bluuebunny/crossref_metadata_2025 huggingface dataset:
Bidirectional dysregulation of synaptic glutamate signaling after transient metabolic failure
Authors: Passlick Stefan , Ullah Ghanim , Henneberger Christian
Published: April 2024

Ischemia leads to a severe dysregulation of glutamate homeostasis and excitotoxic cell damage in the brain. Shorter episodes of energy depletion, for instance during peri-infarct depolarizations, can also acutely perturb glutamate signaling. It is less clear if such episodes of metabolic failure also have persistent effects on glutamate signaling and how the relevant mechanisms such as glutamate release and uptake are differentially affected. We modelled acute and transient metabolic failure by using a chemical ischemia protocol and analyzed its effect on glutamatergic synaptic transmission and extracellular glutamate signals by electrophysiology and multiphoton imaging, respectively, in the hippocampus. Our experiments uncover a duration-dependent bidirectional dysregulation of glutamate signaling. Whereas short chemical ischemia induces a lasting potentiation of presynaptic glutamate release and synaptic transmission, longer episodes result in a persistent postsynaptic failure of synaptic transmission. We also observed unexpected differences in the vulnerability of the investigated cellular mechanisms. Axonal action potential firing and glutamate uptake were unexpectedly resilient compared to postsynaptic cells, which overall were most vulnerable to acute and transient metabolic stress. We conclude that even short perturbations of energy supply lead to a lasting potentiation of synaptic glutamate release, which may increase glutamate excitotoxicity well beyond the metabolic incident.
Macrolide resistance through uL4 and uL22 ribosomal mutations inPseudomonas aeruginosa
Authors: Goltermann Lise , Laborda Pablo , Irazoqui Oihane , Pogrebnyakov Ivan , Molin Søren , Johansen Helle Krogh , Rosa Ruggero La
Published: April 2024

Macrolides are widely used antibiotics for the treatment of bacterial airway infections. Due to its elevated minimum inhibitory concentration in standardized culture media,Pseudomonas aeruginosais considered intrinsically resistant and, therefore, antibiotic susceptibility testing against macrolides is not performed. Nevertheless, due to macrolides’ immunomodulatory effect and suppression of virulence factors, they are used for the treatment of persistentP. aeruginosainfections. Here, we demonstrate that macrolides are, instead, effective antibiotics againstP. aeruginosaairway infections in an air-liquid interface (ALI) infection model system resembling the human airways. Importantly, macrolide treatment in both people with cystic fibrosis and primary ciliary dyskinesia patients leads to the accumulation of uL4 and uL22 ribosomal protein mutations inP. aeruginosawhich causes antibiotic resistance. Consequently, higher concentrations of antibiotics are needed to modulate the macrolide-dependent suppression of virulence. Surprisingly, even in the absence of antibiotics, these mutations also lead to a collateral reduction in growth rate, virulence and pathogenicity in airway ALI infections which are pivotal for the establishment of a persistent infection. Altogether, these results lend further support to the consideration of macrolides asde factoantibiotics againstP. aeruginosaand the need for resistance monitoring upon prolonged macrolide treatment.
The G-Protein-Coupled Receptor Kinase 2 Orchestrates Hair Follicle Homeostasis
Authors: Asensio Alejandro , Sanz-Flores Maria , Liakath-Ali Kif , Palacios-García Julia , Paramio Jesús M , García-Escudero Ramon , Mayor Federico , Ribas Catalina
Published: April 2024

Tightly regulated cell-cell and cell-niche intercommunications via intertwined signaling networks are involved in maintaining normal hair follicle (HF) homeostasis, cycling and cell fate determination. However, knowledge of specific mechanisms by which hair loss takes place under pathological situations is needed. Using a keratinocyte-specific knockout mouse model, we uncover that the G-protein-coupled receptor kinase 2 (GRK2) signaling node plays a key role in HF homeostasis. Epidermal GRK2 ablation causes alterations during anagen induction, giving rise to abnormal cyst-like structures. HF-linked cysts display aberrant growth and differentiation patterns as well as lineage infidelity, displaying features of abortive HFs unable to fully acquire canonical hallmarks. Cysts triggered by GRK2 deletion displace the dermal papilla away from the bulge and promote irreversible changes in HF stem cell architecture, leading to bulge destruction and hair loss. Our data provide unforeseen roles of GRK2 in epidermal physiology and uncover mechanisms linking dystrophic follicular cysts formation with hair loss, with potential connections to pathogenic processes operating in immune-mediated alopecias.
A Lipidomics-Based Method to Eliminate Negative Urine Culture in General Population
Authors: Nartey Linda K , Mikhael Abanoub , Pětrošová Helena , Yuen Victor , Kibsey Pamela , Ernst Robert K , Chen Michael X , Goodlett David R
Published: April 2024

