bluuebunny/crossref_metadata_2025 huggingface dataset:
An analysis of RNA quality metrics in human brain tissue
Authors: Tian Jiahe , Lam Tiffany G. , Ross Sophie K. , Ciener Benjamin , Leskinen Sandra , Sivakumar Sharanya , Bennett David A. , Menon Vilas , McKhann Guy M. , Runnels Alexi , Teich Andrew F.
Published: October 2024

Human brain tissue studies have historically used a range of metrics to assess RNA quality. However, few large-scale cross-comparisons of pre-sequencing quality metrics with RNA-seq quality have been published. Here, we analyze how well metrics gathered before RNA sequencing (post-mortem interval (PMI) and RNA integrity number RIN) relate to analyses of RNA quality after sequencing (Percent of counts in Top Ten genes (PTT), 5’ bias, and 3’ bias) as well as with individual gene counts across the transcriptome. We conduct this analysis across four different human cortical brain tissue collections sequenced with varying library preparation protocols. PMI and RIN have a low inverse correlation, and both PMI and RIN show consistent and opposing correlations with PTT. Unlike PMI, RIN shows strong consistent correlations with measurements of 3’ and 5’ bias, and RIN also correlates with 3,933 genes across datasets, in comparison to 138 genes for PMI. Neuronal and immune response genes correlate positively and negatively with RIN respectively, suggesting that different gene sets have divergent relationships with RIN in brain tissue. In summary, these analyses suggest that conventional metrics of RNA quality have varying degrees of value, and that PMI has an overall minimal but reproducible effect on RNA quality.
Sequential structure probing of cotranscriptional RNA folding intermediates
Authors: Szyjka Courtney E. , Kelly Skyler L. , Strobel Eric J.
Published: October 2024

Cotranscriptional RNA folding pathways typically involve the sequential formation of folding intermediates. Existing methods for cotranscriptional RNA structure probing map the structure of nascent RNA in the context of a terminally arrested transcription elongation complex. Consequently, the rearrangement of RNA structures as nucleotides are added to the transcript can be inferred but is not assessed directly. To address this limitation, we have developed linked-multipointTranscriptionElongationComplex RNA structureprobing (TECprobe-LM), which assesses the cotranscriptional rearrangement of RNA structures by sequentially positioningE. coliRNAP at two or more points within a DNA template so that nascent RNA can be chemically probed. We validated TECprobe-LM by measuring known folding events that occur within theE. colisignal recognition particle RNA,Clostridium beijerinckii pflZTP riboswitch, andBacillus cereus crcBfluoride riboswitch folding pathways. Our findings establish TECprobe-LM as a strategy for detecting cotranscriptional RNA folding events directly using chemical probing.
Apoptosis is increased in cortical neurons of female Marfan Syndrome mice
Authors: Esfandiarei Mitra , Anwar Faizan , Nuthi Manogna , Harrison Alisha , Barrameda Mary Eunice , Curry Tala , Pull Kasey , Currier Thomas Theresa , Jadavji Nafisa M.
Published: October 2024

Marfan Syndrome (MFS) is an autosomal dominant genetic disorder that affects connective tissue throughout the body due to mutations in theFBN1gene. Individuals with MFS display symptoms in different organs, particularly in the vasculature, but the mechanisms of this multi-system dysfunction are still under investigation. There is still a gap in our understanding of the impact of monogenic connective tissue aberrations on the brain. This study aims to determine the impact of MFS on neurodegeneration, in cortical brain tissue of male and female MFS mice. Brain tissue of 6-month-old female and male mice with theFBN1C1041G/+mutation and wildtype litter mates was collected and stained for active caspase-3 (ac3), brain derived neurotrophic factor (BDNF), and neuronal nuclei (NeuN) or with TUNEL and DAPI. Data revealed increased levels of ac3 in neurons within the sensory and motor cortical areas of female MFS mice compared to sex- and age-matched controls. We confirm increased levels of apoptosis in MFS mice using TUNEL staining within the same brain areas. We also report increased levels of neuronal BDNF levels in cortical brain tissue of male and female MFS mice. These results indicate a heightened susceptibility for neurodegeneration in the mouse model of MFS.

Significance Statement

The study revealed that female mice with aFBN1C1041G/+mutation have more apoptotic neurons in sensory and motor cortical brain tissue compared to wildtype litter mates.
A parasite-inclusive food web for the California rocky intertidal zone
Authors: Zilz Zoe L. , Hascall Emily , DiBartolo Athena , Flores Delén , Cameron Sophie , Orli Jaden E. , Kuris Armand M.
Published: October 2024

