bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of the Follow-Up Discourse Observation Protocol (FUDOP) for characterizing instructor active-learning follow-up behaviors
Authors: Cen Xinjian , Kight Maci , Lee Rachel , Kranzfelder Petra , Lo Stanley M. , Maloy Jeffrey , Owens Melinda T.
Published: August 2024

Instructors can provide feedback to their class in multiple ways. One way is through their follow-up behaviors, which are the specific strategies instructors implement after active learning activities. These behaviors could play an important role in student learning as students can receive feedback from the instructor. However, there is little research on the effects of different types of follow-up behaviors. Follow-up after active learning can be seen as a form of discourse between the instructor and the entire class. Previous researchers developed the Classroom Discourse Observation Protocol (CDOP) to analyze discourse between the instructor and individual students or small groups. We used CDOP as a starting point to develop and validate a new protocol, the Follow-Up Discourse Observation Protocol (FUDOP), to characterize instructional follow-up behaviors to the entire class after active-learning activities. We then used FUDOP to characterize follow-up behaviors of multiple instructors in introductory biology courses at three different universities. We measured consistent differences in these behaviors across instructors but not within instructors, demonstrating that instructors may engage in consistent follow-up behaviors. FUDOP could allow instructors and researchers to better measure and analyze follow-up behaviors and their effects, which could in turn provide guidance to instructors and faculty developers.
Severe disease is not essential for a high neutralizing antibody response post-SARS-CoV-2 infection
Authors: Khairallah Afrah , Jule Zesuliwe , Piller Alice , Bernstein Mallory , Reedoy Kajal , Ganga Yashica , Gosnell Bernadett I. , Karim Farina , Moosa Yunus , Ndung’u Thumbi , Khan Khadija , Sigal Alex
Published: August 2024

Neutralizing antibody responses correlate with protection from SARS-CoV-2 infection, yet higher neutralizing responses associate with more severe disease. Whether people without severe disease can also develop strong neutralizing responses to infection, and the pathways involved, is less clear. We performed a proteomic analysis on sera from 71 individuals infected with ancestral SARS-CoV-2, enrolled during the first South African infection wave. We determined disease severity by whether participants required supplemental oxygen and measured neutralizing antibody levels at convalescence. High neutralizing antibodies were associated with high disease severity, yet 40% of participants with lower disease severity had neutralizing antibody levels comparable to those with severe disease. We found 130 differentially expressed proteins between high and low neutralizers and 40 between people with high versus low disease severity. Five proteins overlapped, including furin, a protease which enhances SARS-CoV-2 infection. High neutralizers with non-severe disease had similar levels of differentially expressed neutralization response proteins to high neutralizers with severe disease, yet similar levels of differentially expressed disease severity proteins to participants with non-severe disease. Furthermore, we could reasonably predict who developed a strong neutralizing response based on a single protein, HSPA8, involved in clathrin pit uncoating. These results indicate that a strong antibody response does not always require severe disease and may involve different pathways.
The transcription factor BATF pioneers the differentiation program of cytolytic effector CD8+T cells through the direct interaction with IRF4
Authors: Fujisawa Sotaro , Tanabe Yamato , Hojo Arisa , Shiga Ryotaro , Kurachi Junko , Koura Miki , Tamai Toshikatsu , Miyanari Yusuke , Wherry Edward John , Kurachi Makoto
Published: August 2024

The transcription factor BATF plays critical roles in the differentiation of various immune cells, including CD8+T cells. Here, we demonstrated that BATF controls epigenomic and transcriptomic reprogramming of CD8+T cells at an early phase of acute viral infection, thereby promoting the differentiation of cytolytic effector CD8+T cells. Loss of BATF drastically perturbed gene expression, chromatin accessibility, and the bindings of key transcription factors including Jun, T-bet, and IRF4. The direct interaction with IRF4 was essential for BATF-mediated effector differentiation, as the BATF mutant lacking this interaction failed to induce proper chromatin remodeling and proliferation of antigen-specific CD8+T cells. Notably, IRF4 binding was exhaustively dependent on BATF, whereas BATF retained binding capacity even in IRF4-deficient CD8+T cells. Furthermore, BATF initiated chromatin remodeling in the absence of IRF4, whereas subsequent dynamic epigenomic reorganization required IRF4. Our data proposed that BATF serves as a “pioneer transcription factor” spearheading the reorganization of chromatin architecture upon antigen encounter, followed by further rearrangement of epigenomic and transcriptomic landscapes through the cooperation with IRF4.
An autonomous robotic system for high-throughput phenotyping and behavioral studies of individual fruit flies
Authors: Woo Seung Je , Huang Cheng , Savall Joan , Conrad Benjamin L , Luo Junjie , Schnitzer Mark J
Published: August 2024