Urinary tract infections (UTIs) pose a significant challenge to human health. Accurate and timely detection remains pivotal for effective intervention. Current urine culture techniques, while essential, often encounter challenges where urinalysis yields positive results, but subsequent culture testing produces a negative result. This highlights potential discrepancies between the two methods and emphasizes the need for improved correlation in urinary tract infection (UTI) detection. Employing advanced lipidomics techniques, we deployed the fast lipid analysis technique (FLAT) on a clinical cohort suspected of having UTIs. Lipid fingerprinting by MALDI-TOF MS, directly from urine samples withoutex vivogrowth, correctly identified the common uropathogens within a 1-hour timeframe when compared to urine culture. FLAT analysis also identified urine samples without culturable pathogens (negative UTIs) with 99% agreement, whereas urinalysis showed 37% agreement with the gold standard urine culture. In 402 urine samples suspected for UTI from out-patients, FLAT assay rapidly ruled out negative urines without the need for culture in 77% of all cases. The potential impact of this innovative lipidomic-based approach extends beyond conventional diagnostic limitations, offering new avenues for early detection and targeted management of urinary tract infections. This research marks a paradigm shift in urine culture methodology, paving the way for improved clinical outcomes and public health interventions.
Plasma pTau181 reveals a pathological signature that predicts cognitive outcomes in Lewy body disease
Authors: Abdelnour Carla , Young Christina B , Shahid-Besanti Marian , Smith Alena , Wilson Edward N. , Ramos Benitez Javier , Vossler Hillary , Plastini Melanie J. , Winer Joseph R. , Kerchner Geoffrey A. , Cholerton Brenna , Andreasson Katrin I. , Henderson Victor W. , Yutsis Maya , Montine Thomas J , Tian Lu , Mormino Elizabeth C. , Poston Kathleen L.
Published: April 2024

Lewy body disease (LBD) often co-exists with Alzheimer’s disease (AD), influencing disease progression, cognitive decline, and neurodegeneration. This study aims to determine whether plasma phosphorylated-Tau181 (pTau181) could be used as diagnostic biomarker of concurrent Alzheimer’s disease neuropathologic change (ADNC) or amyloidosis alone, as well as a prognostic, monitoring, and susceptibility/risk biomarker for clinical outcomes in LBD. Our sample comprised 565 Stanford research participants: 94 LBD with normal cognition, 83 LBD with abnormal cognition, 114 AD, and 274 who were cognitively normal. We measured plasma pTau181 levels with the LumipulseGplatform. Diagnostic accuracy for concurrent ADNC and amyloidosis was assessed with receiver-operating-characteristic curves in a subset of participants with CSF pTau181/Aβ42, and CSF Aβ42/Aβ40 or amyloid-β PET, respectively. We used linear mixed effects models to examine the associations between baseline and longitudinal plasma pTau181 levels and clinical outcomes. Plasma pTau181 predicted concurrent ADNC and amyloidosis in LBD with abnormal cognition with 87% and 72% accuracy, respectively. In the LBD with abnormal cognition, higher baseline plasma pTau181 was associated with worse baseline MoCA and CDR-SB, as well as accelerated decline in CDR-SB. Additionally, in this group rapid increases in plasma pTau181 over 3 years predicted a faster decline in CDR-SB and memory. In LBD with normal cognition, there was no association between baseline or longitudinal plasma pTau181 levels and clinical outcomes; however, elevated pTau181 at baseline increased the risk of conversion to cognitive impairment. These findings suggest that plasma pTau181 is a promising biomarker for concurrent ADNC and amyloidosis in LBD. Furthermore, plasma pTau181 holds potential as a prognostic, monitoring, and susceptibility/risk biomarker, predicting disease progression in LBD.
Assessing the role of bacterial innate and adaptive immunity as barriers to conjugative plasmids
Authors: Siedentop Berit , Mediavilla Carlota Losa , Kouyos Roger D. , Bonhoeffer Sebastian , Chabas Hélène
Published: April 2024