We present a highly resolved, species-rich food web, including parasitic interactions, for the California rocky intertidal zone. The food web is comprised of 1809 nodes, representing 1845 taxa, and 13,222 links representing trophic interactions between nodes. While only 670 links represent parasitic interactions, we have assembled possibly the most speciose parasite-inclusive food web ever published. The inclusion of all nodes and links are justified using multiple lines of evidence which are built into the dataset. In addition, metadata, including trophic strategy, taxonomic information, habitat, and other ecological attributes allow the data user to filter the food web to their specifications. The food web is a powerful and flexible tool for researchers with questions about large network properties, ecological dynamics of rocky shores, and the role of parasites in ecosystems. Our food web can be used to predict how complex ecosystems like the California rocky intertidal will respond to anthropogenic change and management strategies.
Tumors with mutations in chromatin regulators are associated with higher mutational burden and improved response to checkpoint immunotherapy
Authors: Kungulovski Goran , Gjorgjievska Marija , Mehandziska Sanja , Bukovec Djansel , Risteski Milan , Kungulovski Ivan , Mitrev Zan
Published: October 2024

In recent years, it has been demonstrated that many of the pervasive genetic defects throughout cancerogenesis occur in genes encoding chromatin regulators (CRs). We analyzed the distribution and characteristics of well-studied CRs across tens of thousands of tumor samples. Our analysis revealed that tumors with mutations in CRs are associated with high tumor mutational burden (TMB). The co-occurrence of mutations in multiple CRs was linked with a further increase in TMB. Given that TMB may predict the clinical response to immune checkpoint inhibitor (ICI) treatment, we investigated the relationship between mutations in CRs and ICI response. We found that patients harboring mutations in CRs exhibited improved responses to ICI treatment, comparable to those with deficiencies in canonical DNA repair pathways. Overall, this study uncovered significant relationships between mutations in chromatin regulators and critical features of cancer, underscoring the need for further functional and clinical studies.
Digital biomechanical biomarkers in the clinical assessment of patients with peripheral neuropathies
Authors: Tejada-Illa Clara , Pegueroles Jordi , Claramunt-Molet Mireia , Pi-Cervera Ariadna , Heras-Delgado Ainhoa , Gascón-Fontal Jesus , Idelsohn-Zielonka Sebastian , Rico Mari , Vidal Nuria , Martín-Aguilar Lorena , Caballero-Ávila Marta , Lleixà Cinta , Collet-Vidiella Roger , Llansó Laura , Carbayo Álvaro , Vesperinas Ana , Querol Luis , Pascual-Goñi Elba
Published: October 2024

The clinical status and treatment response of patients with peripheral neuropathies (PN) rely on subjective and inaccurate clinical scales. Wearable sensors have shown success in evaluating gait and balance in individuals with other neurological disorders. We aimed to explore the ability of biomechanical analysis via wearable technology to monitor disease activity in PN by conducting a single-center, longitudinal study to analyze gait parameters in PN patients and healthy controls using wearable sensors. First, we analyzed the sensor’s ability to detect changes in ataxia and steppage gait severity and found significant differences in spatiotemporal and angular variables. Second, we found correlations between biomechanical features and clinical scales linked to specific gait phenotypes. Finally, we demonstrated that this technology captures clinical changes in gait features over time. Our study provides proof-of-concept that wearable technology effectively detects and grades gait impairment, captures clinically relevant changes, and could enhance gait assessment in routine care and research for PN patients.
Mathematical Model of Disease Transmission and Control: Incorporating Age and Deprivation Decile
Authors: Oyedele Gbeminiyi J. , Idowu Oluwarimi J. , Tildesley Michael J.
Published: October 2024

The epidemic of COVID-19 has opened a significant interest in developing mathematical models that could incorporate more complexities into the dynamics of disease transmission and control. This study aims to perform a rigorous mathematical analysis on incorporating the effects of age mixing and deprivation decile into an epidemic model of infectious diseases using deterministic models. We consider a mathematical model consisting of nine compartments: susceptible, exposed, asymptomatic, unreported and untested, tested and awaiting test results, positively tested symptomatic and hospitalised, recovered, and dead. The basic reproduction number was estimated using the next generation matrix approach. The analysis shows that the most deprived group in the population demonstrated disproportionately higher number of infections compared with the least deprived groups, and this was consistent across the deprivation spectrum. Our work suggests that in order to effectively control disease, support should be given to those individuals with higher levels of deprivation in order to improve uptake of intervention measures in those groups to reduce the burden of disease.
Investigating Sex Bias in Machine Learning Research: A Systematic Review in Rheumatoid Arthritis
Authors: Talwar Anahita , Turner Shruti , Maw Claudia , Quayle Georgina , Watt Thomas N , Gohil Sunir , Duckworth Emma , Ciurtin Coziana
Published: October 2024

Unchecked sex bias in machine learning (ML) algorithms used in healthcare can exacerbate disparities in care and treatment. We aimed to assess the acknowledgment and mitigation of sex bias within studies using supervised ML for improving clinical outcomes in Rheumatoid Arthritis (RA). For this systematic review, we searched PUBMED and EMBASE for original, English language studies published between 2018 to November 2023. We scored papers on whether the authors reported, attempted to mitigate or successfully mitigated the following types of bias: training data bias, test data bias, input variable bias, output variable bias, analysis bias, and assessed the quality of ML research in all papers. This study is registered on PROSPERO with ID CRD42023431754. We identified 52 papers to include in our review. All but one had a female skew in their study participants, yet 42 papers did not acknowledge any potential sex bias. Three papers assessed bias in model performance by sex disaggregating their results. One paper acknowledged potential sex bias in input variables, and six papers in their output variables, predominantly disease activity scores. No paper attempted to mitigate for any type of sex bias. The findings demonstrate the requirement for increased promotion of inclusive and equitable ML practices in healthcare.
Post Intensive care outcomes and follow-up in Children: A Collaboration of Health care providers, researchers, and families Utilizing knowledge co-production
Authors: Dunphy Michelle , Yang Gaby , Marchand Jason , Retallack Jenny
Published: October 2024