The fruit fly, Drosophila melanogaster, is a widely used model species in biomedical research. Despite its importance, conducting manual experiments with individual fruit flies can be challenging and time-consuming, especially for studies of individual fly behaviors. Such studies often involve cumbersome preparatory steps, such as manually tethering a fly and then positioning it within an experimental setup1,2. These procedures commonly require the fly to be anesthetized, and, before behavioral assessments begin, the fly must recover from anesthesia. Hence, the introduction of automated phenotyping and behavioral assays would expedite important aspects of fly research, by minimizing manual handling of flies and decreasing the net time needed for experiments. Here, we introduce FlyMAX (Fly Manipulation and Autonomous eXperimentation), an autonomous robotic system for manipulating adult flies without use of anesthesia. FlyMAX collects individual flies from a standard vial, analyzes them with computer vision, and achieves a throughput of >1,000 flies per day for high-throughput inspection and characterization assays. Robotic handling had no detectable adverse effects on fly longevity or our assessments of fly health. Moreover, the behavioral performance of flies, especially of males, was better and less variable than of flies handled manually. Our system employs deep learning-based machine vision for real-time assessments of picking quality and fly phenotypes. This enables fully pipelined, autonomous experimentation for behavioral assays with individual flies in controlled environments, which was previously infeasible. Overall, FlyMAX constitutes a promising technology to enhance the efficiency and reproducibility of research with flies and other insects in fields such as genetics, neuroscience, and drug screening.
Histone deacetylase inhibition expands cellular proteostasis repertoires to enhance neuronal stress resilience
Authors: Taylor Caitlin A , Maor-Nof Maya , Metzl-Raz Eyal , Hidalgo Aaron , Yee Callista , Gitler Aaron D , Shen Kang
Published: August 2024

Neurons are long-lived, terminally differentiated cells with limited regenerative capacity. Cellular stressors such as endoplasmic reticulum (ER) protein folding stress and membrane trafficking stress accumulate as neurons age and accompany age-dependent neurodegeneration. Current strategies to improve neuronal resilience are focused on using factors to reprogram neurons or targeting specific proteostasis pathways. We discovered a different approach. In an unbiased screen for modifiers of neuronal membrane trafficking defects, we unexpectedly identified a role for histone deacetylases (HDACs) in limiting cellular flexibility in choosing cellular pathways to respond to diverse types of stress. We show that genetic or pharmacological inactivation of HDACs results in improved neuronal health in response to ER protein folding stress and endosomal membrane trafficking stress in C. elegans and mammalian neurons. Surprisingly, HDAC inhibition enabled neurons to activate latent proteostasis pathways tailored to the nature of the individual stress, instead of generalized transcriptional upregulation. These findings shape our understanding of neuronal stress responses and suggest new therapeutic strategies to enhance neuronal resilience.
Reverse-breaking CFS (rev-bCFS): Disentangling conscious and unconscious effects by measuring suppression and dominance times during continuous flash suppression
Authors: Ciorli Tommaso , Pia Lorenzo , Stein Timo
Published: August 2024

Breaking continuous flash suppression (bCFS) is a widely used experimental paradigm that exploits detection tasks to measure the time an initially invisible stimulus requires to escape interocular suppression and access awareness. One pretty contentious and unresolved issue is whether differences in detection times reflect unconscious or conscious processing. To answer this question, here we introduce a novel approach (i.e., reverse-bCFS [rev-bCFS]) that measures the time an initially visible stimulus requires to be suppressed from awareness. Results from two experiments using face stimuli indicate that rev-bCFS can capture conscious effects, which indicates that contrasting standard bCFS with rev-bCFS can isolate unconscious processing occurring specifically during bCFS. For example, while face inversion impacted both bCFS and rev-bCFS, effects were larger in bCFS, suggesting a distinct contribution of unconscious processing to the advantage of upright over inverted faces in accessing awareness. Combining standard bCFS and rev-bCFS may offer a fruitful approach able to disentangle conscious and unconscious effects occurring during interocular suppression.
Genomes of the Caribbean reef-building corals Colpophyllia natans, Dendrogyra cylindrus, and Siderastrea siderea
Authors: Locatelli Nicolas Shogo , Baums Iliana B
Published: August 2024

Corals populations worldwide are declining rapidly due to elevated ocean temperatures and other human impacts. The Caribbean harbors a high number of threatened, endangered, and critically endangered coral species compared to reefs of the larger Indo-Pacific. The reef corals of the Caribbean are also long diverged from their Pacific counterparts and may have evolved different survival strategies. Most genomic resources have been developed for Pacific coral species which may impede our ability to study the changes in genetic composition of Caribbean reef communities in response to global change. To help fill the gap in genomic resources, we used PacBio HiFi sequencing to generate the first genome assemblies for three Caribbean, reef-building corals, Colpophyllia natans, Dendrogyra cylindrus, and Siderastrea siderea. We also explore the genomic novelties that shape scleractinian genomes. Notably, we find abundant gene duplications of all classes (e.g., tandem and segmental), especially in S. siderea. This species has one of the largest genomes of any scleractinian coral (822Mb) which seems to be driven by repetitive content and gene family expansion and diversification. As the genome size of S. siderea was double the size expected of stony corals, we also evaluated the possibility of an ancient whole genome duplication using Ks tests and found no evidence of such an event in the species. By presenting these genome assemblies, we hope to develop a better understanding of coral evolution as a whole and to enable researchers to further investigate the population genetics and diversity of these three species.
Anti-correlation of LacI association and dissociation rates observed in living cells
Authors: Kandavalli Vinodh , Zikrin Spartak , Elf Johan , Jones Daniel
Published: August 2024