Plasmids are ubiquitous mobile genetic elements, that can be either costly or beneficial for their bacterial host. In response to constant viral threat, bacteria have evolved various immune systems, such as the prevalent restriction modification (RM) (innate immunity) and CRISPR-Cas systems (adaptive immunity). At the molecular level, both systems also target plasmids, but the consequences of these interactions for plasmid spread are unclear. Using a modeling approach, we show that RM and CRISPR-Cas are effective as barriers against the spread of costly plasmids, but not against beneficial ones. Consequently, bacteria can profit from the adaptive advantages that beneficial plasmids confer even in the presence of bacterial immunity. While plasmids that are costly for bacteria may persist for a certain period in the bacterial population, RM and CRISPR-Cas pose a substantial burden for such plasmids, which can eventually drive them to extinction. Finally, we demonstrate that the selection pressure imposed by bacterial immunity on costly plasmids can be circumvented through a diversity of escape mechanisms and highlight how plasmid carriage might be common despite bacterial immunity. In summary, the population-level outcome of interactions between plasmids and defense systems in a bacterial population is closely tied to plasmid cost: Beneficial plasmids can persist at high prevalence in bacterial populations despite defense systems, while costly plasmids may face substantial reduction in prevalence or even extinction.
Essential and virulence-related protein interactions of pathogens revealed through deep learning
Authors: Humphreys Ian R. , Zhang Jing , Baek Minkyung , Wang Yaxi , Krishnakumar Aditya , Pei Jimin , Anishchenko Ivan , Tower Catherine A. , Jackson Blake A. , Warrier Thulasi , Hung Deborah T. , Peterson S. Brook , Mougous Joseph D. , Cong Qian , Baker David
Published: April 2024

Identification of bacterial protein–protein interactions and predicting the structures of the complexes could aid in the understanding of pathogenicity mechanisms and developing treatments for infectious diseases. Here, we developed a deep learning-based pipeline that leverages residue-residue coevolution and protein structure prediction to systematically identify and structurally characterize protein-protein interactions at the proteome-wide scale. Using this pipeline, we searched through 78 million pairs of proteins across 19 human bacterial pathogens and identified 1923 confidently predicted complexes involving essential genes and 256 involving virulence factors. Many of these complexes were not previously known; we experimentally tested 12 such predictions, and half of them were validated. The predicted interactions span core metabolic and virulence pathways ranging from post-transcriptional modification to acid neutralization to outer membrane machinery and should contribute to our understanding of the biology of these important pathogens and the design of drugs to combat them.
Identification of bacteria involved in non-sulfate based hydrogen sulfide production in an aquaculture environment
Authors: Nguyen-tiet Alexandre Minh , Puente-Sanchez Fernando , Bertilsson Stefan , Aalto Sanni L
Published: April 2024

Unwanted microbiological production of hydrogen sulfide (H2S) is a major challenge in engineered systems, such as sewage treatment plants, landfills, and aquaculture systems. While sulfur-rich amino acids and other substrates for non-sulfate-based H2S production are commonly present, the ability and potential of different microorganisms to perform sulfate-free H2S production has not yet been resolved. Here, we reveal the identity, activity, and genomic characteristics of bacteria that degrade cysteine to produce H2S in anaerobic enrichment bioreactors seeded with material from aquaculture systems. We compared them with canonical sulfate reducing bacteria and found that both sulfur sources led to microbial H2S production, yet with the process being more rapid with cysteine than with sulfate. 16S rRNA amplicon sequencing and metagenomic analysis showed four bacterial families, Dethiosulfatibacteraceae, Fusobacteriaceae, Vibrionaceae, and Desulfovibrionaceae to be centrally involved in non-sulfate H2S production. Metagenome/metatranscriptome assembled genomes uncovered the main cysteine-degradation pathway mediated by cysteine desulfidase cyuA and revealed that some bacteria potentially also use cysteine as a carbon source in sulfate-based H2S production.
Tumor spheroid elasticity estimation using mechano-microscopy combined with a conditional generative adversarial network
Authors: Foo Ken Y. , Shaddy Bryan , Murgoitio-Esandi Javier , Hepburn Matt S. , Li Jiayue , Mowla Alireza , Vahala Danielle , Amos Sebastian E. , Choi Yu Suk , Oberai Assad A. , Kennedy Brendan F.
Published: April 2024

Techniques for imaging the mechanical properties of cells are needed to study how cell mechanics influence cell function and disease progression. Mechano-microscopy (a high-resolution variant of compression optical coherence elastography) generates elasticity images of a sample undergoing compression from the phase difference between optical coherence microscopy (OCM) B-scans. However, the existing mechano-microscopy signal processing chain (referred to as the algebraic method) assumes the sample stress is uniaxial and axially uniform, such that violation of these assumptions reduces the accuracy and precision of elasticity images. Furthermore, it does not account for prior information regarding the sample geometry or mechanical property distribution. In this study, we investigate the feasibility of training a conditional generative adversarial network (cGAN) to generate elasticity images from phase difference images of samples containing a cell spheroid embedded in a hydrogel. To train and test the cGAN, we constructed 30,000 elasticity and phase difference image pairs, where elasticity images were generated using a parametric model to simulate artificial samples, and phase difference images were computed using finite element analysis to simulate compression applied to the artificial samples. By applying both the cGAN and algebraic methods to simulated phase difference images, our results indicate the cGAN elasticity images exhibit better spatial resolution and sensitivity. We also evaluated the cGAN on experimental phase difference images of real spheroids embedded in hydrogels and compared the cGAN elasticity with the algebraic elasticity, OCM, and confocal fluorescence microscopy, and found the cGAN elasticity is often more robust to noise, especially within stiff nuclei.
A stress-dependent TDP-43 SUMOylation program preserves neuronal function
Authors: Suk Terry R. , Part Caroline E. , Zhang Jenny L. , Nguyen Trina T. , Heer Meghan M. , Caballero-Gómez Alejandro , Grybas Veronica S. , McKeever Paul M. , Nguyen Benjamin , Callaghan Steve M. , Woulfe John M. , Robertson Janice , Rousseaux Maxime W.C.
Published: April 2024

Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Dementia (FTD) are overwhelmingly linked to TDP-43 dysfunction. Mutations in TDP-43 are rare, indicating that the progressive accumulation of exogenous factors – such as cellular stressors – converge on TDP-43 to play a key role in disease pathogenesis. Post translational modifications such as SUMOylation play essential roles in response to such exogenous stressors. We therefore set out to understand how SUMOylation may regulate TDP-43 in health and disease. We find that TDP-43 is regulated dynamically via SUMOylation in response to cellular stressors. When this process is blockedin vivo, we note age-dependent TDP-43 pathology and sex-specific behavioral deficits linking TDP-43 SUMOylation with aging and disease. We further find that SUMOylation is correlated with human aging and disease states. Collectively, this work presents TDP-43 SUMOylation as an early physiological response to cellular stress, disruption of which may confer a risk for TDP-43 proteinopathy.
Huntingtin polyglutamine expansions misdirect axonal transport by perturbing motor and adaptor recruitment
Authors: Prowse Emily N. P. , Turkalj Brooke A. , Sébastien Muriel , Beaudet Daniel , McBride Heidi M. , Brouhard Gary J. , Pouladi Mahmoud A. , Hendricks Adam G.
Published: April 2024

Huntington’s disease (HD) is caused by polyglutamine (polyQ) expansions in huntingtin (HTT). Polyglutamine repeat lengths >35Q lead to neurodegeneration and longer repeats correspond to earlier symptom onset. HTT scaffolds kinesin-1 and dynein to a variety of vesicles and organelles directly and through adaptors. To characterize the effects of HTT polyQ expansions on axonal transport, we tracked BDNF vesicles, mitochondria, and lysosomes in neurons induced from an isogenic set of human stem cell lines with repeat lengths of 30, 45, 65, and 81Q. Mild and intermediate pathogenic polyQ expansions caused increased BDNF motility, while HTT-81Q misdirected BDNF towards the distal tip. In comparison, mitochondria and lysosome transport showed mild defects with polyQHTT. We next examined the effect of polyQHTT in combination with neuroinflammatory stress. Under stress, BDNF cargoes in HTT-30Q neurons were more processive. Stress in HTT-81Q resulted in a stark decrease in the number of BDNF cargoes. However, the few remaining BDNF cargoes displayed more frequent long-range motility in both directions. Under neuroinflammatory stress, lysosomes were more abundant in HTT-81Q neurons, and motile lysosomes moved less processively and had an anterograde bias while lysosomes in HTT-30Q where not strongly affected. To examine how HTT-polyQ expansions altered the motors and adaptors on vesicular cargoes, we isolated BDNF cargoes from neurons and quantified the proteins associated with them. BDNF-endosomes isolated from HTT-81Q neurons associated with 2.5 kinesin-1 and 3.9 HAP1 molecules on average, compared to 1.0 kinesin-1 and 1.0 HAP1 molecule for HTT-30Q neurons. Together, these results show that polyQ expansions in HTT cause aberrant motor and adaptor recruitment to cargoes, resulting in dysregulated transport and responses to neuroinflammatory stress.
Structure ofEscherichia coliDNA gyrase with chirally wrapped DNA supports ratchet-and-pawl mechanism for an ATP-powered supercoiling motor
Authors: Michalczyk Elizabeth , Pabiś Marta , Heddle Jonathan , Ghilarov Dmitry
Published: April 2024

