bluuebunny/crossref_metadata_2025 huggingface dataset:
MACROPHAGES COORDINATE IMMUNE RESPONSE TO LASER-INDUCED INJURY VIA EXTRACELLULAR TRAPS
Authors: Conedera Federica M. , Kokona Despina , Zinkernagel Martin S. , Stein Jens V. , Alt Clemens , Enzmann Volker , Lin Charles P.
Published: October 2023

Macrophages/monocytes, the primary contributors to chronic inflammation in degenerated retinas, orchestrate intricate immune responses. They remain enigmatic in their local coordination and activation mechanisms. Innovations in experimental systems enable real-time exploration of immune cell interactions and temporal dimensions in response. In preclinical mouse models, we usein vivomicroscopy to unravel how macrophages/monocytes govern microglia and PL responses spatio-temporally.

Our findings underscore the pivotal role of innate immune cells, especially macrophages/monocytes, in regulating retinal repair. The absence of neutrophil and macrophage infiltration aids parenchymal integrity restoration, while their depletion, particularly macrophages/monocytes, impedes vascular recovery. Innate immune cells, when activated, release chromatin and granular proteins, forming extracellular traps (ETs), critical for tissue repair by modulating neutrophil and T-cell responses.

Our investigations demonstrate that pharmacological inhibition of ETosis with Cl-amidine enhances retinal and vascular repair, surpassing the effects of blocking innate immune cell recruitment. Simultaneously, Cl-amidine treatment reshapes the inflammatory response, causing neutrophils, helper, and cytotoxic T-cells to cluster primarily in the superficial capillary plexus, affecting retinal microvasculature perfusion. Our data offer novel insights into innate immunity’s role in responding to retinal damage, potentially informing more effective immunotherapeutic strategies for neurodegenerative diseases.
The breath shape controls intonation of mouse vocalizations
Authors: MacDonald Alastair , Hebling Alina , Wei Xin Paul , Yackle Kevin
Published: October 2023

Intonation in speech is the control of vocal pitch to layer expressive meaning to communication, like increasing pitch to indicate a question. Also, stereotyped patterns of pitch are used to create distinct sounds with different denotations, like in tonal languages and, perhaps, the ten sounds in the murine lexicon. A basic tone is created by exhalation through a constricted laryngeal voice box, and it is thought that more complex utterances are produced solely by dynamic changes in laryngeal tension. But perhaps, the shifting pitch also results from altering the swiftness of exhalation. Consistent with the latter model, we describe that intonation in most vocalization types follows deviations in exhalation that appear to be generated by the re-activation of the cardinal breathing muscle for inspiration. We also show that the brainstem vocalization central pattern generator, the iRO, can create this breath pattern. Consequently, ectopic activation of the iRO not only induces phonation, but also the pitch patterns that compose most of the vocalizations in the murine lexicon. These results reveal a novel brainstem mechanism for intonation.
Surface Generative Modelling of Neurodevelopmental Trajectories
Authors: Fawaz Abdulah , Masui Saga N. B. , Williams Logan Z. J. , Dahan Simon , Edwards A. David , Robinson Emma C.
Published: October 2023

Cortical neurodevelopment is sensitive to disruption following preterm birth, with lasting impact on cognitive outcomes. The creation of generative models of neurodevelopment could aid clinicians in identifying atrisk subjects but is complicated by the degree of subject variability in cortical folding, and significant heterogeneity in the effect of preterm birth. In this work, we propose a graph convolutional generative adversarial network (GAN) and a training scheme to simulate neonatal cortical surface developmental trajectories. The proposed model is used to smoothly modify two cortical phenotypes: post-menstrual age at scan (PMA) and gestational age at birth (GA) on data from the developing Human Connectome Project (dHCP) [1]. The synthetic images were validated with an independently trained regression network, and compared against follow up scans, indicating that the model can realistically age individuals whilst preserving subject-specific cortical morphology. Deviation between simulated ‘healthy’ scans, and preterm follow up scans generated a metric of individual atypicality, which improved prediction of 18-month cognitive outcome over GA alone.
Learning enhances representations of taste-guided decisions in the mouse gustatory insular cortex
Authors: Kogan Joshua F. , Fontanini Alfredo
Published: October 2023

Learning to discriminate overlapping gustatory stimuli that predict distinct outcomes – a feat known as discrimination learning – can mean the difference between ingesting a poison or a nutritive meal. Despite the obvious importance of this process, very little is known on the neural basis of taste discrimination learning. In other sensory modalities, this form of learning can be mediated by either sharpening of sensory representations, or enhanced ability of “decision-making” circuits to interpret sensory information. Given the dual role of the gustatory insular cortex (GC) in encoding both sensory and decision-related variables, this region represents an ideal site for investigating how neural activity changes as animals learn a novel taste discrimination.

