moral elevation.

Findings

The proposed framework emphasizes the processual nature of CME, highlighting the importance of understanding sequences of events rather than merely examining static relationships between variables.

Originality/value

This paper is one of the pioneering academic works to offer a novel perspective on moral elevation, exploring its manifestation at the collective level and elucidating the dynamics of its emergence and evolution within teams and groups in organizational settings. Our proposed framework explicates how moral norms, organizational symbols, social cohesion, emulation and their iterations allow individuals to transition from individual internalization of norms to collective aggregation of moral elevation.