Background

Many children do not return to their pre-admission health status following admission to the paediatric intensive care unit (PICU), facing a range of physical, cognitive, emotional, and social challenges collectively known as Post-Intensive Care Syndrome in Paediatrics (PICS-p). The sequelae associated with PICS-p necessitate comprehensive follow-up care intending to address these multifaceted needs. ThePostIntensive care outcomes and follow-up inChildren:A Collaboration ofHealth care providers, researchers, and familiesUtilizing knowledge co-production (PICACHU) study aims to develop a shared care follow-up service for post-PICU patients and their families. It also seeks to facilitate outcomes research and identify quality improvement (QI) initiatives to mitigate the impact of PICS-p.

Methods

The study employs a pragmatic approach informed by the Medical Research Council (MRC) framework and co-design methodology. The research includes surveys and focus group discussions (FGDs) with purposively sampled post-PICU families, acute care pediatricians, community pediatricians, general practitioners (GPs), and primary care nurse practitioners (NPs). Data collection tools include adapted versions of existing surveys and semi-structured interview guides. The analysis will involve qualitative and quantitative methods, utilising SPSS for statistical analysis and NVivo for thematic analysis of FGDs.

Conclusion

The PICACHU study is the first of its kind to use a co-design approach to create a post-PICU shared care follow-up service in British Columbia (BC), Canada. The findings will provide valuable insights for improving post-PICU care services in BC and potentially other jurisdictions.
Genome-wide association study for circulating metabolites in 619,372 individuals
Authors: Tambets Ralf , Kronberg Jaanika , Abner Erik , Võsa Urmo , Rahu Ida , Taba Nele , Kolde Anastassia ,   Estonian Biobank Research Team, Fischer Krista , Esko Tõnu , Alasoo Kaur , Palta Priit
Published: October 2024

Examining the downstream molecular consequences of genetic variation significantly enhances our understanding of the heritable determinants of complex traits and disease predisposition. Metabolites serve as key indicators of various biological processes and disease states, playing a crucial role in this systematic mapping, also providing opportunities for the discovery of new biomarkers for disease diagnosis and prognosis. Here, we present a genome-wide association study for 249 circulating metabolite traits quantified by nuclear magnetic resonance spectroscopy across various genetic ancestry groups from the Estonian Biobank and the UK Biobank. We generated mixed model associations in the Estonian Biobank and six major genetic ancestry groups of the UK Biobank and performed two separate meta-analyses across the predominantly European genetic ancestry samples (n = 599,249) and across all samples (n = 619,372). In total, we identified 89,489 locus-metabolite pairs and 8,917 independent lead variants, out of which 4,184 appear to be novel associated loci. Moreover, 12.4% of the independent lead variants had a minor allele frequency of less than 1%, highlighting the importance of including low-frequency and rare variants in metabolic biomarker studies. Our publicly available results provide a valuable resource for future GWAS interpretation and drug target prioritisation studies.
Impact of anionic lipids on the energy landscape of conformational transition in anion exchanger 1 (AE1)
Authors: Chen Tianle , Vallese Francesca , Gil-Iturbe Eva , Kim Kookjoo , Quick Matthias , Clarke Oliver , Tajkhorshid Emad
Published: October 2024

Anion Exchanger 1 (AE1) is an elevator-type membrane transporter that plays a key role in erythrocytes by mediating the exchange of chloride and bicarbonate ions across the membrane, thus participating in acid-base homeostasis. While previous studies have provided structural insights into AE1 and its substrate binding, the conformational transitions and the role of lipid interactions remain elusive. In this study, we utilized cryo-electron microscopy (cryo-EM) to resolve three high resolution structures of distinct conformational states of AE1: two inward-facing (IF1 and IF2) and one outward-facing (OF). Furthermore, uptake assay revealed the modulatory effect of phosphatidylinositol 4,5-bisphosphate (PIP2) lipids on AE1. Molecular dynamics (MD) simulations were conducted on these structures to capture anion binding and determine the anion binding sites in AE1. We then used a combination of advanced enhanced sampling techniques together with system-specific collective variables to study the OF⇔IF transition in AE1 and provided refined pathways for the process in three different systems:apo, HCO3−-bound, and an AE1 system in which cryo-EM-determined interfacial PIP2lipids had been removed. The refined pathways were then used to calculate the free energy of the OF⇔IF transition in AE1 under different conditions. The energies show how substrate binding reduces the transition barrier and, therefore, facilitates the transport. Furthermore, they clearly capture the inhibitory effect of PIP2lipids at the dimer interface. Furthermore, the simulation results provide a molecular mechanism for this inhibitory effect. These results provide a molecular-level understanding of the mechanistic basis for ion transport in AE1 and the regulatory role of PIP2on its function.
A bounded accumulation model of temporal generalization outperforms existing models and captures modality differences and learning effects
Authors: Ofir Nir , Landau Ayelet N.
Published: October 2024