Here we present results from experiments relying on two photon calcium imaging of GC neural activity in mice performing a taste-guided mixture discrimination task. The task allows for recording of neural activity before and after learning induced by training mice to discriminate increasingly similar pairs of taste mixtures. Single neuron and population analyses show a time-varying pattern of activity, with early sensory responses emerging after taste delivery and binary, choice encoding responses emerging later in the delay before a decision is made. Our results demonstrate that while both sensory and decision-related information is encoded by GC in the context of a taste mixture discrimination task, learning and improved performance are associated with a specific enhancement of decision-related responses.
Revisiting Hox gene evolution and Hox cluster linkage across Nematoda
Authors: Kirangwa Joseph , Laetsch Dominik R , King Erna , Stevens Lewis , Blaxter Mark , Holovachov Oleksandr , Schiffer Philipp
Published: October 2023

Hox genes are central to metazoan body plan formation, patterning and evolution, playing a critical role in cell fate decisions early in embryonic development in invertebrates and vertebrates. While the archetypical Hox gene cluster consists of members of nine ortholog groups (HOX1-HOX9), arrayed in close linkage in the order in which they have their anterior-posterior patterning effects, nematode Hox gene sets do not fit this model. TheCaenorhabditis elegansHox gene set is not clustered and contains only six Hox genes from four of the ancestral groups. The pattern observed inC. elegansis not typical of the phylum, and variation in orthologue set presence and absence and in genomic organisation has been reported. Recent advances in genome sequencing have resulted in the availability of many novel genome assemblies in Nematoda, especially from taxonomic groups that had not been analysed previously. Here, we explored Hox gene complements in high-quality genomes of 80 species from all major clades of Nematoda to understand the evolution of this key set of body pattern genes and especially to probe the origins of the “dispersed” cluster observed inC. elegans. We also included the recently available high-quality genomes of some Nematomorpha as an outgroup. We find that nematodes can have Hox genes from up to six orthology groups. While nematode Hox “clusters” are often interrupted by unrelated genes we identify species in which the cluster is intact and not dispersed.
Chst9Marks a Spatially and Transcriptionally Unique Population ofOprm1-Expressing Neurons in the Nucleus Accumbens
Authors: Andraka Emma , Phillips Robert A. , Brida Kasey L. , Day Jeremy J.
Published: October 2023

Opioids produce addictive, analgesic, and euphoric effects via actions at mu opioid receptors (μORs). The μOR is encoded by theOprm1gene and is expressed in multiple brain regions that regulate reward and motivation, such as the nucleus accumbens (NAc).Oprm1expression in NAc medium spiny neurons (MSNs) mediates opioid place preference, seeking, and consumption. However, recent single nucleus RNA sequencing (snRNA-seq) studies in rodent, primate, and human NAc have revealed that multiple subpopulations of NAc neurons expressOprm1mRNA, making it unclear which populations mediate diverse behaviors resulting from μOR activation. Using published snRNA-seq datasets from the rat NAc, we identified a novel population of MSNs that express the highest levels ofOprm1of any NAc cell type. Here, we show that this population is selectively marked by expression ofChst9, a gene encoding a carbohydrate sulfotransferase. To validate this observation and characterize spatial localization of this population in the rat NAc, we performed multiplexed RNAscope fluorescencein situhybridization studies to detect expression ofOprm1andChst9mRNA along with well-validated markers of MSNs. Notably,Chst9+ neurons exhibited more abundant expression ofOprm1as compared to other cell types, and formed discrete cellular clusters along the medial and ventral borders of the NAc shell subregion. Moreover,CHST9mRNA was also found to mark specific MSN populations in published human and primate snRNA-seq studies, indicating that this unique population may be conserved across species. Together, these results identify a spatially and transcriptionally distinct NAc neuron population characterized by the expression ofChst9. The abundant expression ofOprm1in this population and the conservation of these cells across species suggests that they may play a key functional role in opioid response and identify this subpopulation as a target for further investigation.
A tale of two phage tails: Engineering the host range of bacteriophages infectingClostridioides difficile
Authors: Steczynska Joanna P. , Kerr Sarah J. , Kelly Michelle L. , Whittle Michaella J. , Bilverstone Terry W. , Minton Nigel P.
Published: October 2023

Clostridioides difficileinfection (CDI) is a leading cause of antibiotic-associated diarrhoea across the globe. Although treatable with a restricted number of antibiotics, the emergence of resistant variants and high relapse rates necessitate alternative countermeasures. Phage therapy represents an attractive option. However, its implementation is handicapped by the narrow host specificity of theC. difficilebacteriophages isolated to date. One strategy to rationally expand phage host range would be to make appropriate modifications to the phage receptor binding protein (RBP). Here, we identify the tail fibre as the RBP of twoMyoviridaephages, ΦCD1801 and ΦCD2301, which were previously isolated and propagated using theC. difficilestrains CD1801 (RT078) and CD2301 (RT014), respectively. Contrary to studies into reprogramming the host ranges of phage of other bacterial other species, exchanging the tail fibre genes (tcf/tfp) alone between the two phage was insufficient to change host specificity. Rather, alterations to host range were dependent their exchange together with a putative chaperone encoded byhyp, localised adjacent to the tail fibre gene. Capitalising on this discovery, CRISPR/Cas9 was used to change the host range of one phage to that of the other by swapping the respectivetcf/tfpandhypgenes. Significantly, one of the resulting mutants, surpassed both parental phages in terms of host range and efficiency of infection. This is the first time that genome engineering has successfully expanded the host range of aC. difficilephage, a prerequisite for implementing phage for the treatment of CDI.