The rate at which transcription factors (TFs) bind their cognate sites has long been assumed to be limited by diffusion, and thus independent of binding site sequence. Here, we systematically test this assumption using cell-to-cell variability in gene expression as a window into the in vivo association and dissociation kinetics of the model transcription factor LacI. Using a stochastic model of the relationship between gene expression variability and binding kinetics, we performed single-cell gene expression measurements to infer association and dissociation rates for a set of 35 different LacI binding sites. We found that both association and dissociation rates differed significantly between binding sites, and moreover observed a clear anticorrelation between these rates across varying binding site strengths. These results contradict the long-standing hypothesis that TF binding site strength is primarily dictated by the dissociation rate, but may confer the evolutionary advantage that TFs do not get stuck in near-operator sequences while searching.
Olfactory receptor coexpression and co-option in the dengue mosquito
Authors: Adavi Elisha David , dos Anjos Vitor L , Kotb Summer , Metz Hillery C , Tian David , Zhao Zhilei , Zung Jessica L , Rose Noah H , McBride Carolyn S
Published: August 2024

The olfactory sensory neurons of vinegar flies and mice tend to express a single ligand-specific receptor. While this ′one neuron-one receptor′ motif has long been expected to apply broadly across insects, recent evidence suggests it may not extend to mosquitoes. We sequenced and analyzed the transcriptomes of 46,000 neurons from antennae of the dengue mosquitoAedes aegyptito resolve all olfactory, thermosensory, and hygrosensory neuron subtypes and identify the receptors expressed therein. We find that half of all olfactory subtypes coexpress multiple receptors. However, coexpression occurs almost exclusively among genes from the same family—among odorant receptors (ORs) or among ionotropic receptors (IRs). Coexpression of ORs with IRs is exceedingly rare. Many coexpressed receptors are recent duplicates. In other cases, the recruitment or co-option of single receptors by multiple neuron subtypes has placed these genes together in the same cells with distant paralogs. Close examination of data fromDrosophilareveal rare cases of both phenomena, indicating that the olfactory systems of these two species are not fundamentally different, but instead fall at different locations along a continuum likely to encompass diverse insects.
Voltage-gated calcium channels generate blastema Ca2+fluxes restraining zebrafish fin regenerative outgrowth
Authors: Le Bleu Heather K. , Kioussi Rea G. , Henner Astra L. , Lewis Victor M. , Stewart Scott , Stankunas Kryn
Published: August 2024

Adult zebrafish fins regenerate to their original size regardless of damage extent, providing a tractable model of organ size and scale control. Gain-of-function of voltage-gated K+channels expressed in fibroblast-lineage blastema cells promotes excessive fin outgrowth, leading to a long-finned phenotype. Similarly, inhibition of the Ca2+-dependent phosphatase calcineurin during regeneration causes dramatic fin overgrowth. However, Ca2+fluxes and their potential origins from dynamic membrane voltages have not been explored or linked to fin size restoration. We used fibroblast-lineage GCaMP imaging of regenerating adult fins to identify widespread, heterogeneous Ca2+transients in distal blastema cells. Membrane depolarization of isolated regenerating fin fibroblasts triggered Ca2+spikes dependent on voltage-gated Ca2+channel activity. Single cell transcriptomics identified the voltage-gated Ca2+channelscacna1c(L-type channel),cacna1ba(N-type), andcacna1g(T-type) as candidate mediators of fibroblast-lineage Ca2+signaling. Small molecule inhibition revealed L- and/or N-type voltage-gated Ca2+channels act during regenerative outgrowth to restore fins to their original scale. Strikingly,cacna1ghomozygous mutant zebrafish regenerated extraordinarily long fins due to prolonged outgrowth. The regenerated fins far exceeded their original length but with otherwise normal ray skeletons. Therefore,cacna1gmutants uniquely provide a genetic loss-of-function long-finned model that decouples developmental and regenerative fin outgrowth. Live GCaMP imaging of regenerating fins showed T-type Cacna1g channels enable Ca2+dynamics in distal fibroblast-lineage blastemal mesenchyme during the outgrowth phase. We conclude “bioelectricity” for fin size control likely entirely reflects voltage-modulated Ca2+dynamics in fibroblast-lineage blastemal cells that specifically and steadily decelerates outgrowth at a rate tuned to restore the original fin size.
Adult male Lar gibbon sings the female great-call: A case study of inter-sex song production in a non-human primate
Authors: Varkevisser Judith , Berger Stijn , van der Loo Judith , Kriengwatana Buddhamas Pralle , Spierings Michelle
Published: August 2024

Gibbons are known as one of the most vocal non-human primates. They vocally advertise and reinforce their pair-bonds by singing complex duets, in which both the male and female perform a predetermined sex-specific set of song phrases, including the loud and elongated great-calls. Only females and sub-adult male gibbons have been previously observed performing great-calls. Once a male gibbon matures, he normally stops great-call production completely but continues singing other and less high-pitched song phrases. This case study describes a fully adult, castrated male lar gibbon (Hylobates lar, 32 years old, zoo-housed) who performs both male phrases of the duet, including the female great-call. The male regularly produced great-calls despite being in a, relatively weak, pair bond with a female conspecific. His great-calls adhered to the general structure of typical female great-calls but were shorter and had a lower maximum frequency. Notably, he produced these great-calls predominantly when the female was absent, especially when she was in their inside enclosure whilst he was outside. Behavioural observations indicate that the occurrence of great-calls by the male cannot be predicted based on pre-song behaviour or his interaction with the female. The recurrence of sub-adult singing behaviour in a fully grown adult is most likely due to his reduced testosterone levels. This study sheds light on the intricate dynamics of duetting and the unique occurrence of cross-sex song production in gibbons, emphasizing the complexity of pair-bond communication in this species.
Investigating the impact of the interstitial fluid flow and hypoxia interface on cancer biology using a spheroid-on-chip perfusion system
Authors: Pyne Emily , Reardon Mark , Christensen Martin , Mateos Pablo Rodriguez , Taylor Scott , Iles Alexander , Choudhury Ananya , Pamme Nicole , Pires Isabel M.
Published: August 2024

