bluuebunny/crossref_metadata_2025 huggingface dataset:
Ensuring Robustness in Scientific Research, Split-root assays as an example case
Authors: Salvatore L , Pierik R , Kajala K , ten Tusscher K.H
Published: November 2024

Scientific progress relies on reproducibility, replicability, and robustness of research outcomes. After briefly discussing these terms and their significance for reliable scientific discovery, we argue for the importance of investigating robustness of outcomes to experimental protocol variations. We highlight challenges in achieving robust, replicable results in multi-step plant science experiments, using split-root assays in Arabidopsis thaliana as a case study. These experiments are important for unraveling the contributions of local, systemic and long-distance signalling in plant responses and play a central role in nutrient foraging research. The complexity of these experiments allows for extensive variation in protocols. We investigate what variations do or do not result in similar results and provide concrete recommendations for enhancing replicability and robustness of these and other complex experiments through extending the level of detail in research protocols.
AnnotIEM: novel tool for microbiome species-level annotation of 16S gene based microbial sequencing
Authors: Bhattacharyya Madhumita , Rauer Luise , Reiger Matthias , Afghani Jamie , Huelpuesch Claudia , Traidl-Hoffmann Claudia , Neumann Avidan U.
Published: November 2024

Identification of microbial species is essential for the generation of meaningful results from microbiome analysis. However, correct annotation of 16S microbial sequences remains a challenge, especially down to the species-level, because most available databases of 16S sequences are not well curated. AnnotIEM is a new tool for species-level annotation of sequences derived from 16S rRNA gene sequencing. AnnotIEM’s novel hit-selection algorithm combines top-hit and majority-hit alignment results from multiple databases. Benchmarking using in-vitro and in-silico mock community control datasets showed that AnnotIEM’s annotation precision on species-level (median=0.83) is significantly (p<0.0001) better than any currently available annotation tool. Benchmarking using a number of real-world environmental microbiome studies demonstrated that AnnotIEM gives higher fraction (58-68%) of species-level annotated sequences, as compared to any other currently available tool. In conclusion, AnnotIEM significantly improves bacterial annotation, which can greatly enhance the results of any microbiome study, and could be potentially used also for other organisms.
Four ZIPs contribute to Zn, Fe, Cu and Mn acquisition at the outer root domain
Authors: Robe Kevin , Lefebvre-Legendre Linnka , Cleard Fabienne , Barberon Marie
Published: November 2024

Zinc (Zn), an essential micronutrient, plays a crucial role in plant development. However, the specific transporters involved in Zn uptake from the soil remain unclear in dicotyledonous. Using promoter-reporter lines inArabidopsis thaliana, we identified severalZIP(Zn-regulated transporter, Iron-regulated transporter (IRT)-like Protein) family members that are expressed in the epidermis and potentially involved in Zn acquisition from the outer root domain. ZIP2, ZIP3, ZIP5 and ZIP8 predominantly localize to the plasma membrane of epidermal and cortical cells, supporting their potential roles in metal uptake from the soil. Through physiology studies, ionomic profiling and genetic analysis, we determined that ZIP3 and ZIP5 are key contributors to Zn acquisition, while ZIP2 and ZIP8 are primarily involved in copper (Cu) and iron (Fe) acquisition respectively. Notably, ZIP3 and ZIP8 exhibit outer polarity in root epidermal cells, similar to IRT1, underscoring the significance of transporter polarity in mineral acquisition. These findings provide new insights into the mechanisms of metal uptake in plant roots and offer potential strategies for biofortification to enhance metal content in plants.
MAPK signaling modulates the partition of DCP1 between P-bodies and stress granules in plant cells
Authors: He Siou-Luan , Wang Ying , Shan Libo , He Ping , Jang Jyan-Chyun
Published: November 2024

Processing bodies (PBs) and stress granules (SGs) are membrane-less cellular compartments consisting of ribonucleoprotein complexes. Whereas PBs are more ubiquitous, SGs are assembled mainly in response to stress. PBs and SGs are known to physically interact and molecules exchange between the two have been documented in mammals. However, the molecular mechanisms underpinning these processes are virtually unknown in plants. We have reported recently that tandem CCCH zinc finger 1 (TZF1) protein can recruit MAPK signaling components to SGs. Here we have found that TZF1-MPK3/6-MKK4/5 form a protein-protein interacting network in SGs. The mRNA decapping factor 1 (DCP1) is a core component of PBs. MAPK signaling mediated phosphorylation triggers a rapid reduction of DCP1 partition into PBs, concomitantly associated with an increase of DCP1 assembly into SGs. Furthermore, we have found that plant SG marker protein UBP1b (oligouridylate binding protein 1b) plays a role in maintaining DCP1 in PBs by suppressing the accumulation of MAPK signaling components. Together, we propose that MAPK signaling and UBP1b mediate the dynamics of PBs and SGs in plant cells.
Brain functional connectivity, but not neuroanatomy, captures the interrelationship between sex and gender in preadolescents
Authors: Metoki Athanasia , Chauvin Roselyne J. , Gordon Evan M. , Laumann Timothy O. , Kay Benjamin P. , Krimmel Samuel R. , Marek Scott , Wang Anxu , Van Andrew N. , Baden Noah J. , Suljic Vahdeta , Scheidter Kristen M. , Monk Julia , Whiting Forrest I. , Ramirez-Perez Nadeshka J. , Barch Deanna M. , Sotiras Aristeidis , Dosenbach Nico U.F.
Published: November 2024