Importance

Alternatives to antibiotics for treatingClostridioides difficileinfection (CDI) are urgently required. Phage therapy presents an attractive option as it has the potential to clear the infection with minimal microbiome disruption and eliminate the possibility of recurrence. However, theC. difficilebacteriophages isolated to date have highly restricted host ranges. Moreover, rational strategies to alter specificity have till now been precluded as the identity of the phage receptor binding proteins involved was largely unknown. Here, we demonstrated that tail fibre proteins and an associated putative chaperone determine the host range of twoMyoviridaephage. This enabled the alteration of specificity through CRISPR-mediated genome editing and the creation of a phage derivative with a host range and infection efficiency exceeding that of the parental phages. This is the first time that the host range of aC. difficilephage has been successfully expanded through rational genome engineering.
Exhaustive search for DNA binding sites ofBasillus subtilistranscription factor YsiA by KaScape method
Authors: Huang Bing-yao , Huang Mia , Chen Hong , Su Xiao-dong
Published: October 2023

Basillus subtilis(B. subtilis) YsiA is also known as FadR is a pre-formed dimeric repressor to regulate fatty acid degradation. However, the knowledge about double-stranded DNA(dsDNA) binding sites of YsiA in the whole genome level is limited so far. In this report, we have applied a newly established high-throughput method, KaScape, to exhaustively study the relative binding sites and energy landscape of YsiA and confirmed the resuls with gel-shift experiments. We’ve found that half-binding site is enough for YsiA to bind with dsDNA. Besides detecting the known consensus sequence which is bound by YsiA, we have also detected other minor binding site sequences through the KaScape method. It thus demonstrates that KaScape can be used to study dimeric transcription factors (TFs) in general.
Adaptive modeling and inference of higher-order coordination in neuronal assemblies: a dynamic greedy estimation approach
Authors: Mukherjee Shoutik , Babadi Behtash
Published: October 2023

Central in the study of population codes, coordinated ensemble spiking activity is widely observable in neural recordings with hypothesized roles in robust stimulus representation, interareal communication, and learning and memory formation. Model-free measures of synchrony characterize coherent pairwise activity but not higher-order interactions, a limitation transcended by statistical models of ensemble spiking activity. However, existing model-based analyses often impose assumptions about the relevance of higher-order interactions and require repeated trials to characterize dynamics in the correlational structure of ensemble activity. To address these shortcomings, we propose an adaptive greedy filtering algorithm based on a discretized mark point-process model of ensemble spiking and a corresponding statistical inference framework to identify significant higher-order coordination. In the course of developing a precise statistical test, we show that confidence intervals can be constructed for greedily estimated parameters. We demonstrate the utility of our proposed methods on simulated neuronal assemblies. Applied to multi-electrode recordings from human and rat cortical assemblies, our proposed methods provide new insights into the dynamics underlying localized population activity during transitions between brain states.

Author summary

Simultaneous ensemble spiking is hypothesized to have important roles in neural encoding; however, neurons can also spike simultaneously by chance. In order to characterize the potentially time-varying higher-order correlational structure of ensemble spiking, we propose an adaptive greedy filtering algorithm that estimates the rate of all reliably-occurring simultaneous ensemble spiking events. Moreover, we propose an accompanying statistical inference framework to distinguish the chance occurrence of simultaneous spiking events from coordinated higher-order spiking. We demonstrate the proposed methods accurately differentiate coordinated simultaneous spiking from chance occurrences in simulated data. In application to human and rat cortical data, the proposed methods reveal time-varying dynamics in higher-order coordination that coincide with changing brain states.
HIV incidence among women engaging in sex work in sub-Saharan Africa: a systematic review and meta-analysis
Authors: Jones Harriet S , Anderson Rebecca L , Cust Henry , McClelland R. Scott , Richardson Barbra A. , Thirumurthy Harsha , Malama Kalonde , Hensen Bernadette , Platt Lucy , Rice Brian , Cowan Frances M , Imai-Eaton Jeffrey W. , Hargreaves James R , Stevens Oliver
Published: October 2023

Introduction

HIV incidence among women in sub-Saharan Africa (SSA) has declined steadily, but it is unknown whether new infections among women who engage in sex work (WESW) have declined at a similar rate. We synthesised estimates of HIV incidence among WESW in SSA and compared these to the wider female population to understand levels and trends in incidence over time.

Methods

We searched Medline, Embase, Global Health, Popline, Web of Science, and Google Scholar from January 1990 to October 2022, and grey literature for estimates of HIV incidence among WESW in SSA. We included studies reporting empirical estimates in any SSA country. We calculated incidence rate ratios (IRR) compared to age-district-year matched total female population incidence estimates. We conducted a meta-analysis of IRRs and used a continuous mixed-effects model to estimate changes in IRR over time.