Solid tumours are complex and heterogeneous systems, which exist in a dynamic biophysical microenvironment. Conventional cancer research methods have long relied on two-dimensional (2D) static cultures which neglect the dynamic, three-dimensional (3D) nature of the biophysical tumour microenvironment (TME), especially the role and impact of interstitial fluid flow (IFF). To address this, we undertook a transcriptome-wide analysis of the impact of IFF-like perfusion flow using a spheroid-on-chip microfluidic platform, which allows 3D cancer spheroids to be integrated into extracellular matrices (ECM)-like hydrogels and exposed to continuous perfusion, to mimic IFF in the TME. Importantly, we have performed these studies both in experimental (normoxia) and pathophysiological (hypoxia) oxygen conditions. Our data indicated that gene expression was altered by flow when compared to static conditions, and for the first time showed that these gene expression patterns differed in different oxygen tensions, reflecting a differential role of spheroid perfusion in IFF-like flow in tumour-relevant hypoxic conditions in the biophysical TME. We were also able to identify factors primarily linked with IFF-like conditions which are linked with prognostic value in cancer patients and therefore could correspond to a potential novel biomarker of IFF in cancer. This study therefore highlights the need to consider relevant oxygen conditions when studying the impact of flow in cancer biology, as well as demonstrating the potential of microfluidic models of flow to identify IFF-relevant tumour biomarkers.
Aging and viral evolution impair immunity against dominant pan-coronavirus-reactive T cell epitope
Authors: Loyal Lucie , Jürchott Karsten , Reimer Ulf , Meyer-Arndt Lil , Henze Larissa , Mages Norbert , Kostrzanowski Jak , Reus Bernhard , Mangold Maike , Kruse Beate , Dingeldey Manuela , Sawitzki Birgit , Michel Janine , Grossegesse Marica , Schnatbaum Karsten , Wenschuh Holger , Nitsche Andreas , Lachmann Nils , Timmermann Bernd , Giesecke-Thiel Claudia , Braun Julian , Kern Florian , Thiel Andreas
Published: August 2024

Immune evasion by escape mutations subverts immunity against SARS-CoV-2. A role of pan-coronavirus immunity for more durable protection is being discussed but has remained understudied. We here investigated the effects of age, mutations, and homo-/heterologous vaccination regimens on the dominant pan-coronavirus-specific cellular and humoral epitope iCope after SARS-CoV-2 infection and vaccination in detail. In the older, quantitatively, and qualitatively reduced iCope-reactive CD4+T cell responses with narrow TCR repertoires could not be enhanced by vaccination and were further compromised by emerging spike mutations. In contrast pan-coronavirus-reactive humoral immunity was affected only by mutations and not by age. Our results reveal a distinct deficiency of the dichotomous layer of pan-coronavirus immunity in the older, critical for long-term protection against SARS-CoV-2 variants.

One-Sentence Summary

Aging and viral evolution impair dominant pan-coronavirus immunity, a hallmark of efficient and broad immune competence against SARS-CoV-2
Large serine integrases utilise scavenged phage proteins as directionality cofactors
Authors: Alsaleh Abdulrazak , Pena Reyes Tania , Baksh Aron , Taiwo-Aiyerin Oluwateniola T. , Holland Alexandria , Pigli Ying , Rice Phoebe A. , Olorunniji Femi J.
Published: August 2024

Recombination directionality factors (RDFs) for large serine integrases (LSIs) are cofactor proteins that control the directionality of recombination to favor excision over insertion. Although RDFs are predicted to bind their cognate LSIs in similar ways, there is no overall common structural theme across LSI RDFs, leading to the suggestion that some of them may be moonlighting proteins with other primary functions. To test this hypothesis, we searched for characterized proteins with structures similar to the predicted structures of known RDFs. Our search shows that the RDFs for two LSIs, TG1 integrase and Bxb1 integrase, show high similarities to a single stranded DNA binding (SSB) protein and an editing exonuclease, respectively. We present experimental data to show that TG1 RDF is a functional SSB protein. We used mutational analysis to validate the integrase-RDF interface predicted by AlphaFold2 multimer for TG1 integrase and its RDF, and establish that control of recombination directionality is mediated via protein-protein interaction at the junction of recombinase’s second DNA binding domain and the base of the coiled coil domain.
Quantifying the seasonal reproductive cycle in three species of Malagasy fruit bats with implications for pathogen and population dynamics
Authors: Cornelius Ruhs Emily , Kettenburg Gwenddolen , Andrianiaina Angelo , Andry Santino , Ranaivoson Hafaliana Christian , Grewe Felix , Brook Cara E
Published: August 2024