Gyrase is essential for replication and transcription in bacteria, and as such is an important target for antibiotics including fluoroquinolones. Gyrase is a molecular machine that channels the energy of ATP hydrolysis into negative supercoiling of DNA. The mechanism proposed more than 40 years ago involves stabilising and inverting a chiral DNA loop; however, the molecular basis for this is poorly understood, as the loop was never directly observed. We present high-resolution cryoEM structures of theEscherichia coligyrase - 217 bp DNA holocomplex, and of the moxifloxacin-bound gyrase complex with cleaved 217 bp DNA. Each structure constrains an intact figure-of-eight positively supercoiled DNA loop, poised for strand passage. The loop is stabilised by a GyrA β-pinwheel domain which how we here show has a structure of a flat disc, and functions akin to a mini-nucleosome. Our data implies that during catalysis the ATPase domains of the enzyme undergo a large movement to push the transported DNA segment through the break in DNA. By comparing the catalytic site between native drug-free and moxifloxacin-bound gyrase structures that both contain a single metal ion we demonstrate that the enzyme is observed in a native pre-catalytic state. Finally, we propose a ‘ratchet and pawl’ mechanism for energy coupling in gyrase. These unexpected findings call for re-evaluation of existing data and offer a framework for further experiments designed to dissect the details of how gyrase molecular motor converts chemical energy into mechanical tension.
Differential maturation of the brain networks required for the sensory, emotional and cognitive aspects of pain in human newborns
Authors: Jones Laura , Batalle Dafnis , Meek Judith , Edwards David , Fitzgerald Maria , Arichi Tomoki , Fabrizi Lorenzo
Published: April 2024

Pain is multidimensional and complex, including sensory-discriminative, affective-motivational, and cognitive-evaluative components. While the concept of pain is learned through life experience, it is not known when and how the brain networks that are required to encode these different dimensions of pain develop. Using the two largest databases of human brain magnetic resonance (MR) images in the world - the developing Human Connectome Project and the Human Connectome Project - we have mapped the development of the neural pathways required for pain perception in the human brain in infants from <32 weeks to 42 weeks postmenstrual age (n = 372), compared to adults (n = 98). Partial correlation analysis of 15 mins resting BOLD signal between all possible pairwise combinations of 12 pain-related regions of interest showed that overall functional connectivity is significantly weaker in 32-week infants compared to adults. However, over the following weeks, significantly different developmental patterns of connectivity emerge in sensory-discriminative, affective-motivational, and cognitive-evaluative pain networks. The first subnetwork to reach adult levels in strength and proportion of connections is the sensory-discriminative subnetwork (34-36 weeks PMA), followed by the affective-motivational subnetwork (36-38 weeks PMA), while the cognitive-evaluative subnetwork has still not reached adult levels at 42 weeks. This study reveals a previously unknown pattern of postnatal development of connectome subnetworks necessary for mature pain processing. The brain networks that form the infrastructure to encode different components of pain experience, change rapidly in the equivalent of the last gestational trimester but are still immature at the time of normal birth. Newborn neural pathways required for mature pain processing in the brain are incomplete in newborns compared to adults, particularly with respect to the emotional and evaluative aspects of pain. This data suggests that pain-related networks may have distinct periods of vulnerability to untimely noxious procedures during hospitalization, particularly in preterm infants.
Soluble αβ-tubulins reversibly sequester TTC5 to regulate tubulin mRNA decay
Authors: Batiuk Alina , Höpfler Markus , Almeida Ana C. , En-Jie Deryn Teoh , Vadas Oscar , Vartholomaiou Evangelia , Hegde Ramanujan S. , Lin Zhewang , Gasic Ivana
Published: April 2024

Microtubules, built from heterodimers of α- and β-tubulins, control cell shape, mediate intracellular transport and power cell division. The concentration of αβ-tubulins is tightly controlled through a post-transcriptional mechanism involving selective and regulated degradation of tubulin-encoding mRNAs. Degradation is initiated by TTC5, which recognizes tubulin-synthesizing ribosomes and recruits downstream effectors to trigger mRNA deadenylation. Here, we have investigated how cells regulate TTC5 activity. Biochemical and structural proteomic approaches reveal that under normal conditions, soluble αβ-tubulins bind to and sequester TTC5, preventing it from engaging nascent tubulins at translating ribosomes. We identify the flexible C-terminal tail of TTC5 as a molecular switch, toggling between soluble αβ-tubulin-bound and nascent tubulin-bound states. Loss of sequestration by soluble αβ-tubulins constitutively activates TTC5, leading to diminished tubulin mRNA levels and compromised microtubule-dependent chromosome segregation during cell division. Our findings provide a paradigm for how cells regulate the activity of a specificity factor to adapt posttranscriptional regulation of gene expression to cellular needs.
Problem-Solving as a Language: A Computational Lens into Human and Monkey Intelligence
Authors: Yang Qianli , Zhu Zhihua , Si Ruoguang , Li Yunwei , Zhang Jiaxiang , Yang Tianming
Published: April 2024