Results

From 32 studies between 1985 and 2020, 2,194 new HIV infections were observed in WESW over 51,000 person-years (py). Median HIV incidence was 4.3/100py (IQR 2.8-7.0/100py), declining from a median of 5.96/100py between 1985 and 1995 to a median of 3.2/100py between 2010 and 2020. Incidence among WESW was nine times higher than in matched total population women (RR 8.6, 95%CI: 5.7-12.9), and greater in Western and Central Africa (RR 22.4, 95%CI: 11.3-44.3) than in Eastern and Southern Africa (RR 5.3, 95%CI: 3.7–7.6). Annual changes in log IRRs were minimal (–0.1% 95%CI: −6.9 to +6.8%).

Conclusions

Across SSA, HIV incidence among WESW remains disproportionately high compared to the total female population but showed similar rates of decline between 1990 and 2020. Improved surveillance and standardisation of approaches to obtain empirical estimates of sex worker incidence would enable a clearer understanding of whether we are on track to meet global targets for this population and better support data-driven HIV prevention programming.
Understanding and Predicting Polycystic Ovary Syndrome through Shared Genetics with Testosterone, SHBG, and Chronic Inflammation
Authors: Petersen Lillian Kay , Brixi Garyk , Li Jun , Hu Jie , Wang Zicheng , Han Xikun , Meir Anat Yaskolka , Tyrmi Jaakko , Mahalingaiah Shruthi , Piltonen Terhi , Liang Liming
Published: October 2023

Polycystic ovary syndrome (PCOS) is a common hormonal disorder that affects one out of eight women and has high metabolic and psychological comorbidities. PCOS is thought to be associated with increased systemic low-grade inflammation, but the underlying mechanisms remain unclear. Here we study the genetic relationship between PCOS and obesity, testosterone, sex hormone binding globulin (SHBG), and chronic inflammation. First we create a large meta-analysis of PCOS (7,747 PCOS cases and 498,227 controls) and identify four novel genetic loci associated with PCOS. These novel loci have been previously associated with changes in gene expression in multiple tissues including the thyroid and ovary. We then analyze the PCOS meta analysis alongside GWASs for obesity (n=681,275), SHBG (n=190,366), testosterone (n=176,687), and meta-analyses of 130 inflammatory biomarkers (average n=30,000). We replicate potential causal relationships (via Mendelian randomization) from obesity and SHBG to PCOS and find extensive genetic correlations and causality between these traits and inflammatory biomarkers. We identify significant genetic correlations between PCOS and eight inflammatory biomarkers, including new relationships such as a strong correlation to death receptor 5 (LDSC rg = 0.54, FDR = 0.043). Although these results point to a shared genetic architecture between PCOS and inflammation, we did not find statistically significant causality between them; however, we did find 27 inflammatory biomarkers with significant causal effects on SHBG and four biomarkers with significant causal effects on testosterone. These results support the hypothesis that chronic inflammation can influence androgen and SHBG levels, though more research is needed to verify these results. Finally, we show that combining the polygenic risk scores of PCOS-related traits improves genetic prediction of PCOS cases in the UK Biobank and MGB Biobank compared to using only PCOS risk scores (0.72 AUC from 0.59 AUC and 0.61 AUC from 0.59 AUC in each biobank respectively).
Cerebrospinal Fluid Pharmacokinetics of Nicardipine Following Intrathecal Administration in Subarachnoid Hemorrhage Patients
Authors: Sadan Ofer , Jeong Yoo-Seong , Cohen-Sadan Shany , Sathialingam Eashani , Buckley Erin M. , Kandiah Prem A. , Grossberg Jonathan A. , Asbury William , Jusko William J , Samuels Owen B.
Published: October 2023

Subarachnoid hemorrhage (SAH) is a devastating type of stroke, leading to high mortality and morbidity rates. Cerebral vasospasm and delayed cerebral ischemia (DCI) are common complications following SAH and contribute significantly to the poor outcomes observed in these patients. Intrathecal (IT) nicardipine delivered via an existing external ventricular drain has been shown to be correlated with reduced DCI and improved patient outcomes. The current study aims to characterize population pharmacokinetic (popPK) properties of intermittent IT nicardipine. Following informed consent, serial cerebrospinal fluid (CSF) samples were obtained from 16 SAH patients (50.4 ± 9.3 years old; 12 females) treated with IT nicardipine every 6 hours (n=8) or every 8 hours (n=8), which were subject to high-performance liquid chromatography for measurement of its CSF concentration. Our popPK analysis showed that the CSF PK of IT nicardipine in the cohort was adequately described by a two-compartment model with a lag time, with reliable parameter estimates (relative standard error < 50%). The intracranial pressure influenced both the total clearance and the central volume. Calculated PK parameters were similar between q6h and q8h dosing regimens. Despite a small cohort of SAH patients, we successfully developed a popPK model to describe the nicardipine disposition kinetics in the CSF following IT administration. These findings may help inform future clinical trials designed to examine the optimal dosing of IT nicardipine.
Multiple imputation assuming missing at random: auxiliary imputation variables that only predict missingness can increase bias due to data missing not at random
Authors: Curnow Elinor , Cornish Rosie P , Heron Jon E , Carpenter James R , Tilling Kate
Published: October 2023