Bats (order Chiroptera) are hosts for highly virulent zoonotic pathogens. Many bats demonstrate seasonally varying antiviral responses, including antibody responses which have been observed to peak during the nutritionally depleted dry-season and female gestation periods, suggesting some impact of resource deficits on bat virus immunity. Given the frequent overlap in these energetically demanding periods, it is likely that endocrinological changes associated with pregnancy might partially explain the aforementioned pattern in antibody dynamics. Regardless, we know little about the seasonality of reproduction in many fruit bat species, despite the importance of reproductive biology to informing conservation management (e.g. population viability) and disease dynamics. Here, we aimed to elucidate the reproductive biology of three species of endemic fruit bat native to the island of Madagascar: Pteropus rufus, Eidolon dupreanum, and Rousettus madagascarensis. To do so, we leveraged plasma samples collected in part with a longitudinal field study, from 2018 to 2020. We adapted three standard reproductive assays previously validated in humans to quantify seasonal changes in reproductive hormones for bats and applied a mixture model approach to determine hormone cutoffs for pregnancy. As expected, we found that pregnant females showed the highest levels of estradiol and progesterone and adult males the highest levels of testosterone. Additionally, female P. rufus and R. madagascariensis showed clear seasonality in reproduction with peaks in estradiol and progesterone in August and October, respectively. Seasonality was less clearly discernible in the female E. dupreanum and male data. In general, we found that the commercially available assays were successful in quantifying endocrinological hormones for bats; when paired with histological embryo sections or field data, these offer a powerful tool to elucidate bat reproductive calendars.
Discovery of Novel R-Selective Aminotransferase Motifs through Computational Screening
Authors: Runthala Ashish , Satya Sri Pulla Sai , Nair Aayush S , Puttagunta Murali Krishna , Sekhar Rao T Chandra , Sreya Vajrala , Sowmya Ganugapati Reshma , Reddy G Koteshwara
Published: August 2024

Transaminases, enzymes facilitating amino group transfers, are divided into four subfamilies: D-alanine transaminase (DATA), L-selective Branched chain aminotransferase (BCAT), 4-amino-4-deoxychorismate lyase (ADCL), and R-selective aminotransferase (RATA). RATA enzymes are particularly valuable in biocatalysis for synthesizing chiral amines and resolving racemic mixtures, yet their identification in sequence databases is challenging due to the lack of robust motif-based screening methods. By constructing a transaminase sequence dataset and categorizing them into subfamilies, we re-screened conserved motifs and explored novel ones. Phylogenetic clustering and structural localization of these motifs on Alphafold-predicted protein models validated their importance. For ADCL, BCAT, DATA, and RATA datasets, we discovered 5, 7, 10, and 2 novel motifs, respectively. Additionally, unique residue patterns were identified, underscoring their structural significance. This motif-based computational approach promises to unveil novel RATA enzymes for biocatalytic applications.
Investigation of pair-wise single-cell interactions by statistically interpreting spatial cell state correlation learned by self-supervised graph inductive bias transformer
Authors: Xiao Xiao
Published: August 2024

Image-based spatial transcriptomics (ST) offers spatial gene expression profile at the single-cell resolution and provides information to understand intercellular communication that is critical for maintaining tissue development and organ function. Disruption of normal cell-cell interactions (CCI) can lead to disease onset and progression. Current CCI analysis methods face several limitations, including subjection to the number of measured ligand-receptor genes in image-based spatial transcriptomics, limited graph encoding power, inadequate use of spatial information, and low interpretability. Here, we present GITIII, an interpretable self-supervised graph transformer- based language model that treats cells as words (nodes) and their cell neighborhood as a sentence to explore the communications among cells. Enhanced by multilayer perceptron-based distance scaler, physics-informed attention mechanism, and a state-of-the-art, expressive, and lightweight graph transformer model, GITIII infers CCI by investigating how the state of a cell is influenced by the spatial organization, ligand expression, cell types and states of neighboring cells. With its interpretable architecture, GITIII can be used to understand how the sender cell influences target genes in the receiver cell, visualize the spatial pattern and utility of CCI, identify significant CCI networks, perform CCI-informed cell subtyping, and compare CCI strength between disease groups. Applications to four ST datasets from several species, organs, and platforms, GITIII effectively identified and quantitatively interpreted key CCI patterns driving within-sample heterogeneity and disease progression, thus improving our understanding of brain structures, tumor microenvironments, and the interplay among different cell types responding to neighboring CCIs.
Neural Adaptation to the Eye's Optics Through Phase Compensation
Authors: Barbot Antoine , Pirog John T , Ng Cherlyn J , Yoon Geunyoung
Published: August 2024