Understanding sex differences in the adolescent brain is crucial, as these differences are linked to neurological and psychiatric conditions that vary between males and females. Predicting sex from adolescent brain data may offer valuable insights into how these variations shape neurodevelopment. Recently, attention has shifted toward exploring socially-identified gender, distinct from sex assigned at birth, recognizing its additional explanatory power. This study evaluates whether resting-state functional connectivity (rsFC) or cortical thickness more effectively predicts sex and sex/gender alignment (the congruence between sex and gender) and investigates their interrelationship in preadolescents. Using data from the Adolescent Brain Cognitive Development (ABCD) Study, we employed machine learning to predict both sex (assigned at birth) and sex/gender alignment from rsFC and cortical thickness. rsFC predicted sex with significantly higher accuracy (86%) than cortical thickness (75%) and combining both did not improve the rsFC model’s accuracy. Brain regions most effective in predicting sex belonged to association (default mode, dorsal attention, and parietal memory) and visual (visual and medial visual) networks. The rsFC sex classifier trained on sex/gender aligned youth was significantly more effective in classifying unseen youth with sex/gender alignment than in classifying unseen youth with sex/gender unalignment. In females, the degree to which their brains’ rsFC matched a sex profile (female or male), was positively associated with the degree of sex/gender alignment. Lastly, neither rsFC nor cortical thickness predicted sex/gender alignment. These findings highlight rsFC’s predictive power in capturing the relationship between sex and gender and the complexity of the interplay between sex, gender, and the brain’s functional connectivity and neuroanatomy.
Bias-accounting meta-analyses overcome cerebellar neglect to refine the cerebellar behavioral topography
Authors: Magielse Neville , Manoli Aikaterina , Eickhoff Simon B. , Fox Peter T. , Saberi Amin , Valk Sofie L.
Published: November 2024

The cerebellum plays important roles in motor, cognitive, and emotional behaviors. Previous cerebellar coordinate-based meta-analyses and mappings have attributed different behaviors to cerebellar subareas, but an accurate behavioral topography is lacking. Here, we show overrepresentation of superior activation foci, which may be exacerbated by historical cerebellar neglect. Unequal foci distributions render the null hypothesis of standard activation likelihood estimation unsuitable. Our new method, cerebellum-specific activation-likelihood estimation (C-SALE), finds behavioral convergence beyond baseline activation rates. It does this by testing experimental foci versus null models sampled from a data-driven, biased probability distribution of finding foci at any cerebellar location. Cerebellar mappings were made across five BrainMap task domains and thirty-five subdomains, illustrating improved specificity of the new method. Twelve of forty (sub)domains reached convergence in specific cerebellar subregions, supporting dual motor representations and placing cognition in posterior-lateral regions. Repeated subsampling revealed that whereas action, language and working memory were relatively stable, other behaviors produced unstable meta-analytic maps. Lastly, meta-analytic connectivity modeling in the same debiased framework was used to reveal coactivation networks of cerebellar behavioral clusters. In sum, we created a new method for cerebellar meta-analysis that accounts for data biases and can be flexibly adapted to any part of the brain. Our findings provide a refined understanding of cerebellar involvement in human behaviors, highlighting regions for future investigation in both basic and clinical applications.
Speech in noise performance in adults with cochlear implants using a combined channel deactivation strategy with a variable number of dynamic focused channels
Authors: Wohlbauer Dietmar M. , Hem Charles , McCallick Caylin , Arenberg Julie G.
Published: November 2024

Abstract

Objectives and Methods

Cochlear implant listeners show difficulties in understanding speech in noise. Channel interactions from activating overlapping neural populations reduce the signal accuracy necessary to interpret complex signals. Optimizing programming strategies based on focused detection thresholds to reduce channel interactions has led to improved performance. In the current study, two previously suggested methods, channel deactivation and focused dynamic tripolar stimulation, were combined to create three cochlear implant programs. Utilizing an au-tomatic channel selection algorithm from focused detection threshold profiles, three programs were created with the same deactivated channels but varying proportions of channels employing focused stimulation, monopolar, dynamic focused and a mixed program. Thirteen ears in eleven adult cochlear implant listeners with Advanced Bionics HiRes90k devices were tested. Vowel identification and sentence perception in quiet and noise served as outcome measures, and the influences of listening experience, age, clinical consonant-nucleus-consonant performance, and perceptual thresholds on speech performance were assessed.

Results

Across subjects, different degrees of focusing showed individual performance improvements for vowels and sentences over the monopolar program. However, only slight trends and no significant group improvements were observed. Focused listening benefits were shown for individuals with less cochlear implant experience, and clinically poor performers seem to benefit more from focusing than good per-formers.