Epidemiological studies often have missing data, which are commonly handled by multiple imputation (MI). MI is valid (given correctly-specified models) if data are missing at random, conditional on the observed data, but not (unless additional information is available) if data are missing not at random (MNAR). In this paper we explore a previously-suggested strategy, namely, including an auxiliary variable predictive of missingness but not the missing data in the imputation model, when data are MNAR. We quantify, algebraically and by simulation, the magnitude of additional bias of the MI estimator, over and above any bias due to data MNAR, from including such an auxiliary variable. We demonstrate that where missingness is caused by the outcome, additional bias can be substantial when the outcome is partially observed. Furthermore, if missingness is caused by the outcome and the exposure, additional bias can be even larger, when either the outcome or exposure is partially observed. When using MI, it is important to identify, through a combination of data exploration and considering plausible casual diagrams and missingness mechanisms, the auxiliary variables most predictive of the missing data (in addition to all variables required for the analysis model and/or to minimise bias due to MNAR).
A qualitative analysis of community health worker perspectives on the implementation of the preconception and pregnancy phases of theBukhalirandomised controlled trial
Authors: Soepnel Larske M , Norris Shane A , Mabetha Khuthala , Motlhatlhedi Molebogeng , Nkosi Nokuthula , Lye Stephen , Draper Catherine E
Published: October 2023

Community health workers (CHWs) play an important role in health systems in low– and middle-income countries, including South Africa.Bukhaliis a CHW-delivered intervention as part of a randomised controlled trial, to improve the health trajectories of young women in Soweto, South Africa. This study aimed to qualitatively explore factors influencing implementation of the preconception and pregnancy phases ofBukhali, from the perspective of the CHWs (Health Helpers, HHs) delivering the intervention. As part of theBukhalitrial process evaluation, three focus group discussions were conducted with the 13 HHs employed by the trial. A thematic approach was used to analyse the data, drawing on elements of a reflexive thematic and codebook approach. The following six themes were developed, representing factors impacting implementation of the HH roles: interaction with the existing public healthcare sector; participant perceptions of health; health literacy and language barriers; participants’ socioeconomic constraints; family, partner, and community views of trial components; and the HH-participant relationship. HHs reported uses of several trial-based tools to overcome implementation challenges, increasing their ability to implement their roles as planned. The relationship of trust between the HH and participants seemed to function as one important mechanism for impact. The findings supported a number of adaptations to the implementation ofBukhali, such as intensified trial-based follow-up of referrals that do not receive management at clinics, continued HH training and community engagement parallel to trial implementation, with an increased emphasis on health-related stigma and education.

HH perspectives on intervention implementation highlighted adaptations relevant to theBukhaliintervention, other CHW-delivered preconception and pregnancy trials, and ‘real-world’ CHW roles, across three broad strategic areas: navigating and bridging healthcare systems, adaptability to individual participant needs, and navigating stigma around disease.
Feeding secondary fermentations with mammalian and fungal culture waste streams increases productivity and resource efficiency
Authors: Lynch Ciara , Cerrone Federico , O’Connor Kevin E , O’Connell David J
Published: October 2023

The evolution of the circular bioeconomy will require the realisation of new value from waste streams generated from all manufacturing processes. Bioprocessing of recombinant proteins and functional foods using animal and microbial fermentations are fast growing industries with increasing volumes of spent culture media waste resulting in significant resource inefficiency. Here Chinese hamster ovary cell spent media (CSM) andTrametes versicolorfungal cell spent media (FSM) were used as model waste streams to feedEscherichia coliin secondary fermentations. Expression of a recombinant fusion protein was used to measure the value of these streams as feedstuff.E. colicultures fed with either waste stream in bioreactors produced equivalent yields of the protein as those fed with rich microbiological media. Separately CSM was tested as a replacement feed for the fungal cell fermentation producing beta and alpha glucans. This waste-fed fermentation resulted in a 2-fold higher glucan yield than when using standard corn steep liquor feed. Quantitative analysis of the spent media content with mass spectrometry and hplc methods showed significant differences in elemental composition profiles, quantities of individual amino acids and carboxylic acids and levels of carbon sources. These findings underline the versatility ofE.coliin utilisation of waste media as a feedstuff and show that the range of applications of CHO cell culture media waste are not limited to feeding bacterial fermentation. Exploration of cellular bioprocesses that can efficiently use cell media waste as fermentation feed will be a valuable step towards increased resource efficiency in bioprocessing industries. (249/250).

Significance Statement

The expanding range and scale of valuable biomolecular products developed with bioprocessing activities using animal and microbial cells is responsible for the production of hundreds of millions of litres of waste culture media annually. Recycling this waste stream has the potential to decrease the impact of the associated high water and energy consumption contributing to meeting targets for the Paris 2050 Agreement and UN Sustainable Development Goals. This work shows that waste media from distinct bioprocesses can be reused to sustain high-level recombinant protein production in a secondary fermentation and the notable finding that a waste media can add value to a secondary process by increasing its productivity. Efficient valorisation of waste media is an urgent and scientifically valuable objective. (120/120)
A purine salvage bottleneck leads to bacterial adenine cross-feeding
Authors: Chuang Ying-Chih , Haas Nicholas W. , Pepin Robert , Behringer Megan , Oda Yasuhiro , LaSarre Breah , Harwood Caroline S. , McKinlay James B.
Published: October 2023