How does the brain achieve a seemingly veridical and ‘in-focus’ perception of the world, knowing how severely corrupted visual information is by the eye’s optics? Optical blur degrades retinal image quality by reducing the contrast and disrupting the phase of transmitted signals. Neural adaptation can attenuate the impact of blur on image contrast, yet vision rather relies on perceptually-relevant information contained within the phase structure of natural images. Here we show that neural adaptation can compensate for the impact of optical aberrations on phase congruency. We used adaptive optics to fully control optical factors and test the impact of specific optical aberrations on the perceived phase of compound gratings. We assessed blur-induced changes in perceived phase over three distinct exposure spans. Under brief blur exposure, perceived phase shifts matched optical theory predictions. During short-term (~1h) exposure, we found a reduction in blur-induced phase shifts over time, followed by after-effects in the opposite direction–a hallmark of adaptation. Finally, patients with chronic exposure to poor optical quality showed altered phase perception when tested under fully-corrected optical quality, suggesting long-term neural compensatory adjustments to phase spectra. These findings reveal that neural adaptation to optical aberrations compensates for alterations in phase congruency, helping restore perceptual quality over time.
Spatial population dynamics of bacterial colonies with social antibiotic resistance
Authors: Denk-Lobnig Marlis K. , Wood Kevin B.
Published: August 2024

Bacteria frequently inhabit surface-attached communities where rich “social” interactions can significantly alter their population-level behavior, including their response to antibiotics. Understanding these collective effects in spatially heterogeneous communities is an ongoing challenge. Here, we investigated the spatial organization that emerges from antibiotic exposure in initially randomly distributed communities containing antibiotic-resistant and -sensitive strains ofE. faecalis, an opportunistic pathogen. We identified that a range of complex spatial structures emerged in the population homeland—the inoculated region that microbes inhabit prior to range expansion—, which depended on initial colony composition and antibiotic concentration. We found that these arrangements were explained by cooperative interactions between resistant and sensitive subpopulations with a variable spatial scale, the result of dynamic zones of protection afforded to sensitive cells by growing populations of enzyme-producing resistant neighbors. Using a combination of experiments and mathematical models, we explored the complex spatiotemporal interaction dynamics that create these patterns, and predicted spatial arrangements of sensitive and resistant subpopulations under new conditions. We illustrated how spatial population dynamics in the homeland affect subsequent range expansion, both because they modulate the composition of the initial expanding front, and through long-range cooperation between the homeland and the expanding region. Finally, we showed that these spatial constraints resulted in populations whose size and composition differed markedly from matched populations in well-stirred (planktonic) cultures. These findings underscore the importance of spatial structure and cooperation, long-studied features in theoretical ecology, for determining the fate of bacterial communities under antibiotic exposure.

Significance

Interactions between bacteria are common, particularly in the crowded surface-associated communities that occur anywhere from natural ecosystems to the human body to medical devices. Antibiotic resistance can be influenced by these “social” interactions, making it difficult to predict how spatial communities respond to antibiotic. Here, we show that complex spatial arrangements emerge when initially randomly distributed populations of antibiotic-resistant and -sensitiveE. faecalis, a microbial pathogen, are exposed to antibiotic. Using mathematical models and experiments, we show how local competition and dynamic-range cross-protection drive pattern formation. As a result, these spatially structured populations respond differently to antibiotics than well-mixed communities. Our findings elucidate how “social” antibiotic resistance affects spatially structured bacterial communities, a step towards predicting and controlling resistance.
Facial and body colouration is linked to social rank in the African cichlidAstatotilapia burtoni
Authors: Peroš M. , Chang A. , Martashvili A. , Alvarado S.G.
Published: August 2024

Animal colouration is fundamentally important for social communication within conspecifics to advertising threat to competitors or fitness to possible mates. Social status and animal colouration are covarying traits that are plastic in response to dynamic environments. In the African cichlid,Astatotilapia burtoni, body colouration and behaviour have been extensively reported to vary with social rank. However, the nature of the interaction between these two traits is poorly understood. We hypothesise that pigmentation patterns could be linked to the behavioural repertoires underlying social status and can be resolved to regions on the cichlid body plan. To test this hypothesis, we generated Territorial (T) and Non-territorial (NT) males and employed computer vision tools to quantify and visualise patterns/colour enrichment associated with stereotyped T/NT male behaviour. We report colour-behaviour interactions localised in specific areas of the body and face for two colour morphs illustrating a more nuanced view of social behaviour and pigmentation. Since behavioural and morphological variation are key drivers of selection in the East African Great Rift Lakes, we surmise our data may be translatable to other cichlid lineages and underline the importance of trait covariance in sexual selection and male competition.
Unsupervised domain classification of AlphaFold2-predicted protein structures
Authors: Barone Federico , Laio Alessandro , Punta Marco , Cozzini Stefano , Ansuini Alessio , Cazzaniga Alberto
Published: August 2024

Abstract

The release of the AlphaFold database, which contains 214 million predicted protein structures, represents a major leap forward for proteomics and its applications. However, lack of comprehensive protein annotation limits its accessibility and usability. Here, we present DPCstruct, an unsupervised clustering algorithm designed to provide domain-level classification of protein structures. Using structural predictions from AlphaFold2 and comprehensive all-against-all local alignments from Foldseek, DPCstruct identifies and groups recurrent structural motifs into domain clusters. When applied to the Foldseek Cluster database, a representative set of proteins from the AlphaFoldDB, DPCstruct successfully recovers the majority of protein folds catalogued in established databases such as SCOP and CATH. Out of the 28,246 clusters identified by DPCstruct, 24% have no structural or sequence similarity to known protein families. Supported by a modular and efficient implementation, classifying 15 million entries in less than 48 hours, DPCstruct is well suited for large-scale proteomics and metagenomics applications. It also facilitates the rapid incorporation of updates from the latest structural prediction tools, ensuring that the classification remains up-to-date. The DPCstruct pipeline and associated database are freely available in a dedicated repository, enhancing the navigation of the AlphaFoldDB through domain annotations and enabling rapid classification of other protein datasets.
Atomic-Level Free Energy Landscape Reveals Cooperative Symport Mechanism of Melibiose Transporter
Authors: Liang Ruibin , Guan Lan
Published: August 2024