Multiple systems in the brain track the passage of time and can adapt their activity to temporal requirements (Paton & Buonomano, 2018). While the neural implementation of timing varies widely between neural substrates and behavioral tasks, at the algorithmic level many of these behaviors can be described as bounded accumulation (Balcı & Simen, 2024). So far, from the range of temporal psychophysical tasks, the bounded accumulation model has only been applied to temporal bisection, in which participants are requested to categorize an interval as “long” or “short” (Balcı & Simen, 2014; Ofir & Landau, 2022). In this work, we extend the model to fit performance in the temporal generalization task, in which participants are required to categorize an interval as being the same or different compared to a standard, or reference, duration (Wearden, 1992). Previous models of performance in this task focused on either the group level or performance of highly trained animals (Birngruber et al., 2014; Church & Gibbon, 1982; Wearden, 1992). Whether the same models can fit performance from a few hundreds of trials of single participants, necessary for comparing performance across experimental manipulations, has not been tested. A drift-diffusion model with two decision boundaries fits the data of single participants better than the previous models. We ran two experiments, one comparing performance between vision and audition and another examining the effect of learning. We found that decision boundaries can be modified independently: While the upper boundary was higher in vision compared to audition, the lower boundary decreased with learning in the task.
Saving the Dinaric lynx: multidisciplinary monitoring and stakeholder engagement support large carnivore restoration in human-dominated landscape
Authors: Krofel Miha , Fležar Urša , Černe Rok , Hočevar Lan , Konec Marjeta , Skrbinšek Aleksandra Majić , Skrbinšek Tomaž , Wilson Seth , Bele Bernarda , Črtalič Jaka , Gomerčić Tomislav , Hvala Tilen , Kubala Jakub , Kvapil Pavel , Mavec Meta , Molinari-Jobin Anja , Molinari Paolo , Pazhenkova Elena , Potočnik Hubert , Sin Teodora , Sindičić Magda , Topličanec Ira , Oliveira Teresa
Published: October 2024

Translocations are central to large carnivore restoration efforts, but inadequate monitoring often inhibits effective conservation decision-making. Extinctions, reintroductions, poaching and high inbreeding levels of the Central European populations of Eurasian lynx (Lynx lynx) typify the carnivore conservation challenges in the Anthropocene. Recently, several conservation efforts were initiated to improve the genetic and demographic status, but were met with variable success. Here, we report on a successful, stakeholder-engaged translocation effort to reinforce the highly-inbred Dinaric lynx population and create a new stepping-stone subpopulation in the Southeastern Alps. We used multidisciplinary and internationally-coordinated monitoring using systematic camera- trapping, non-invasive genetic sampling, GPS-tracking of translocated and remnant individuals, recording of reproductive events and interspecific interactions, as well as the simultaneous tracking of the public and stakeholders’ support of carnivore conservation before, during and after the translocation process across the three countries. Among the 22 translocated wild-caught Carpathian lynx, 68% successfully integrated into the population and local ecosystems and at least 59% reproduced. Probability of dispersing from the release areas was 3-times lower when soft-release rather than hard-release method was used. Translocated individuals had lower natural mortality, higher reproductive success and similar ungulate kill rates compared to the remnant lynx. Cooperation with local hunters and protected area managers enabled us to conduct multi-year camera-trapping and non-invasive genetic monitoring across a 12,000-km2transboundary area. Results indicate a reversal in population decline, as the lynx abundance increased for >40% during the 4-year translocation period. Effective inbreeding decreased from 0.32 to 0.08-0.19, suggesting a 2- to 4-fold increase in fitness. Furthermore, successful establishment of a new stepping-stone subpopulation represents an important step towards restoring the Central European lynx metapopulation. Robust partnerships with local communities and hunters coupled with transparent communication helped maintain high public and stakeholder support for lynx conservation throughout the translocation process. Lessons learned about the importance of stakeholder involvement and multidisciplinary monitoring conducted across several countries provide a successful example for further efforts to restore large carnivores in human-dominated ecosystems.
Background optic flow modulates responses of multiple descending interneurons to object motion in locusts
Authors: Zhang Sinan , Gray John R.
Published: October 2024

Animals flying within natural environments are constantly challenged with complex visual information. Therefore, it is necessary to understand the impact of the visual background on the motion detection system. Locusts possess a well-identified looming detection pathway, compromised of the lobula giant movement detector (LGMD) and the descending contralateral movement detector (DCMD). The LGMD/DCMD pathway responds preferably to objects on a collision course, and the response of this pathway is affected by the background complexity. However, multiple other neurons are also responsive to looming stimuli. In this study, we presented looming stimuli against different visual backgrounds to a rigidly-tethered locust, and simultaneously recorded the neural activity with a multichannel electrode. We found that the number of discriminated units that responded to looms was not affected by the visual background. However, the peak times of these units were delayed, and the rise phase was shortened in the presence of a flow field background. Dynamic factor analysis (DFA) revealed that fewer types of common trends were present among the units responding to looming stimuli against the flow field background, and the response begin time was delayed among the common trends as well. These results suggest that background complexity affects the response of multiple motion-sensitive neurons, yet the animal is still capable of responding to potentially hazardous visual stimuli.
What’s in it for the dogs? Assessing the outcomes of a prison-based dog training program from an animal behavior and welfare perspective
Authors: Baria-Unwalla Parizad , Munhoz Morello Gabriela , Queiroz Maria , Olsson I. Anna S. , Vieira de Castro Ana Catarina
Published: October 2024