1

Human intelligence is characterized by our remarkable ability to solve complex problems. This involves planning a sequence of actions that leads us from an initial state to a desired goal state. Quantifying and comparing problem-solving capabilities across species and finding its evolutional roots is a fundamental challenge in cognitive science, and is critical for understanding how the brain carries out this intricate process. In this study, we introduce the Language of Problem-Solving (LoPS) model as a novel quantitative framework that investigates the structure of problem-solving behavior through a language model. We adapted the classic Pac-Man game as a cross-species behavioral paradigm to test both humans and macaque monkeys. Using the LoPS model, we extracted the latent structure — or grammar — embedded in the agents’ gameplay, revealing the non-Markovian temporal structure of their problem-solving behavior. The LoPS model captured fine-grained individual differences among the players and revealed the striking differences in the complexity and hierarchical organization of problem-solving behavior between humans and monkeys, reflecting the distinct cognitive capabilities of each species. Furthermore, both humans and monkeys evolved their LoPS grammars during learning, progressing from simpler to more complex ones, suggesting that the language of problem-solving is not fixed, but rather evolves to support more sophisticated and efficient problem-solving. Through the lens of a language model, our study provides insights into how humans and monkeys break down problem-solving into compositional units and navigate complex tasks. This framework deepens our understanding of human intelligence and its evolution, and establishes a foundation for future investigations of the neural mechanisms of problem-solving.
Building better genome annotations across the tree of life
Authors: Freedman Adam H , Sackton Timothy B
Published: April 2024

Recent technological advances in long read DNA sequencing accompanied by dramatic reduction in costs have made the production of genome assemblies financially achievable and computationally feasible, such that genome assembly no longer represents the major hurdle to evolutionary analysis for most non-model organisms. Now, the more difficult challenge is to properly annotate a draft genome assembly once it has been constructed. The primary challenge to annotation is how to select from the myriad gene prediction tools that are currently available, determine what kinds of data are necessary to generate high quality annotations, and evaluate the quality of the annotation. To determine which methods perform the best and determine whether the inclusion of RNA-seq data is necessary to obtain a high-quality annotation, we generated annotations with 10 different methods for 21 different species spanning vertebrates, plants, and insects. We found that the RNA-seq assembler Stringtie and the annotation transfer method TOGA were consistently top performers across a variety of metrics including BUSCO recovery, CDS length, and false positive rate, with the exception that TOGA performed less in plants with larger genomes. RNA-seq alignment rate was best with RNA-seq assemblers. HMM-based methods such as BRAKER, MAKER, and multi-genome AUGUSTUS mostly underperformed relative to Stringtie and TOGA. In general, inclusion of RNA-seq data will lead to substantial improvements to genome annotations, and there may be cases where complementarity among methods may motivate combining annotations from multiple sources.
Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID pipeline
Authors: Lu Dan , Kalantar Katrina L. , Chu Victoria T. , Glascock Abigail L. , Guerrero Estella S. , Bernick Nina , Butcher Xochitl , Ewing Kirsty , Fahsbender Elizabeth , Holmes Olivia , Hoops Erin , Jones Ann E. , Lim Ryan , McCanny Suzette , Reynoso Lucia , Rosario Karyna , Tang Jennifer , Valenzuela Omar , Mourani Peter M. , Pickering Amy J. , Raphenya Amogelang R. , Alcock Brian P. , McArthur Andrew G. , Langelier Charles R.
Published: April 2024

Antimicrobial resistant (AMR) pathogens represent urgent threats to human health, and their surveillance is of paramount importance. Metagenomic next generation sequencing (mNGS) has revolutionized such efforts, but remains challenging due to the lack of open-access bioinformatics tools capable of simultaneously analyzing both microbial and AMR gene sequences. To address this need, we developed the Chan Zuckerberg ID (CZ ID) AMR module, an open-access, cloud-based workflow designed to integrate detection of both microbes and AMR genes in mNGS and whole-genome sequencing (WGS) data. It leverages the Comprehensive Antibiotic Resistance Database and associated Resistance Gene Identifier software, and works synergistically with the CZ ID short-read mNGS module to enable broad detection of both microbes and AMR genes. We highlight diverse applications of the AMR module through analysis of both publicly available and newly generated mNGS and WGS data from four clinical cohort studies and an environmental surveillance project. Through genomic investigations of bacterial sepsis and pneumonia cases, hospital outbreaks, and wastewater surveillance data, we gain a deeper understanding of infectious agents and their resistomes, highlighting the value of integrating microbial identification and AMR profiling for both research and public health. We leverage additional functionalities of the CZ ID mNGS platform to couple resistome profiling with the assessment of phylogenetic relationships between nosocomial pathogens, and further demonstrate the potential to capture the longitudinal dynamics of pathogen and AMR genes in hospital acquired bacterial infections. In sum, the new AMR module advances the capabilities of the open-access CZ ID microbial bioinformatics platform by integrating pathogen detection and AMR profiling from mNGS and WGS data. Its development represents a critical step toward democratizing pathogen genomic analysis and supporting collaborative efforts to combat the growing threat of AMR.
Affective Symptoms in Pregnancy are Associated with the Vaginal Microbiome
Authors: Scheible Kristin , Beblavy Robert , Sohn Michael B. , Qui Xing , Gill Ann L. , Narvaez-Miranda Janiret , Brunner Jessica , Miller Richard K. , Barrett Emily S. , O’Connor Tom G. , Gill Steven R.
Published: April 2024