Conclusion

The current findings suggest that deactivating and focusing subsets of channels improves speech performance for some individuals, especially poor performers, a possi-ble effect of reduced channel interactions. The findings also show that individual performance is largely variable, possibly due to listening experience, age or the underlying detection threshold.
Fitness trade-off and the discovery of a novel missense mutation in the PmrB sensor kinase of a colistin-resistantPseudomonas aeruginosastrain developed by adaptive laboratory evolution
Authors: Padhy Indira , Dwibedy Sambit K. , Mohapatra Saswat S.
Published: November 2024

Pseudomonas aeruginosais a prominent bacterial pathogen that causes several nosocomial infections and is notorious for its environmental resilience and rapid development of resistance to frontline antibiotics. A major cause of mortality and morbidity among cystic fibrosis patients, multidrug-resistantP. aeruginosais often targeted with the antibiotic colistin as a last option. However, increasing reports of colistin resistance amongP. aeruginosais a matter of significant concern. Though the molecular mechanisms responsible for the development of colistin resistance are well known, the evolutionary trajectory to colistin resistance is an important area of investigation. In this work, using the adaptive laboratory evolution (ALE) approach we have evolved a colistin-sensitiveP. aeruginosaancestral strain to a resistant one. During the process of laboratory evolution in 106 generations, colistin MIC was increased 32-fold. The evolved strain had lower fitness than the ancestral strain as evidenced by a lower growth rate and higher doubling time. Moreover, the evolved strain produced more biofilm and less pyocyanin. Interestingly, the evolved strain showed collateral sensitivity to several antibiotics such as co-trimoxazole, rifampicin, kanamycin, tigecycline, penicillin, ampicillin, and teicoplanin. On analysing various TCS modules involved in the development of colistin resistance a novel missense mutation (V136G) was detected in the PmrB sensor kinase. Bioinformatics prediction indicated that the mutation could be deleterious, though the functionality of the PmrB mutant remains to be validated experimentally.
Early life adversity increases risk for chronic posttraumatic pain, data from humans and rodents
Authors: McKibben Lauren A. , Woolard Alice , McLean Samuel A. , Zhao Ying , Verma Taanvii , Mickelson Jacqueline , Lu Hongxia , Lobo Jarred , House Stacey L. , Beaudoin Francesca L. , An Xinming , Stevens Jennifer S. , Neylan Thomas C. , Jovanovic Tanja , Germine Laura T. , Rauch Scott L. , Haran John P. , Storrow Alan B. , Lewandowski Christopher , Hendry Phyllis L. , Sheikh Sophia , Jones Christopher W. , Punches Brittany E. , Hudak Lauren A. , Pascual Jose L. , Seamon Mark J. , Pearson Claire , Peak David A. , Merchant Roland C. , Domeier Robert M. , Rathlev Niels K. , O’Neil Brian J. , Sanchez Leon D. , Bruce Steven E. , Sheridan John F. , Kessler Ronald C. , Koenen Karestan C. , Ressler Kerry J. , Linnstaedt Sarah D.
Published: November 2024

Traumatic stress exposures (TSE) are common in life. While most individuals recover following a TSE, a substantial subset develop adverse posttraumatic neuropsychiatric sequelae such as chronic posttraumatic musculoskeletal pain (CPMP). Vulnerability factors for CPMP are poorly understood, which hinders identification of high-risk individuals for targeted interventions. One known vulnerability factor for many pain types is exposure to early life adversity (ELA), but few studies have assessed whether ELA increases risk for CPMP. This study used data from the AURORA study, a prospective human cohort study of TSE survivors, to test the hypothesis that ELA increases risk for CPMP. In addition, in secondary analyses, we assessed which subtypes of ELA (including childhood bullying) were most predictive of CPMP and whether a rat ELA model consisting of neonatal limited bedding (NLB), combined with single prolonged stress (SPS) in adulthood, would accurately model human findings. In AURORA study participants (n=2,480), using multinomial logistic regression modeling of four identified latent pain classes, we found that ELA increased vulnerability to the high unremitting pain class (OR=1.047,p<0.001), the moderate pain class (OR=1.031,p<0.001), and the moderate recovery pain class (OR=1.018,p=0.004), with physical abuse, emotional abuse, and bullying being the strongest predictors of high pain class assignment. Similarly, in male and female Sprague Dawley rats, in comparison to SPS alone NLB combined with SPS caused increased baseline sensitivity and prolonged mechanical hypersensitivity (F(11,197)=3.22,p<0.001). Further studies in animals and humans are needed to understand mechanisms by which ELA confers vulnerability to CPMP.

In humans and rats, early life adversity is associated with a greater duration of musculoskeletal pain and mechanical hypersensitivity following traumatic stress exposures during adulthood.
Does frequency or diversity of leisure activity matter more for epigenetic ageing? Analyses of arts engagement and physical activity in the UK Household Longitudinal Study
Authors: Fancourt Daisy , Masebo Lehané , Finn Saoirse , Mak Hei Wan , Bu Feifei
Published: November 2024

Over the past decade, ageing clocks have become widely adopted as important tools for understanding biological ageing and have been redefining notions of “pro-longevity” lifestyles. However, this work is still at an early stage. Some leisure activities, such as arts and cultural engagement (ACEng) have never been studied at all, while others such as physical activity (PA) have only received scant attention. In particular, there is little understanding of whether frequency of engagement or diversity (which provides access to more active ingredients) is more important. This study used 3,354 adults in the UK Household Longitudinal Study - a large, nationally-representative cohort study, which includes six derived epigenetic clocks. We used a doubly robust estimation using the inverse-probability-weighted regression adjustment estimator adjusted for demographic, socioeconomic, behavioural and health covariates, data collection gaps and technical covariates of epigenetic clocks. ACEng and PA were related to slower biological ageing in the PhenoAge and DunedinPoAm clocks, although not to the other measured clocks, with comparable effect sizes between ACEng and PA (Lin, Horvath2018, Horvath2013 and Hannum). For ACEng, diversity and frequency of engagement were related to DunedinPoAm, while for PhenoAge, there was a slightly clearer relationship for frequency than diversity. For PA, higher levels of frequency, diversity, and activeness were related to DunedinPoAm, while only the highest diversity and activeness were related to PhenoAge. These findings were all stronger amongst middle-aged and older adults. This was the first study to show a relationship between ACEng and epigenetic ageing, with comparable effect sizes to PA, suggesting the value of its exploration alongside other lifestyle factors. Decelerations in ageing clocks, including those within our study, have been demonstrated to have clinical (as well as statistical) importance, supporting future exploration as to whether lifestyle changes have any value to slowing or potentially reversing epigenetic ageing.
Positive and negative affect, related mental health traits, and cognitive performance: shared genetic architecture and potential causality
Authors: Slaney Chloe , Mac Giollabhui Naoise , van der Most Peter J. , Palacios Ensor R. , Snieder Harold , Nivard Michel , Hemani Gibran , Hartman Catharina A. , Khandaker Golam M.
Published: November 2024