Prison-Based Dog Training Programs (PBDTPs) are gaining popularity across the world for their benefits to inmates in terms of mental and emotional health, and reduced recidivism. However, research on the implications for the dogs is limited. The aim of the present study was to assess the outcomes of a PBDTP from an animal behavior and welfare perspective. Shelter dogs (N=42) were transported to and from the prisons twice a week where they received training from inmates for a total duration of 12 weeks. Dogs were tested for potential improvements in socialization and handling skills and basic training skills using standard tests (Temperament Test and Basic Education Test). Dog welfare was assessed using behavioral, physiological, and cognitive measures, namely stress-related behaviors and overall behavior states during training sessions, salivary cortisol levels, and cognitive bias tests. Results showed that participating in the PBDTP improved the dogs’ sociability towards humans and increased playful behavior, and improved basic training skills including not jumping on people, walking on a leash without pulling, responding to commands (sit, down, and staying in place) and staying calm when separated from the handler. Furthermore, behaviors indicative of stress were generally rare during training sessions and no impact of the PBDTP was found on the levels of salivary cortisol nor on the dogs’ affective states (as measured with cognitive bias tests). In conclusion, the present study suggests that PBDPTs are beneficial for dogs, with animals showing no indicators of compromised welfare while displaying improved behavior skills, which will likely facilitate their future rehoming.
Optimization of citric acid production from sugarcane molasses usingAspergillus nigerby submerged Fermentation
Authors: Amin Al , Ahmmed Hd. Razu , Ismail Mohammad , Islam Tajreen Naziba , Mohasin Mohammed
Published: October 2024

The potentiality of citric acid on economy is high because of its multi-purpose uses, particularly in the food and pharmaceutical industries. Bangladesh spent more than million US dollars to import citric acid mostly from India and China. Its consumption is increasing 3.5–4%, annually, indicating the need for better manufacturing alternatives. Globally, citric acid is primarily produced through microbial fermentation withAspergillus niger. To support the massive scale of production of citrate, the manufacturing process must be eco-friendly which should be inexpensive and available raw materials for maintaining high yielding in a cost-effective manner. In Bangladesh prospective, the current study has undertaken to optimize citric acid production using one of the most abundant raw materials sugarcane molasses. Moreover, the aim of this study was to determine the optimum conditions to produce citric acid from sugarcane molasses usingAspergillus niger (F-81)by submerged fermentation. The amount of citric acid production was determined by Marier-Boulet colorimetric method. The optimization data suggested that 10% substrate (from processed cane molasses), 4% inoculum size ofA. niger, and initial pH 6.0 allowed to produce around 25.8 g/L citric acid. Further study is warranted to assess the feasibility of citrate production in an industrial level as well as improvement of microbial strains is needed to further enhance citric acid production.
Coma pattern-based autofocusing unlocks superior performance in unravelling single-cell dynamics during bacterial cold shock response
Authors: Li Sihong , Ma Zhixin , Yu Yue , Wang Jinjuan , Shen Yaxin , Cui Xiaodong , Fu Xiongfei , Huang Shuqiang
Published: October 2024

Cutting-edge studies in live cell dynamics place increasing demands on microscopy imaging, and focus stability during acquisition is a critical factor in obtaining high-quality image data. Current autofocusing solutions are limited to focusing precision and range, thus impeding their application in high-accuracy research. Here, we introduce LUNA (locking under nanoscale accuracy), an innovative autofocusing method that leverages the coma pattern of detection light to characterize focus drift. LUNA improves the focusing precision down to 3 nm and extends the focusing range to at least 40 times the objective depth-of-focus. These advancements enable us to investigate how bacteria adapt to temperature change at the single-cell level, revealing a series of novel insights into bacterial cold shock response mechanisms. This approach addresses the complexities of growth dynamics, growth mode transition, division synchronization, and size regulation during the adaptation period, which present significant challenges for traditional analytical methods. Notably, the controversies between the growth lag of batch culture and continuous growth at the single-cell level are successfully explained based on scattering theory. LUNA shows enhanced performance in improving existing advanced microscopy technologies and demonstrates excellent potential for expanding state-of-the-art research in biology.
Systematic annotation of hyper-variability hotspots in phage genomes and plasmids
Authors: Egorov Artyom A. , Hauryliuk Vasili , Atkinson Gemma C.
Published: October 2024