The Major Facilitator Superfamily (MFS) transporters are an essential class of secondary active transporters involved in various physiological and pathological processes. The melibiose permease (MelB), which catalyzes the stoichiometric symport of the disaccharide melibiose and monovalent cations (e.g., Na+, H+, or Li+), is a key model for understanding the cation-coupled symport mechanisms. Extensive experimental data has established that positive cooperativity between the cargo melibiose and the coupling cation is central to the symport mechanism. However, the structural and energetic origins of this cooperativity remain unclear at the atomistic level for MelB and most other coupled transporters. Here, leveraging recently resolved structures in inward- and outward-facing conformations, we employed the string method and replica-exchange umbrella sampling simulation techniques to comprehensively map the all-atom free energy landscapes of the Na+-coupled melibiose translocation across the MelB in Salmonella enterica serovar Typhimurium (MelBSt), in comparison with the facilitated melibiose transport in a uniporter mutant. The simulation results unravel asymmetrical free energy profiles of melibiose translocation, which is tightly coupled to protein conformational changes in both the N- and C-terminal domains. Notably, the cytoplasmic release of the melibiose induces the simultaneous opening of an inner gate, resulting in a high-energy state of the system. Periplasmic sugar binding and cytoplasmic melibiose released are dynamically coupled with changes in the internal gating elements along the translocation pathway. The outward-facing sugar-bound state is thermodynamically most stable, while the occluded state is a transient state. The binding of Na+ facilitates melibiose translocation by increasing the melibiose-binding affinity and decreasing the overall free energy barrier and change. The cooperative binding of the two substrates results from the allosteric coupling between their binding sites instead of direct electrostatic interaction. These findings add substantial new atomic-level details into how Na+ binding facilitates melibiose translocation and deepen the fundamental understanding of the molecular basis underlying the symport mechanism of cation-coupled transporters.
Epigenetic and transcriptional regulation of ovarian development altered inErβKOovaries
Authors: Mohamadi Ryan , Vo Kevin , Sharma Yashica , Mohamadi Amelia , Bahadursingh Elizabeth S. , Fields Patrick E. , Karim Rumi M. A.
Published: August 2024

We analyzed the transcriptome of wildtype and estrogen receptor β knockout (ErβKO) rat ovaries during the early postnatal period and detected remarkable changes in epigenetic regulators and transcription factors. Compared to postnatal day (PD) 4.5 wildtype ovaries, 17 differentially expressed epigenetic regulators (DEERs), and 23 differentially expressed transcription factors (DETFs) were detected in PD6.5 wildtype ovaries. Subsequently, compared to PD 6.5 wildtype ovaries, 24 DEERs and 68 DETFs were detected in PD8.5 ovaries. Changes in DEERs and DEFTs resulted in 581 differentially expressed downstream genes (DEDGs) in PD6.5 and 920 DEDGs in wildtype PD8.5 ovaries. The DEERs, DETFs, and DEDGs in wildtype ovaries represented primordial follicle activation (PFA) and development of the first-wave follicles because the second-wave follicles remain dormant during this period. However, the changes in DEERs, DETFs, and DEDGs during this postnatal period were markedly different in ErβKOrat ovaries, which suffered from increased PFA in both waves. Compared to 17 DEERs and 23 DETFs in wildtype, 46 DEERs and 55 DETFs were identified in PD 6.5 ErβKOovaries. The differences were more remarkable in PD 8.5 ErβKOovaries; compared to 24 DEERS and 68 DETFs in wildtype, only 8 DEERs and 10 DETFs were detected in ErβKOovaries. Such dysregulation resulted in altered DEDGs in PD 6.5 (581 vs. 744) and in PD8.5 (920 vs. 191) ErβKOovaries. These findings also suggest that the number of DEDGs depends directly on the numbers of DEERS and DETFs. In addition to the quantitative differences in DEERs and DETFs between the wildtype and ErβKOovaries, we detected distinct differences in the identities of the regulators. Our observations indicate that loss of ERβ dysregulates the epigenetic regulators and transcription factors in ErβKOovaries, which disrupts the downstream genes in ovarian follicles and increases follicle activation.
High-Intensity Interval Training Decreases Circulating HMGB1 in Individuals with Insulin Resistance; Plasma Lipidomics Identifies Associated Cardiometabolic Benefits
Authors: Bravo Gabriela Martinez , Paramasivam Prabu , Bellissimo Gabriella F. , Jacquez Quiteria , Zheng Huayu , Amorim Fabiano , Alvidrez Roberto Ivan Mota
Published: August 2024