Altered affect and cognitive dysfunction are transdiagnostic, burdensome, and pervasive features of many psychiatric conditions which remain poorly understood and have few efficacious treatments. Research on the genetic architecture of these phenotypes and causal relationships between them may provide insight into their aetiology and comorbidity. Using data from the Lifelines Cohort Study, we conducted genome-wide association studies (GWAS) on positive and negative affect and four cognitive domains (working memory, reaction time, visual learning and memory, executive function). Using publicly available large GWAS on related - albeit distinct-phenotypes (depression, anxiety, wellbeing, general cognitive ability [GCA]) we conducted genetic correlation and Mendelian randomization (MR) analyses to examine genetic overlap and causal relationships. We identified one genome-wide hit (p<5×10-8) for reaction time, and many loci with suggestive associations (p<5×10-6; N range= 11-20 independent hits) for other phenotypes. For most phenotypes, gene mapping and tissue expression analysis of suggestive hits from the GWAS showed increased gene expression in brain tissue compared to other tissues. As predicted, negative affect is genetically correlated with mental health phenotypes (depressionrg=0.51; anxietyrg=0.70; wellbeingrg= −0.71) and cognitive domains are genetically correlated with GCA and brain volume (rg≤ 0.66). Genetic correlations between negative and positive affect suggest that they are dissociable constructs (rg= −0.18) with negative affect having higher genetic overlap with GCA than positive affect (rg=-0.19 vs −0.06). This could indicate that negative affect has a higher shared neural basis with GCA than positive affect and/or GCA and negative affect may exhibit causal relationships. MR analyses suggest potential causal effects of higher GCA on reduced negative affect, reduced risk of depression and anxiety, and higher wellbeing, but little impact on positive affect. We also report evidence for potential causal effects of depression and lower wellbeing on reduced GCA. Taken together, these results suggests that GCA may be a valid target for negative affect (but not positive affect) and depression and wellbeing may be valid targets for GCA.
Interplay between polygenic effects and polypharmacy on dementia: An investigation in an elderly Scottish cohort
Authors: Raptis Vasilis , Mullin Donncha , Syed Sumbul , Deary Ian J , Cox Simon R , Russ Tom C , Luciano Michelle
Published: November 2024

INTRODUCTION

Polygenic Risk Scores for Alzheimer dementia (AD-PRS), a measure of aggregate AD genetic risk and polypharmacy have been associated with dementia. Here, we test their interaction’s association with future dementia among older adults without baseline neurodegenerative diagnoses.

METHODS

Using Cox proportional hazards and mortality-adjusted competing risk regression models we analysed up to 17.5 years all-cause incident dementia in the Lothian Birth Cohort 1936 (n=759, 105 dementia patients). We used polypharmacy (total or nervous-system-acting medications count), AD-PRS, and their interaction as main predictors.

RESULTS

A non-significant interaction was found between AD-PRS and total polypharmacy (HR=1.06; p=0.15) or nervous-system-acting polypharmacy (HR=0.98; p=0.86) in shaping dementia risk. Omitting interaction, mortality-adjusted models showed significant AD-PRS prediction of dementia (HR ∼1.40; p<0.001), non-significant total (HR=1.03; p=0.49), and nervous-system-acting polypharmacy effects (HR=1.27; p=0.069).

DISCUSSION

Elucidating the complex interplay between polypharmacy and genetics could improve management of inappropriate medication in older adults genetically prone to dementia/AD.
Nanophysiology Approach Reveals Diversity in Calcium Microdomains across Zebrafish Retinal Bipolar Ribbon Synapses
Authors: Rameshkumar Nirujan , Shrestha Abhishek P , Boff Johane M. , Hoon Mrinalini , Matveev Victor , Zenisek David , Vaithianathan Thirumalini
Published: November 2024