Diverse ecosystems host microbial relationships that are stabilized by nutrient cross-feeding. Cross-feeding can involve metabolites that should hold value for the producer. Externalization of such communally valuable metabolites is often unexpected and difficult to predict. Previously, we fortuitously discovered purine externalization byRhodopseudomonas palustrisby its ability to rescue growth of anEscherichia colipurine auxotroph. Here we found that anE. colipurine auxotroph can stably coexist withR. palustrisdue to purine cross-feeding. We identified the cross-fed purine as adenine. Adenine was externalized byR. palustrisunder diverse growth conditions. Computational models suggested that adenine externalization occurs via passive diffusion across the cytoplasmic membrane. RNAseq analysis led us to hypothesize that accumulation and externalization of adenine stems from an adenine salvage bottleneck at the enzyme encoded byapt. Ectopic expression ofapteliminated adenine externalization, supporting our hypothesis. A comparison of 49R. palustrisstrains suggested that purine externalization is relatively common, with 15 of the strains exhibiting the trait. Purine externalization was correlated with the genomic orientation ofaptorientation, butaptorientation alone could not explain adenine externalization in some strains. Our results provide a mechanistic understanding of how a communally valuable metabolite can participate in cross-feeding. Our findings also highlight the challenge in identifying genetic signatures for metabolite externalization.
Repressor sequestration activates translation of germ granule localized mRNA
Authors: Chen Ruoyu , Stainier William , Dufourt Jeremy , Lagha Mounia , Lehmann Ruth
Published: October 2023

Biomolecular condensates organize and compartmentalize biochemical processes within cells1. Among these, ribonucleoprotein (RNP) granules are characterized as storage depots for translationally repressed mRNA2–8. Whether RNP granules can also activate translation and how such translation is achieved remains unclear9. This question is particularly relevant for embryonic germ granules, whose activity has been linked to germ cell fate10–13. Here, we use single-molecule imaging to show that embryonic germ cell RNP granules inDrosophilaare the sites of active translation fornanosmRNA. TranslatingnanosmRNA is oriented with the 5’end preferentially at the germ granule surface while the 3’UTR is buried within the granule. UntranslatednanosmRNAs remain internal within the granule. Quantitative analysis of translational kinetics demonstrates that germ granules activate translation by antagonizing translational repression rather than changing the rate or efficiency of translation. We generated separation-of-function mutations in the disordered linker region of the scaffold protein Oskar that specifically impedenanostranslation without affecting germ granule morphology or RNA localization. These mutations reveal thatnanostranslation is dependent on the sequestration of translational repressors within germ granules. Together, our findings show that RNP granules regulate localized protein synthesis through compartmentalized relief of translational repression raising the possibility that similar repressor-activator switches control translation in other condensates.
A single pair of pharyngeal neurons functions as a commander to reject high salt inDrosophila melanogaster
Authors: Sang Jiun , Dhakal Subash , Shrestha Bhanu , Nath Dharmendra Kumar , Kim Yunjung , Ganguly Anindya , Montell Craig , Lee Youngseok
Published: October 2023

Salt is an essential nutrient for survival, while excessive NaCl can be detrimental. In the fruit fly,Drosophila melanogaster, internal taste organs in the pharynx are critical gatekeepers impacting the decision to accept or reject a food. Currently, our understanding of the mechanism through which pharyngeal gustatory receptor neurons (GRNs) sense high salt are rudimentary. Here, we found that a member of the ionotropic receptor family,Ir60b, is expressed exclusively in a pair of GRNs activated by high salt. Using a two-way choice assay (DrosoX) to measure ingestion volume, we demonstrate that IR60b and two coreceptors IR25a and IR76b, are required to prevent high salt consumption. Mutants lacking external taste organs but retaining the internal taste organs in the pharynx exhibit much higher salt avoidance than flies with all taste organs but missing the three IRs. Our findings highlight the vital role for IRs in a pharyngeal GRN to control ingestion of high salt.
Cut it out: Out-of-plane stresses in cell sheet folding ofVolvoxembryos
Authors: Haas Pierre A. , Höhn Stephanie S. M. H.
Published: October 2023

The folding of cellular monolayers pervades embryonic development and disease. It results from stresses out of the plane of the tissue, often caused by cell shape changes including cell wedging via apical constriction. These local cellular changes need not however be compatible with the global shape of the tissue. Such geometric incompatibilities lead to residual stresses that have out-of-plane components in curved tissues, but the mechanics and function of these out-of-plane stresses are poorly understood, perhaps because their quantification has proved challenging. Here, we overcome this difficulty by combining laser ablation experiments and a mechanical model to reveal that such out-of-plane residual stresses exist and also persist during the inversion of the spherical embryos of the green algaVolvox. We show how to quantify the mechanical properties of the curved tissue from its unfurling on ablation, and reproduce the tissue shape sequence at different developmental timepoints quantitatively by our mechanical model. Strikingly, this reveals not only clear mechanical signatures of out-of-plane stresses associated with cell shape changes away from those regions where cell wedging bends the tissue, but also indicates an adaptive response of the tissue to these stresses. Our results thus suggest that cell sheet folding is guided mechanically not only by cell wedging, but also by out-of-plane stresses from these additional cell shape changes.
Single cell transcriptomics-level Cytokine Activity Prediction and Estimation (SCAPE)
Authors: Javaid Azka , Frost H. Robert
Published: October 2023