Composition of the vaginal microbiome in pregnancy is associated with adverse maternal, obstetric, and child health outcomes. Identifying the sources of individual differences in the vaginal microbiome is therefore of considerable clinical and public health interest. The current study tested the hypothesis that vaginal microbiome composition during pregnancy is associated with an individual’s experience of affective symptoms and stress exposure. Data were based on a prospective longitudinal study of a diverse and medically healthy community sample of 275 mother-infant pairs. Affective symptoms and stress exposure and select measures of associated biomarkers (diurnal salivary cortisol, serum measures of sex hormones) were collected at each trimester; self-report, clinical, and medical records were used to collect detailed data on socio-demographic factors and health behavior, including diet and sleep. Vaginal microbiome samples were collected in the third trimester (34-40 weeks) and characterized by 16S rRNA sequencing. Identified taxa were clustered into three community state types (CST1-3) based on dissimilarity of vaginal microbiota composition. Results indicate that depressive symptoms during pregnancy were reliably associated with individual taxa and CST3 in the third trimester. Prediction of functional potential from 16S taxonomy revealed a differential abundance of metabolic pathways in CST1-3 and individual taxa, including biosynthetic pathways for the neuroactive metabolites, serotonin and dopamine. With the exception of bioavailable testosterone, no significant associations were found between symptoms- and stress-related biomarkers and CSTs. Our results provide further evidence of how prenatal psychological distress during pregnancy alters the maternal-fetal microbiome ecosystem that may be important for understanding maternal and child health outcomes.

Importance

Prenatal affective symptoms and stress are associated with maternal, obstetric, and child health outcomes, but the mechanisms underlying these links and their application to intervention remain unclear. The findings from this investigation extend prior microbiome-oriented research by demonstrating that the maternal vaginal microbiome composition has a biologically plausible mechanistic link with affective symptoms that also suggest additional clinical applications for assessment and intervention.
Chk2 homologue Mek1 limits Exo1-dependent DNA end resection during meiotic recombination inS. cerevisiae
Authors: Grubb Jennifer , Bishop Douglas K.
Published: April 2024

The conserved Rad2/XPG family 5’—3’ exonuclease, Exonuclease 1 (Exo1), plays many roles in DNA metabolism including during resolution of DNA double strand breaks (DSBs) via homologous recombination. Prior studies provided evidence that the end-resection activity of Exo1 is downregulated in yeast and mammals by Cdk1/2 family cyclin-dependent and checkpoint kinases, including budding yeast kinase Rad53 which functions in mitotic cells. Here we provide evidence that the master meiotic kinase Mek1, a paralogue of Rad53, limits 5’-3’ single strand resection at the sites of programmed meiotic DNA breaks. Mutational analysis suggests that the mechanism of Exo1 suppression by Mek1 differs from that of Rad53.

Article Summary

Meiotic recombination involves formation of programmed DNA double strand breaks followed by 5’ to 3’ single strand specific resection by nucleases including Exo1. We find that the activity of budding yeast Exo1 is downregulated during meiotic recombination by the master meiotic kinase Mek1. The mechanism of downregulation of Exo1 by Mek1 in meiosis does not depend on the same phospho-sites as those used by the mitotic kinase Rad53, a relative of Mek1 that downregulates Exo1 in mitosis.
Engineering inducible signaling receptors to enable erythropoietin-free erythropoiesis
Authors: Shah Aadit P. , Majeti Kiran R. , Ekman Freja K. , Selvaraj Sridhar , Soupene Eric , Chati Prathamesh , Sinha Roshani , Luna Sofia E. , Charlesworth Carsten T. , McCreary Travis , Lesch Benjamin J. , Tran Tammy , Sharma Devesh , Chu Simon N. , Porteus Matthew H. , Cromer M. Kyle
Published: April 2024