Rapid and high local calcium (Ca2+) signals are essential for triggering neurotransmitter release from presynaptic terminals. In specialized bipolar ribbon synapses of the retina, these local Ca2+signals control multiple processes, including the priming, docking, and translocation of vesicles on the ribbon before exocytosis, endocytosis, and the replenishment of release-ready vesicles to the fusion sites for sustained neurotransmission. However, our knowledge about Ca2+signals along the axis of the ribbon active zone is limited. Here, we used fast confocal quantitative dual-color ratiometric line-scan imaging of a fluorescently labeled ribbon binding peptide and Ca2+indicators to monitor the spatial and temporal aspects of Ca2+transients of individual ribbon active zones in zebrafish retinal rod bipolar cells (RBCs). We observed that a Ca2+transient elicited a much greater fluorescence amplitude when the Ca2+indicator was conjugated to a ribeye-binding peptide than when using a soluble Ca2+indicator, and the estimated Ca2+levels at the ribbon active zone exceeded 26 μM in response to a 10-millisecond stimulus, as measured by a ribbon-bound low-affinity Ca2+indicator. Our quantitative modeling of Ca2+diffusion and buffering is consistent with this estimate and provides a detailed view of the spatiotemporal [Ca2+] dynamics near the ribbon. Importantly, our data demonstrates that the local Ca2+levels may vary between ribbons of different RBCs and within the same cells. The variation in local Ca2+signals is correlated to ribbon size, which in turn correlates with active zone extent, as serial electron microscopy provides new information about the heterogeneity in ribbon size, shape, and area of the ribbon in contact with the plasma membrane.
Collagen binding adhesin restricts Staphylococcus aureus skin infection
Authors: Bhattacharya Mohini , Spencer Brady L , Kwiecinski Jakub M , Podkowik Magdalena , Putzel Gregory , Pironti Alejandro , Shopsin Bo , Doran Kelly S , Horswill Alexander R
Published: November 2024

Staphylococcus aureus causes approximately 80% of skin and soft tissue infections (SSTIs). Collagen is the most abundant human extracellular matrix protein with critical roles in wound healing, and S. aureus encodes a collagen binding adhesin (Cna). The role of this protein during skin infections is unknown. Here we report that inability to bind collagen results in worsened pathology of intradermal δcna S. aureus infection. WT/Cna+ S. aureus showed reduced infection severity, aggregate formation, and significantly improved clearance of bacteria. Cna binds to the collagen-like domain of serum C1q protein to reduce its opsonophagocytic functions. We demonstrate that infection of C1qKO mice with WT bacteria show results similar to the δcna group. Conversely, inability to bind collagen resulted in an amplified inflammatory response caused in part by macrophage and neutrophil small molecule mediators released at the infection site (MMP-9, MMP-12, LTB4), resulting in increased immune cell infiltration and death.
Single-cell profiling of trabecular meshwork identifies mitochondrial dysfunction in a glaucoma model that is protected by vitamin B3 treatment
Authors: Tolman Nicholas , Li Taibo , Balasubramanian Revathi , Li Guorong , Bupp-Chickering Violet , Kelly Ruth A. , Simón Marina , Peregrin John , Montgomery Christa , Stamer W. Daniel , Qian Jiang , John Simon W.M.
Published: November 2024

Since the trabecular meshwork (TM) is central to intraocular pressure (IOP) regulation and glaucoma, a deeper understanding of its genomic landscape is needed. We present a multimodal, single-cell resolution analysis of mouse limbal cells (includes TM). In total, we sequenced 9,394 wild-type TM cell transcriptomes. We discovered three TM cell subtypes with characteristic signature genes validated by immunofluorescence on tissue sections and whole-mounts. The subtypes are robust, being detected in datasets for two diverse mouse strains and in independent data from two institutions. Results show compartmentalized enrichment of critical pathways in specific TM cell subtypes. Distinctive signatures include increased expression of genes responsible for 1) extracellular matrix structure and metabolism (TM1 subtype), 2) secreted ligand signaling to support Schlemm’s canal cells (TM2), and 3) contractile and mitochondrial/metabolic activity (TM3). ATAC-sequencing data identified active transcription factors in TM cells, including LMX1B. Mutations inLMX1Bcause high IOP and glaucoma. LMX1B is emerging as a key transcription factor for normal mitochondrial function and its expression is much higher in TM3 cells than other limbal cells. To understand the role of LMX1B in TM function and glaucoma, we single-cell sequenced limbal cells fromLmx1bV265D/+mutant mice. InV265D/+mice, TM3 cells were uniquely affected by pronounced mitochondrial pathway changes. This supports a primary role of mitochondrial dysfunction within TM3 cells in initiating the IOP elevation that causes glaucoma in these mice. Importantly, treatment with vitamin B3(nicotinamide), to enhance mitochondrial function and metabolic resilience, significantly protectedLmx1bmutant mice from IOP elevation.
Astrocytes control UP state and slow oscillation periodicity in human cortical networks
Authors: Crowe James A , Bazzari Amjad H , Nagel David A , Sokolovski Sergei G , Rafailov Edik U , Hill Eric J , Parri Rhein H
Published: November 2024

Astrocytes are well known for homeostatic roles in energy maintenance, neurotransmitter recovery and immunoreactivity, however their contributing role in active modulation of neuronal activity remains controversial. Recent evidence highlights astrocytes as a potential signalling partner in ongoing high-order neuronal activity, and a modulator of baseline activity.

Here we utilise an iPSC-derived in vitro cortical network model to describe a slow-wave oscillation and examine the contributions of astrocytes to development of this oscillatory activity, dependant upon generation of UP/DOWN state phenomena. To examine the role of astrocytes we invoke an acetylcholinergic oscillation in the neuronal population by addition of carbachol, which proved to be a robust mechanism for eliciting prolonged and synchronised network bursting. Pharmalogical interrogation determined oscillatory maintenance was dependent on both glutamatergic and purinergic signalling pathways. Upon further interrogation, we determined that astrocytic calcium signalling was essential to timing of the oscillatory signal. By utilising chemogenetic actuators we showed that whilst neurons are essential and sufficient for instigating the oscillatory signal, astrocytes played a key role in timing.