Bacterial and bacteriophage genomes contain genomic regions of hyper-variability (diversity hotspots) caused by insertions of mobile genetic elements (MGEs), non-homologous recombination events and non-horizontal hypermutation. Accessory genes encoded in the diversity hotspots are involved in anti-MGE defence and counter-defence, virulence and antimicrobial resistance (AMR), thus playing key roles in interactions amongst phages, MGEs, bacteria and eukaryotic hosts. To date the majority of research has been focused on either individual hotspots or on relatively limited sets of hotspots in a small set of genomes, typically from a single species. A global understanding of hotspot diversity and dynamics still lacking. To address this gap, we developed iLund4u, an algorithm for the systematic annotation of hotspots across millions of sequences. Using a proteome composition approach, iLund4u detects proteome communities, annotates accessory proteins and identifies hotspots. By analysing 873K phage genomes and 696K plasmid sequences we identified 13.7K hotspots and 171K diverse protein families encoded there as cargo. Furthermore, iLund4u allows for protein search and proteome annotation functions versus a precomputed iLund4u database. In the protein search mode iLund4u identifies all hotspots that encode homologues of a query protein. In the proteome annotation mode iLund4u annotates hotspots by searching for communities of similar proteomes. Detailed documentation, user guide and the source code are available at the iLund4u home page: art-egorov.github.io/ilund4u.
Are you my mother?: When host genetics and gut microbiota tell different phylogenetic stories in the Africanized honey bee hybrid (Apis mellifera scutellatax sspp.)
Authors: Soares Kilmer Oliveira , de Oliveira Celso José Bruno , Villegas Luis Eduardo Martínez , Vasconcelos Priscylla Carvalho , Rodrigues Adriana Evangelista , Madden Christopher , Hale Vanessa L.
Published: October 2024

Africanized honey bees (Apis mellifera scutellatax sspp.) originated in Brazil through the crossbreeding of African (A. mellifera scutellata) and European (A. melliferasspp.) honey bee subspecies. African genes came to dominate in these hybrid honey bees over time. Gut microbiota co-evolve with their hosts and generally reflect host phylogeny. To examine if this was true in Africanized honey bee hybrids, we compared the gut microbiota (16S rRNA) of 3 honey bee subspecies: African, European, and Africanized honey bees. Publicly available sequencing data from five honey bee studies were downloaded from NCBI. European bee samples (n=42) came from United Kingdom, Switzerland, and United States. African bee samples (n=82) came from Kenya. Africanized bee samples (n=10) came from Brazil. Unexpectedly, Africanized honey bee gut microbiota was far more similar to European bees than to African bees despite the closer host genetic relationship between African and Africanized bees. All three subspecies shared similar relative abundances of core taxa. We posit that the similarity in gut microbiota between Africanized and European honey bees arose from the nature of the crossbreeding, and the social / environmental transmission of gut microbiota within hives. Namely, African queens took over European hives. However, the hybrid offspring acquired their gut microbiota from European nurse bees and European hive materials, resulting in the stable transmission of European gut microbiota across generations. Our results provide an intriguing insight into the potential ecological, social, and environmental factors that shape the gut microbiota of the Africanized honey bee hybrid.

Importance

Africanized honey bee hybrids originated in Brazil through the crossbreeding of African and European honey bee subspecies. In this study, we examined the gut microbiota of all 3 honey bee subspecies (African, European, Africanized). A few core microbiota were shared across all subspecies. Interestingly, while African honey bee genes dominated in the Africanized honey bee hybrids, their gut microbial composition was most similar to European bees. This is likely related to the way these bees were crossbred – with African queens taking over European hives, while gut microbial inoculation of hybrids came from European nurse bees and European hive matierals. Gut microbiota are critical to honey bee health, and studying the gut microbiota of closely related honey bee subspecies helps understand the factors that influence gut microbial composition. This is important for our broader understanding of honey bee health, conservation, and evolution.
The restricted N-glycome of neurons is programmed during differentiation
Authors: Kiwimagi Katherine , Noel Maxence , Cetinbas Murat , Sadreyev Ruslan I. , Wang Lei , Smoller Jordan W. , Cummings Richard D. , Weiss Ron , Mealer Robert G.
Published: October 2024

The protein glycome of individual cell types in the brain is unexplored, despite the critical function of these modifications in development and disease. In aggregate, the most abundant asparagine (N-) linked glycans in the adult brain are high mannose structures, and specifically Man5GlcNAc2(Man-5), which normally exits the ER for further processing in the Golgi. Mannose structures are uncommon in other organs and often overlooked or excluded in most studies. To understand cell-specific contributions to the unique brain N-glycome and its abundance of Man-5, we performed RNAseq and MALDI-MS TOF protein N-glycomics at several timepoints during differentiation of multiple cell types. To this end, homogeneous cultures of glutamatergic neurons, GABAergic neurons, and brain-specific endothelial cells were generated from monoclonal human inducible pluripotent stem cells (hiPSCs) through cellular reprogramming. Small molecule induction of stably integrated synthetic transcription units driving morphogen expression generated differentiated cells with distinct patterns mirroring intact tissue. Comparing uninduced hiPSCs for each cell type revealed identical transcriptomic and glycomic profiles before differentiation, with low quantities of Man-5. In differentiated glutamatergic and GABAergic neurons, the most abundant N-glycans became Man-5 and its immediate precursor Man-6, despite the presence of transcripts encoding enzymes for their subsequent modification. Differentiation to brain-specific endothelial cells showed an opposite effect, with the N-glycome displaying an abundance of complex N-glycans and terminal modifications of the late secretory pathway. These results confirm that the restricted N-glycome profile of brain is programmed into neuronal differentiation, with regulation independent of the transcriptome and under tight evolutionary constraint.
A Reproducibility Focused Meta-Analysis Method for Single-Cell Transcriptomic Case-Control Studies Uncovers Robust Differentially Expressed Genes
Authors: Nakatsuka Nathan , Adler Drew , Jiang Longda , Hartman Austin , Cheng Evan , Klann Eric , Satija Rahul
Published: October 2024