Cytokine interaction activity modeling is a pressing problem since uncontrolled cytokine influx is at fault in a variety of medical conditions, including viral infections like COVID19, and cancer. Accurate knowledge of cytokine activity levels can be leveraged to provide tailored treatment recommendations based on individual patients’ transcriptomics data. Here, we describe a novel method named Single cell transcriptomics-level Cytokine Activity Prediction and Estimation (SCAPE) that can predict cell-level cytokine activity from scRNA-seq data. SCAPE generates activity estimates using cytokine-specific gene sets constructed using information from the CytoSig and Reactome databases and scored with a modified version of the Variance-adjusted Mahalanobis (VAM) method adjusted for negative weights. We validate SCAPE using both simulated and real single cell RNA-sequencing (scRNA-seq) data. For the simulation study, we perturb real scRNA-seq data to reflect the expected stimulation signature of up to 41 cytokines, including chemokines, interleukins and growth factors. For the real data evaluation, we use publicly accessible scRNA-seq data that captures cytokine stimulation and blockade experiment conditions and a COVID19 transcriptomics data. As demonstrated by these evaluations, our approach can accurately estimate cell-level cytokine activity from scRNA-seq data. Our model has the potential to be incorporated in clinical settings as a way to estimate cytokine signaling for different cell populations within an impacted tissue sample.
Genetically- and spatially-defined basolateral amygdala neurons control food consumption and social interaction
Authors: Lim Hansol , Zhang Yue , Peters Christian , Straub Tobias , Mayer Johanna Luise , Klein Rüdiger
Published: October 2023

The basolateral amygdala (BLA) contains discrete neuronal circuits that integrate positive or negative emotional information and drive the appropriate innate and learned behaviors. Whether these circuits consist of genetically-identifiable and anatomically segregated neuron types, is poorly understood. Also, our understanding of the response patterns and behavioral spectra of genetically-identifiable BLA neurons is limited. Here, we classified 11 glutamatergic BLA cell clusters and found that several of them were anatomically segregated in lateral versus basal amygdala, and anterior versus posterior regions of the BLA. Two of these BLA subpopulations innately responded to valence-specific, whereas one responded to mixed - aversive and social - cues. Positive-valence BLA neurons promoted normal feeding, while mixed selectivity neurons promoted fear learning and social interactions. These findings enhance our understanding of cell type diversity and spatial organization of the BLA and the role of distinct BLA populations in representing valence-specific and mixed stimuli.

Highlights

Classification of molecularly-defined glutamatergic neuron types in mouse BLA with distinct spatial expression patterns.

BLALypd1neurons are positive-valence neurons innately responding to food and promoting normal feeding.

BLAEtv1neurons innately represent aversive and social stimuli.

BLAEtv1neurons promote fear learning and social interactions.
Detecting time-varying genetic effects in Alzheimer’s disease using a longitudinal GWAS model
Authors: Zhuang Xiaowei , Xu Gang , Amei Amei , Cordes Dietmar , Wang Zuoheng , Oh Edwin C. ,   Alzheimer’s Disease Neuroimaging Initiative
Published: October 2023

Background

The development and progression of Alzheimer’s disease (AD) is a complex process that can change over time, during which genetic influences on phenotypes may also fluctuate. Incorporating longitudinal phenotypes in genome wide association studies (GWAS) could help unmask genetic loci with time-varying effects. In this study, we incorporated a varying coefficient test in a longitudinal GWAS model to identify single nucleotide polymorphisms (SNPs) that may have time- or age-dependent effects in AD.

Methods

Genotype data from 1,877 participants in the Alzheimer’s Neuroimaging Data Initiative (ADNI) were imputed using the Haplotype Reference Consortium (HRC) panel, resulting in 9,573,130 SNPs. Subjects’ longitudinal impairment status at each visit was considered as a binary and clinical phenotype. Participants’ composite standardized uptake value ratio (SUVR) derived from each longitudinal amyloid PET scan was considered as a continuous and biological phenotype. The retrospective varying coefficient mixed model association test (RVMMAT) was used in longitudinal GWAS to detect time-varying genetic effects on the impairment status and SUVR measures. Post-hoc analyses were performed on genome-wide significant SNPs, including 1) pathway analyses; 2) age-stratified genotypic comparisons and regression analyses; and 3) replication analyses using data from the National Alzheimer’s Coordinating Center (NACC).

Results

Our model identified 244 genome-wide significant SNPs that revealed time-varying genetic effects on the clinical impairment status in AD; among which, 12 SNPs on chromosome 19 were successfully replicated using data from NACC. Post-hoc age-stratified analyses indicated that for most of these 244 SNPs, the maximum genotypic effect on impairment status occurred between 70 to 80 years old, and then declined with age. Our model further identified 73 genome-wide significant SNPs associated with the temporal variation of amyloid accumulation. For these SNPs, an increasing genotypic effect on PET-SUVR was observed as participants’ age increased. Functional pathway analyses on significant SNPs for both phenotypes highlighted the involvement and disruption of immune responses- and neuroinflammation-related pathways in AD.