This previously unreported mechanism may contribute to initial development of brain activity, and may underlie a basal activity present later during adulthood. In collaboration with recent results highlighting the role of active gliotransmission, this highlights astrocytes as an important research target for understanding brain activity alterations during development and disease.
The role of the LysR-type transcription factor PacR in regulating nitrogen metabolism inAnabaenasp. PCC7120
Authors: Werner E. , Huokko T. , Santana-Sanchez A. , Picossi S. , Nikkanen L. , Herrero A. , Allahverdiyeva Y.
Published: November 2024

In the filamentous model cyanobacteriumAnabaenasp. PCC 7120 heterocyst formation is triggered by changes in the C/N-ratio and relies on transcriptional reprogramming in cells. The transcription factor PacR is thought to serve as a global regulator of carbon assimilation under photoautotrophic conditions. In response to Ci-availability, PacR may modulate the carbon concentrating mechanism and photosynthesis, balancing reducing power generation while protecting the photosynthetic apparatus from oxidative damage. However, PacR also binds to promoters of genes associated with heterocyst formation, although the underlying mechanisms remain unclear. To explore this, we studied a response of a PacR-deletion mutant to a nitrogen source shift from ammonium to nitrate. The absence of PacR led to the heterocyst formation in nitrate containing media, as well as reduced growth and chlorophyll-content. We observed impaired nitrate uptake and disrupted ammonium assimilation via the GOGAT-cycle. This phenotype may be exacerbated by reduced PSI-yield and reduced expression of ferredoxin, which may lead to less reducing equivalents for nitrogen assimilation.

Our results provide insights into the regulation of heterocyst-formation inAnabaena, potentially advancing its use in biotechnological applications that utilize heterocyst as microoxic cell factories for N2-fixation and hydrogen production.
Acute and early stress axis modulation in joint disease permanently reduces pain and emotional comorbidities
Authors: Hestehave Sara , Florea Roxana , Singleton Samuel , Fedorec Alexander J.H. , Caxaria Sara , Morgan Oakley , Kopp Katharina Tatjana , Brown Laurence A. , Heymann Tim , Sikandar Shafaq , Hausch Felix , Peirson Stuart N. , Géranton Sandrine M.
Published: November 2024

Chronic secondary musculoskeletal pain affects 20-30% of the population and includes sensory disturbances and emotional comorbidities, such as anxiety and depression, which reduce quality of life. We monitored a pre-clinical model of persistent joint pain for 6 months and found that sensory and functional changes were immediate while anxio-depressive comorbidities appeared from 3 months onwards. Modulating the stress axisviagenetic deletion or pharmacological blockade of the stress driver FKBP51 reduced both sensory and emotional symptoms, including injury-induced disruptions in sleep and activity patterns, and did not worsen joint damage. FKBP51 pharmacological blockade after the establishment of the hypersensitive state provided temporary relief while acute inhibition at disease onset, when sensory and affective responses were most severe, provided at least 6 months of pain relief and reduced or prevented late anxiety- and depressive-like behavior. RNA sequencing suggested that FKBP51 inhibition at disease onset downregulated theNaaagene in the superficial dorsal horn, a key regulator of the transition to chronic pain, and reorganized spinal cilia. Our findings suggest that acute and early, but not late, FKBP51 targeting can offer permanent relief from chronic pain and its emotional effects, highlighting the importance for fast therapeutic intervention.
Complex regulatory interactions atGDF5shape joint morphology and osteoarthritis disease risk
Authors: Coveney Clarissa R. , Maridas David , Chen Hao , Muthuirulan Pushpanathan , Liu Zun , Jagoda Evelyn , Yarlagadda Siddharth , Movahhedi Mohammadreza , Proffen Benedikt , Rosen Vicki , Kiapour Ata M. , Capellini Terence D.
Published: November 2024

Our ability to pinpoint causal variants using GWAS is dependent on understanding the dynamic epigenomic and epistatic context of each associated locus. Being the best studied skeletal locus,GDF5associates with many diseases and has a complex cis-regulatory architecture. We interrogateGDF5regulatory interactions and model disease variantsin vitroandin vivo. For all regulatory regions we see that local epigenetic activation/repression impacts patterns of joint-specific expression and disease risk. By modeling the most cited risk variant in mice we found that it had no impact on expression, joint morphology, or disease. Yet, we identified significant epistatic expression interactions between this risk variant and others lying within regulatory regions subject to repression or activation. These findings are important lessons on how regulatory interactions and local epistasis work in the etiology of disease risk, and that assessment of individual variants of high GWAS significance need not alone be considered causal.

Teaser

Genetic interactions at the most studied skeletal disease locus reveal hidden complexities in pinpointing causal mutations.
Daily electric field treatment improves functional outcomes after thoracic contusion spinal cord injury in rats
Authors: Harland Bruce , Matter Lukas , Lopez Salvador , Fackelmeier Barbara , Hazelgrove Brittany , Meissner Svenja , O’Carroll Simon , Raos Brad , Asplund Maria , Svirskis Darren
Published: November 2024