We assessed the reproducibility of differentially expressed genes (DEGs) in previously published Alzheimer’s (AD), Parkinson’s (PD), Schizophrenia (SCZ), and COVID-19 scRNA-seq studies. While transcriptional scores from DEGs of individual PD and COVID-19 datasets had moderate predictive power for case-control status of other datasets (AUC=0.77 and 0.75), genes from individual AD and SCZ datasets had poor predictive power (AUC=0.68 and 0.55). We developed a non-parametric meta-analysis method, SumRank, based on reproducibility of relative differential expression ranks across datasets, and found DEGs with improved predictive power (AUC=0.88, 0.91, 0.78, and 0.62). By multiple other metrics, specificity and sensitivity of these genes were substantially higher than those discovered by dataset merging and inverse variance weighted p-value aggregation methods. The DEGs revealed known and novel biological pathways, and we validateBCAT1as down-regulated in AD mouse oligodendrocytes. Lastly, we evaluate factors influencing reproducibility of individual studies as a prospective guide for experimental design.
OpenASO: RNA Rescue — designing splice-modulating antisense oligonucleotides through community science
Authors: Tse Victor , Guiterrez Martin , Townley Jill , Romano Jonathan , Pearl Jennifer , Chacaltana Guillermo , Players Eterna , Das Rhiju , Sanford Jeremy R. , Stone Michael D.
Published: October 2024

Splice-modulating antisense oligonucleotides (ASOs) are precision RNA-based drugs that are becoming an established modality to treat human disease. Previously, we reported the discovery of ASOs that target a novel, putative intronic RNA structure to rescue splicing of multiple pathogenic variants ofF8exon 16 that cause hemophilia A. However, the conventional approach to discovering splice-modulating ASOs is both laborious and expensive. Here, we describe an alternative paradigm that integrates data-driven RNA structure prediction and community science to discover splice-modulating ASOs. Using a splicing-deficient pathogenic variant ofF8exon 16 as a model, we show that 25% of the top-scoring molecules designed in the Eterna OpenASO challenge have a statistically significant impact on enhancing exon 16 splicing. Additionally, we show that a distinct combination of ASOs designed by Eterna players can additively enhance the inclusion of the splicing-deficient exon 16 variant. Together, our data suggests that crowdsourcing designs from a community of citizen scientists may accelerate the discovery of splice-modulating ASOs with potential to treat human disease.
Modeling compound lipid homeostasis using stable isotope tracing
Authors: Wessendorf-Rodriguez Karl , Ruchhoeft Maureen L. , Ashley Ethan L. , Galvez Hector M. , Murray Christopher W. , Huang Yale , McGregor Grace H. , Kambhampati Shrikaar , Shaw Reuben J. , Metallo Christian M.
Published: October 2024

Lipids represent the most diverse pool of metabolites found in cells, facilitating compartmentation, signaling, and other functions. Dysregulation of lipid metabolism is linked to disease states such as cancer and neurodegeneration. However, limited tools are available for quantifying metabolic fluxes across the lipidome. To directly measure reaction fluxes encompassing compound lipid homeostasis, we applied stable isotope tracing, liquid chromatography-high-resolution mass spectrometry, and network-based isotopologue modeling to non-small cell lung cancer (NSCLC) models. Compound lipid metabolic flux analysis (CL-MFA) enables the concurrent quantitation of fatty acid synthesis, elongation, headgroup assembly, and salvage reactions within virtually any biological system. Here, we resolve liver kinase B1 (LKB1)-mediated regulation of sphingolipid recycling in NSCLC cells and precision-cut lung slice cultures. We also demonstrate that widely used tissue culture conditions drive cells to upregulate fatty acid synthase flux to supraphysiological levels. Finally, we identify previously uncharacterized isozyme specificity of ceramide synthase inhibitors. These results highlight the ability of CL-MFA to quantify lipid cycling in biological systems to discover biological function and elucidate molecular mechanisms in membrane lipid metabolism.
Critical functions and key interactions mediated by the RNase E scaffolding domain inPseudomonas aeruginosa
Authors: Geslain Sandra Amandine Marie , Hausmann Stéphane , Geiser Johan , Allen George Edward , Gonzalez Diego , Valentini Martina
Published: October 2024