Background:Exercise is a fundamental primary standard of care for cardiometabolic health. Body Weight (BW) High-Intensity Interval Training (HIIT) is an effective strategy for reducing cardiometabolic markers in individuals with insulin resistance and Type-2 diabetes (T2D). High-mobility group box 1 (HMGB1), a ubiquitous nuclear factor, plays an ample role beyond an alarmin in T2D development and progression. Our group has described this novel role previously, showing the beneficial effect of whole body HMGB1 silencing in decreasing hyperglycemia in diabetic mice. In the present study we tested the hypothesis that BW-HIIT as an effective exercise training modality will decrease cardiometabolic risk with a concomitant decrease in circulating HMGB1 more prominently in insulin resistant individuals compared to non-insulin resistant individuals contrasting to what we can evidence in a preclinical murine model of insulin resistance;Methods:Human and mouse pre- and post-exercise serum/plasma samples were analyzed for Lipidomics as well as Metabolic and Cytokine Multiplex assays. Standard of care, as well as cardiometabolic parameters, was also performed in human subjects;Results:insulin resistant individuals had the most positive effect, primarily with a decrease in the Homeostatic Model Assessment of Insulin Resistance (HOMA-IR). as an index of insulin resistance as well as decreased HMGB1 post-exercise. Lipidomic analysis illustrated the highly beneficial effect of exercise training using a modified HIIT program, showing an enhanced panel of circulating lipids post-exercise exclusively in insulin resistant individuals. Plasma multiplex revealed significant translational heterogeneity in our studies with distinct metabolic hormone responses to exercise conditioning with a decrease in inflammatory markers in insulin resistant individuals;Conclusions:The current study demonstrated that 6-week BW-HIIT training improves cardiometabolic, anti-inflammatory markers, metabolic hormones, and insulin sensitivity in humans, strongly associated with decreased circulating HMGB1. Overall, these experiments reinforce the potential of HMGB1 as a marker of changes in insulin resistance and the positive effect of exercise training on insulin resistance possibly preventing the development of T2D and associated complications.
Vagal TRPV1+sensory neurons regulate myeloid cell dynamics and protect against influenza virus infection
Authors: Yang Daping , Almanzar Nicole , Xia Jingya , Udit Swalpa , Yeung Stephen T. , Khairallah Camille , Hoagland Daisy A. , Umans Benjamin D. , Sarden Nicole , Erdogan Ozge , Baalbaki Nadia , Beekmayer-Dhillon Anna , Lee Juhyun , Meerschaert Kimberly A. , Liberles Stephen D. , Yipp Bryan G. , Franklin Ruth A. , Khanna Kamal M. , Baral Pankaj , Haber Adam L. , Chiu Isaac M.
Published: August 2024

Influenza viruses are a major global cause of morbidity and mortality. Vagal TRPV1+nociceptive sensory neurons, which innervate the airways, are known to mediate defenses against harmful agents. However, their function in lung antiviral defenses remains unclear. Our study reveals that both systemic and vagal-specific ablation of TRPV1+nociceptors reduced survival in mice infected with influenza A virus (IAV), despite no significant changes in viral burden or weight loss. Mice lacking nociceptors showed exacerbated lung pathology and elevated levels of pro-inflammatory cytokines. The increased mortality was not attributable to the loss of the TRPV1 ion channel or neuropeptides CGRP or substance P. Immune profiling through flow cytometry and single-cell RNA sequencing identified significant nociceptor deficiency-mediated changes in the lung immune landscape, including an expansion of neutrophils and monocyte-derived macrophages. Transcriptional analysis revealed impaired interferon signaling in these myeloid cells and an imbalance in distinct neutrophil sub-populations in the absence of nociceptors. Furthermore, anti-GR1-mediated depletion of myeloid cells during IAV infection significantly improved survival, underscoring a role of nociceptors in preventing pathogenic myeloid cell states that contribute to IAV-induced mortality.

One Sentence Summary: TRPV1+neurons facilitate host survival from influenza A virus infection by controlling myeloid cell responses and immunopathology.
Physiological barriers for glucose utilization inMethanosarcina acetivorans
Authors: Sattler Christian , Richter Marcus , Rother Michael
Published: August 2024

Methanogenesis is a key aspect of anaerobic biomass degradation, and thus of global importance. While methanogenic archaea (methanogens) are ubiquitous in anaerobic habitats, the range of substrates they utilize is very limited. Most methanogens are able to grow chemolithotrophically with H2+CO2, some clades can utilize methylated compounds and/or acetate as well. Organotrophic compounds like amino acids, lipids, nucleotides, or carbohydrates, are not known to support growth of methanogens. This inability to utilize “upstream” intermediates of anaerobic biomass degradation is remarkable considering the presence of cellular metabolism that such intermediates could feed into. Here, we addressed the question why the model methanogenMethanosarcina acetivorans, despite its gluconeogenic and glycolytic capacity, is unable to utilize glucose for methanogenesis and growth. Complementing heterologously with a glucose uptake facilitator allowed a recombinantM. acetivoransstrain to convert glucose to methane at a low rate. However, growth with glucose was not observed, neither as energy source nor as carbon source. Instead, methylotrophic growth of the transgenic strain was impaired in a glucose-dependent fashion, which was aggravated when also glucokinase was heterologuously produced. Glucose-dependent growth inhibition coincided with a significant – and microscopically visible – accumulation of intracellular carbohydrate. Since the glucose-utilizing trait is rapidly lost during methylotrophic growth, accumulating growth-inhibiting metabolites probably makes methanogenic and glycolytic catabolism incompatible. Thus, extensive efforts in strain development would be required to enable direct glucose utilization for methanogenesis.