Spinal cord injury (SCI) can result in permanent loss of sensory, motor, and autonomic functions, with limited therapeutic options to recover the loss. Low-frequency electric fields with changing polarity have shown promise in promoting axon regeneration and improving outcomes. However, the metal electrodes used previously were prone to corrosion, and their epidural placement limited the penetration of the electric field into the spinal cord. Here, we demonstrate that a thin-film implant with supercapacitive electrodes placed under the dura mater can safely and effectively deliver electric field treatment in rats with thoracic SCI. Subdural stimulation enhanced hind limb function and touch sensitivity compared to controls, without inducing a neuroinflammatory response in the spinal cord. While axon density around the lesion site remained unchanged after 12 weeks,in vivomonitoring and electrochemical testing of electrodes indicated that treatment was administered throughout the study. These results highlight the promise of electric field treatment as a viable therapeutic strategy for achieving long-term functional recovery in SCI.
Novel symbionts reveal amoebae as significant hosts for environmental chlamydiae
Authors: Liu Fei , Walker Laura M , Wolf Jason , Thompson Christopher , Haselkorn Tamara S , Shi Yijing , Ding Jijuan , Strassmann Joan E , Queller David , Shu Longfei
Published: November 2024

Chlamydiae represent a diverse group of obligate intracellular bacteria with elusive hosts in environmental settings. This study used one of the largest collections of wild amoebae (Dictyostelium discoideum and D. giganteum, 106 clones) collected over the past two decades to screen for novel environmental chlamydiae. We found that novel environmental chlamydiae are prevalent in two wild Dictyostelium species and assembled 42 novel chlamydiae metagenome-assembled genomes (MAGs). The MAGs represent three chlamydiae species previously only reported using 16S sequencing. Their genomes are divergent enough from other species to warrant placing them in two new genera (tentatively called Ca. Dictychlamydia sp. LF1, Ca. Dictychlamydia sp. LF2, and Ca. Feichlamydia sp. LF3). In addition, these chlamydiae species show strong host specificity with two Dictyostelium amoeba hosts, except one amoeba sample. Ca. Dictychlamydia sp. LF1 and Ca. Feichlamydia sp. LF3 was exclusively observed in D. discoideum, while Ca. Dictychlamydia sp. LF2 was found only in D. giganteum. Phylogenetic and comparative genomic analyses suggest that all three chlamydiae are close to arthropod-associated chlamydiae and likely have some intermediate characteristics between previously reported amoeba-associated and vertebrate-associated chlamydiae. This study significantly broadens our understanding of the chlamydial host range and underscores the role of amoebae as vital hosts for environmental chlamydiae.
Molecular basis underlying specific interaction of mammalian melanopsins with an antagonist AA92593
Authors: Obayashi Kohei , Zou Ruisi , Mori Toshifumi , Tsukamoto Hisao
Published: November 2024

Melanopsin functions in intrinsically photosensitive retinal ganglion cells of mammals to regulate circadian clock and pupil constriction. The opsinamide AA92593 has been reported to specifically inhibit mouse and human melanopsin functions as a competitive antagonist against retinal; however, the molecular mechanisms underlying its specificity have not been resolved. In this study, we attempted to identify amino acid residues responsible for the specific interaction of AA92593 with mammalian melanopsins. Our cell-based assays confirmed that AA92593 effectively inhibited the light-induced cellular responses of mammalian melanopsins, but not those of non-mammalian vertebrate and invertebrate melanopsins. These results suggest that amino acid residues specifically conserved among mammalian melanopsins are important for the antagonistic effect of AA92593, and we noticed Phe-94, Ser-188, and Ser-269 as candidate residues. Substitutions of these residues reduced the antagonistic effect of AA92593. We conducted docking and molecular dynamics simulations based on the AlphaFold-predicted melanopsin structure. The simulations indicated that Phe-94, Ser-188, and Ser-269 are located at the AA92593-binding site, and additionally identified Trp-189 and Leu-207 interacting with the antagonist. Substitutions of Trp-189 and Leu-207 affected the antagonistic effect of AA92593. Furthermore, substitutions of these amino acid residues converted AA92593-insensitive melanopsins susceptible to the antagonist. Based on experiments and molecular simulations, five amino acid residues, at positions 94, 188, 189, 207, and 269, were found to be responsible for the specific interaction with AA92593 in mammalian melanopsins.
The Testing of Copper Intrauterine Devices to Mitigate Uterine Infections in Mares: A Preliminary Study
Authors: Gradil Carlos , Jennette Amelia , Becker Klaus , Haire Teresa , Joone Carolynne , Leibstein Miranda , Minter Lisa
Published: November 2024

This preliminary study evaluated the effectiveness of a novel hormone- and drug-free copper intrauterine device POD (CuiUPOD) with one to three copper-coated magnetic units in controllingStreptococcus equi subsp. zooepidemicusin seven intrauterine-inoculated mares. Initially, one unit was inserted into each mare and animals were followed weekly with trans-rectal ultrasonography, blood progesterone assay, uterine swabs for cytology and microbial culture, uterine specimens for biopsy, and trans-abdominal detection of the CuiUPOD using a handheld magnetic detector or a cell phone compass. Infection persisted after a CuiUPOD with one magnetic unit was inserted, but subsided shortly after two additional magnetic units were added. By day 60, at device removal, and after a 30-day exposure to copper, none of the mares presented with clinical signs of infection. On a scale of I-III (I, IIA, IIB, III), with I representing a healthy uterus, endometrial biopsies at the time of CuiUPOD removal, showed improved biopsy scores in two of seven mares (29%;p< 0.05). Thein vivoexperiments, complemented by anin vitroexperiment, demonstrated a time- (24-96 hours) and dose-dependent response to Cu: three CuiUPODs - OD readings = 0.538; two CuiUPODs - OD = 0.513; and one CuiUPOD - OD = 0.452. As the concentration of copper increased, so did the antimicrobial effect. These findings suggest a promising use for the one-time application of a CuiUPOD with two or three magnetic units to mitigate uterine infections in mares.