The RNA degradosome is a bacterial multi-protein complex mediating mRNA processing and degradation. In Pseudomonadota, this complex assembles on the C-terminal domain (CTD) of RNase E through short linear motifs (SLiMs) that determine its composition and functionality. In the human pathogenPseudomonas aeruginosa, the RNase E CTD exhibits limited similarity to that of model organisms, impeding our understanding of RNA metabolic processes in this bacterium. Our study systematically maps the interactions mediated by theP. aeruginosaRNase E CTD and highlights its critical role in transcript regulation and cellular functions. We identified the SLiMs crucial for membrane attachment, RNA binding and complex clustering, as well as for direct binding to the core components PNPase and RhlB. Transcriptome analyses of RNase E CTD mutants revealed altered expression of genes involved in quorum sensing, type III secretion, and amino acid metabolism. Additionally, we show that the mutants are impaired in cold adaptation, pH response, and virulence in an infection model. Overall, this work establishes the essential role of the RNA degradosome in driving bacterial adaptability and pathogenicity.

Author summary

Bacteria must rapidly adapt to changing environments, whether facing temperature shifts, nutrient scarcity, or antibiotic exposure. A key mechanism enabling this adaptability is the regulation of mRNA levels—the molecular blueprints for protein production. This process is governed by the RNA degradosome, a multi-protein complex that processes and degrades RNA to control gene expression. Although the RNA degradosome core function is conserved across bacteria, its composition and organization differ significantly between species, reflecting diverse lifestyles and environmental challenges each bacterium encounter.

In this study, we investigated the RNA degradosome inPseudomonas aeruginosa, a bacterial pathogen causing difficult-to-treat infections in humans. We identified its components and mapped regions within the complex essential for RNA binding, membrane attachment, and spatial organization. Disrupting these regions compromisedP. aeruginosaability to survive in cold conditions, respond to stress, and establish an infection. Through this work, we uncovered unique features of theP. aeruginosaRNA degradosome that distinguish it from those of other species, emphasizing the RNA degradosome critical role in bacterial adaptability and highlight it as a promising target for therapies againstP. aeruginosainfections.
Isolation of Plastic Digesting Microbes from the Gastrointestinal Tract ofTenebrio Molitor
Authors: Reish Hannah McKinnon , Witty Rebecca F. , Quade Adam H. , Dallas Jason W. , Kirschman Lucas J.
Published: October 2024

Plastics, particularly polystyrene (PS) and polyethylene (PE), are pervasive in ecosystems and degrade slowly, leading to the formation of microplastics and nanoplastics, which pose environmental and health risks. The gut microbiota ofTenebrio molitorlarvae (mealworms) can degrade plastics, making them a potential model for studying microbial plastic digestion. This study investigated how rearingT. molitoron PS-or PE-supplemented diets over three generations affected gut microbiota composition and plastic degradation. Larvae were reared on wheat bran (control), PS, or PE diets, and microbial communities from their guts were cultured to assess plastic metabolism. Results showed that the PE-supplemented diet enhanced bacterial plastic degradation, while the PS-supplemented diet did not lead to similar improvements. Microbes from PE-fed larvae exhibited increased plastic metabolic activity compared to controls, and several bacterial strains with plastic-degrading capabilities were identified. However, microbial digestion of PS was less efficient, and potential dysbiosis due to the presence ofDickeyaphage in PS-fed larvae may have influenced the results. Further research is needed to clarify the mechanisms driving microbial plastic digestion and to determine the applicability of these findings to environmental plastic remediation, particularly for micro– and nanoplastics.
Critical issues found in “Dissecting cell identity via network inference and in silico gene perturbation”
Authors: Nourisa Jalil , Passemiers Antoine , Tomforde Sven
Published: October 2024

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In the 2023 Nature publication “Dissecting cell identity via network inference and in silico gene perturbation” [1], the authors introduced CellOracle (CO), a novel method leveraging mRNA-seq and ATAC-seq data to construct gene regulatory networks (GRNs), which are subsequently used for gene perturbation. They designed CO to account for the role of distal cis-regulatory elements, e.g. enhancers, as well as proximal promoters in the gene regulation system. For this purpose, they employed Cicero to determine the co-accessibility scores between peaks, provided by ATAC-seq data. These scores are then used to identify the interaction of distal regions with the target gene. Using CO, they have conducted multiple perturbation studies on different organisms and identified novel phenotypes resulting from transcriptional factor (TF) perturbation. In addition, they benchmarked CO’s performance using ChIP-seq data as ground truth against other state-of-the-art GRN methods across multiple mouse tissue samples. However, our evaluation reveals critical limitations in the implementation of their methodology, both in terms of ATAC-seq data integration as well as benchmarking. In this report, we first explain the limitations in their approach of integrating ATAC-seq data. We show that the proposed algorithm fails to account for distal regulatory interactions. After, we present the issues associated with their benchmarking algorithm and the data used for benchmarking. We show that their findings regarding the comparative performance of CO against other GRN inference methods is invalid and requires further evaluation. In conclusion, we detect multiple inaccuracies in this paper which undermine the validity of their published protocol and the results. The materials supporting our findings are accessible on GitHub1.