Conclusion

We demonstrate that longitudinal GWAS models with time-varying coefficients can boost the statistical power in AD-GWAS. In addition, our analyses uncovered potential time-varying genetic variants on repeated measurements of clinical and biological phenotypes in AD.
Type II restriction of 2-aminoadenine (dZ) modified DNA and production of dZ-modified plasmid inE. coli
Authors: Yang Weiwei , Kuska Michael , Dai Nan , Ettwiller Laurence , Xu Shuang-yong
Published: October 2023

The modified DNA base 2,6 aminopurine (2-aminoadenine, (d)Z base) was originally found in phages to counteract host encoded restriction systems. However, only a limited number of restriction endonucleases (REases) have been tested on dZ-modified DNA. Herein we report the results of 147 REases activity on dZ-modified PCR DNA. Among the enzymes tested, 53.1% are resistant or partially resistant, and 46.9% are sensitive when the restriction sites contain 1 to 6 modified bases. Sites with 4-6 dZ substitutions are most likely resistant to Type II restriction. Our results support the notion that dZ-modified phage genomes are evolved to combat host- encoded restriction systems. dZ-modified DNA can also “slow down” phage T5 exonuclease degradation, but it has no effect on RecBCD digestion. When two genes for dZ biosynthesis and one gene for dATP hydrolysis fromSalmonellaphage PMBT28 (purZ(adenylosuccinate synthetase),datZ(dATP triphosphohydrolase), andmazZ((d)GTP-specific diphosphohydrolase) were cloned intoE. coliplasmid, dZ incorporation level reached 19-20% dZ/(dZ+dA). dZ level can be further increased to 28.9-44.3% with co-expression of a DNA polymerase gene from the same phage. High level of dZ incorporation in recombinant plasmid is possible by co-expression ofpurZ, mazZ, datZand phage DNA helicase,dpoZ (DNA polymerase) andssb(single-stranded DNA binding protein SSB). This work has a general interest for molecular biologists working on dZ DNA modification and restriction systems. It provides a foundation for future research on screening dZ-dependent Type IV restriction systems. The results presented herein may have implication in gene therapy utilizing dZ-modified DNA, provided that human RNA polymerase variants can efficiently perform transcription from a dZ-modified template.
Bidirectional Generative Adversarial Representation Learning for Natural Stimulus Synthesis
Authors: Reilly Johnny , Goodwin John D. , Lu Sihao , Kozlov Andriy S.
Published: October 2023

Thousands of species use vocal signals to communicate with one another. Vocalisations carry rich information, yet characterising and analysing these complex, high-dimensional signals is difficult and prone to human bias. Moreover, animal vocalisations are ethologically relevant stimuli whose representation by auditory neurons is an important subject of research in sensory neuroscience. A method that can efficiently generate naturalistic vocalisation waveforms would offer an unlimited supply of stimuli with which to probe neuronal computations. While unsupervised learning methods allow for the projection of vocalisations into low-dimensional latent spaces learned from the waveforms themselves, and generative modelling allows for the synthesis of novel vocalisations for use in downstream tasks, there is currently no method that would combine these tasks to produce naturalistic vocalisation waveforms for stimulus playback. In this paper, we demonstrate BiWaveGAN: a bidirectional Generative Adversarial Network (GAN) capable of learning a latent representation of ultrasonic vocalisations (USVs) from mice. We show that BiWaveGAN can be used to generate, and interpolate between, realistic vocalisation waveforms. We then use these synthesised stimuli along with natural USVs to probe the sensory input space of mouse auditory cortical neurons. We show that stimuli generated from our method evoke neuronal responses as effectively as real vocalisations, and produce receptive fields with the same predictive power. BiWaveGAN is not restricted to mouse USVs but can be used to synthesise naturalistic vocalisations of any animal species and interpolate between vocalisations of the same or different species, which could be useful for probing categorical boundaries in representations of ethologically relevant auditory signals.
BTSP, not STDP, Drives Shifts in Hippocampal Representations During Familiarization
Authors: Madar A.D. , Dong C. , Sheffield M.E.J.
Published: October 2023

Synaptic plasticity is widely thought to support memory storage in the brain, but the rules determining impactful synaptic changes in-vivo are not known. We considered the trial-by-trial shifting dynamics of hippocampal place fields (PFs) as an indicator of ongoing plasticity during memory formation. By implementing different plasticity rules in computational models of spiking place cells and comparing to experimentally measured PFs from mice navigating familiar and novel environments, we found that Behavioral-Timescale-Synaptic-Plasticity (BTSP), rather than Hebbian Spike-Timing-Dependent-Plasticity, is the principal mechanism governing PF shifting dynamics. BTSP-triggering events are rare, but more frequent during novel experiences. During exploration, their probability is dynamic: it decays after PF onset, but continually drives a population-level representational drift. Finally, our results show that BTSP occurs in CA3 but is less frequent and phenomenologically different than in CA1. Overall, our study provides a new framework to understand how synaptic plasticity shapes neuronal representations during learning.