Simple Summary

Only a limited number of antimicrobials are effective against most resistant bacteria. Several studies have demonstrated the biocidal effect of copper on bacteria, fungi, and viruses. Copper-containing intrauterine devices provide a non-pharmacological solution to prevent and treat uterine infections in equids. This preliminary study provides evidence of the antimicrobial properties of copper both in vivo and in vitro and explores its possible application in mare reproductive practice. A 30-day intrauterine exposure to copper showed no clinical signs of infection with a common bacterium in horses -Streptococcus equi subsp. zooepidemicus- in intrauterine-inoculated mares. As the concentration of copper increased, so did the antimicrobial effect. Copper intrauterine devices show promise in mitigating uterine infections in mares.
Characterization of a NovelTequatrovirusPhage from Pristine Stretch of The Ganges River, India, in Reducing Bacterial Load from Sewage Water
Authors: Samson Rachel , Pawar Ameya , Khairnar Krishna , Dharne Mahesh
Published: November 2024

Effective treatment of wastewater (WW) and its reuse is necessary to meet certain sustainable development goals and a circular economy.Escherichia coliis one of the primary contaminants in the WW, and its extra-intestinal occurrence poses a considerable threat under one health. This study is the first report of a novel broad-spectrum phage (фERS-1) isolated from a pristine stretch of the Ganges River in the biocontrol ofE. coli, resistant to 3rd-and 4thgeneration cephalosporins and aztreonam. This is the first report of a phage from theTequatrovirusgenus to infectP. aeruginosa. The фERS-1 could reduce the abundance ofE. colicells by 8.22 log10CFU/mL ≤24 hrs. Additionally, □ ERS-1 disrupted the biofilm ofE. coliwith a reduction of 3.88 log10CFU/mL. Further, □ ERS-1 could inhibit biofilm by multiple strains ofE. coliand multiple genera (E. coli, S. boydii,andP. aeruginosa). The phage □ ERS-1 reduced bacterial counts in raw WW by 2 log10CFU/mL and 4 log10CFU/mL reduction in coliform-enriched WW in ≤24 hours. Overall, this study suggests that □ ERS-1 could be used as an effective alternative to be combined with other treatments for improving the quality of WW disposal and environmental health by reducing the bacterial load.

Graphical Abstract

Highlights

Isolation of a novel phage from a pristine stretch of the Ganges River

Antibiofilm activity againstE. coli>8 log10inhibition, >3 log10disruption

Biofilm inhibition of >50% againstP. aeruginosaandS. boydii

2 log10and 4 log10reduction of bacterial counts in phage-treated raw sewage
RNA Binding Protein Khdrbs1 Regulates Hematopoietic Stem and Progenitor Cell Emergence via Splicing
Authors: Karp Ilana , Bowman Teresa V.
Published: November 2024

Definitive hematopoietic stem and progenitor cells (HSPCs) arise through an endothelial-to-hematopoietic transition (EHT), whereby endothelial cells (ECs) acquire a hemogenic fate (HE) and convert to HSPCs. EHT regulators remain incompletely understood. Utilizing published RNA-seq data of ECs, HE/HSPCs, and HSPCs, we defined the alternative splicing landscape of zebrafish EHT and potential RNA binding proteins governing the process. Employing an F0 CRISPR-Cas9 mediated mutagenesis screen, we identified zebrafish homologs of KHDRBS1 as critical for embryonic HSPC formation. Mutagenesis ofkhdrbs1a/bled to diminished HSPCs and a profound lineage shift in differentiated cells, with the greatest decrease observed inrag+T-cells. Treatment of mutagenized embryos with the splicing modulator E7107 partially restored HSPCs to near wildtype levels indicating Khdrbs1 splicing regulation drives EHT. Consistently, Khdrbs1 binding motifs were the only ones enriched in EHT alternative splicing events. Identification of EHT-specific splicing regulation provides a deeper understanding of cell fate tuning by splicing.
Two methodologies and timescales show no promotion of antibiotic resistance from in-water coral disease treatments
Authors: Neely Karen L. , Kellogg Christina A. , Voelschow Julie J. , Cauvin Allison R. , Reed Sydney A. M. , Rubin Ewelina , Meyer Julie L.
Published: November 2024

The decimation of reefs caused by stony coral tissue loss disease prompted the use of a topical amoxicillin treatment to prevent coral mortality. Application of this treatment led to concerns about unintentional impacts such as potential alteration of the coral microbiome and possible spread of antibiotic resistance. We used two different methodologies – microbial RNA sequencing and microbial qPCR array – to assess these concerns. RNA sequencing was conducted on coral mucus samples collected before and 24 hours after amoxicillin application on wildMontastraea cavernosa. No differences in expression of antibiotic resistance genes (ARGs) were detected. Additionally, there were no notable changes in the microbial communities between the before and after samples. Microbial qPCR array was used to assess differences in ARGs over longer timescales in wildColpophylia natans, comparing never-treated corals with ones treated a single time seven months prior and with those treated multiple times seven months and more prior. No clinically relevant ARGs represented in the arrays were detected across any samples. A small number of above-detection reads (4 in the never-treated corals, 2 in the once-treated corals, and 0 in the multi-treated corals) may indicate weak amplification of similar environmental (non-anthropogenic) ARGs in the corals. Results indicate that the localized topical application of amoxicillin to prevent mortality of SCTLD-affected corals is neither disrupting the microbiome of treated corals nor driving the proliferation of antibiotic resistance.