Blood transfusion plays a vital role in modern medicine. However, availability is contingent on donated blood, and frequent shortages pose a significant healthcare challenge.Ex vivomanufacturing of red blood cells (RBCs) derived from universal donor O-negative pluripotent stem cells emerges as a solution, yet the high cost of recombinant cytokines required forex vivoerythroid differentiation remains a major barrier. Erythropoietin (EPO) signaling through the EPO receptor is indispensable to RBC development, and EPO is one of the most expensive components in erythroid-promoting media. Here, we used design-build-test cycles to develop highly optimized small molecule-inducible EPO receptors (iEPORs) which were integrated at a variety of genomic loci using homology-directed repair genome editing. We found that integration of iEPOR at the endogenousEPORlocus in an induced pluripotent stem cell producer line enabled culture with small molecule to yield equivalent erythroid differentiation, transcriptomic changes, and hemoglobin production compared to cells cultured with EPO. Due to the dramatically lower cost of small molecules vs. recombinant cytokines, these efforts eliminate one of the most expensive elements ofex vivoculture media—EPO cytokine. Because dependence on cytokines is a common barrier toex vivocell production, these strategies could improve scalable manufacturing of a wide variety of clinically relevant cell types. More broadly, this work showcases how synthetic biology and genome editing may be combined to introduce precisely regulated and tunable behavior into cells, an advancement which will pave the way for increasingly sophisticated cell engineering strategies.
Neural correlates of flexible sound perception in the auditory midbrain and thalamus
Authors: Ying Rose , Stolzberg Daniel J. , Caras Melissa L.
Published: April 2024

Hearing is an active process in which listeners must detect and identify sounds, segregate and discriminate stimulus features, and extract their behavioral relevance. Adaptive changes in sound detection can emerge rapidly, during sudden shifts in acoustic or environmental context, or more slowly as a result of practice. Although we know that context- and learning-dependent changes in the spectral and temporal sensitivity of auditory cortical neurons support many aspects of flexible listening, the contribution of subcortical auditory regions to this process is less understood. Here, we recorded single- and multi-unit activity from the central nucleus of the inferior colliculus (ICC) and the ventral subdivision of the medial geniculate nucleus (MGV) of Mongolian gerbils under two different behavioral contexts: as animals performed an amplitude modulation (AM) detection task and as they were passively exposed to AM sounds. Using a signal detection framework to estimate neurometric sensitivity, we found that neural thresholds in both regions improved during task performance, and this improvement was driven by changes in firing rate rather than phase locking. We also found that ICC and MGV neurometric thresholds improved and correlated with behavioral performance as animals learn to detect small AM depths during a multi-day perceptual training paradigm. Finally, we reveal that in the MGV, but not the ICC, context-dependent enhancements in AM sensitivity grow stronger during perceptual training, mirroring prior observations in the auditory cortex. Together, our results suggest that the auditory midbrain and thalamus contribute to flexible sound processing and perception over rapid and slow timescales.

Significance statement

What a listener hears depends on several factors, such as whether the listener is attentive or distracted, and whether the sound is meaningful or irrelevant. Practice can also shape hearing by improving the detection of particular sound features, as occurs during language or musical learning. Understanding how changes in sound perception are implemented in the brain is important for developing strategies to optimize healthy hearing, and for treating disorders in which these processes go awry. We report that neurons in auditory midbrain and thalamus exhibit rapid shifts in sound sensitivity that depend on the sound’s behavioral relevance, and slower improvements that emerge over several days of training. Our results suggest that subcortical areas make an important contribution to flexible hearing.
UK BioCoin: Swift Trait-Specific Summary Statistics Regression for UK Biobank
Authors: He Jing-Cheng , Qi Guo-An , Ying Jiacheng , Qian Yu , Han Lide , Mao Yingying , Zheng Hou-Feng , Jiang Hangjin , Chen Guo-Bo
Published: April 2024

Summary statistics derived from large-scale biobanks facilitate the sharing of genetic discoveries while minimizing the risk of compromising individual-level data privacy. However, these summary statistics, such as those from the UK Biobank (UKB) provided by Neale’s lab, are often adjusted by a fixed set of covariates to all traits (12 covariates including 10 PCs, sex and age), preventing the exploration of trait-specific summary statistics. In this study, we present a novel computational device UK BioCoin (UKC), which is designed to provide an efficient framework for trait-specific adjustment for covariates. Without requiring access to individual-level data from UKB, UKC leverages summary statistics regression technique and resources from UKB (289 GB of 199 phenotypes and 10 million SNPs), to enable the generation of GWAS summary statistics adjusted by user-specified covariates. Through a comprehensive analysis of height under trait-specific adjustments, we demonstrate that the GWAS summary statistics generated by UKC closely mirror those generated from individual-level UKB GWAS (ρ ≥0.99 for effect sizes andρ ≥0.99 forp-values). Furthermore, we demonstrate the results for GWAS, SNP-heritability estimation, polygenic score, and Mendelian randomization, after various trait-specific covariate adjustments as allowed by UKC, indicating UKC a platform that harnesses in-depth exploration for researchers lacking access to UKB. The whole framework of UKC is portable for other biobank, as demonstrated in Westlake Biobank, which can equivalently be converted to a ‘UKC-like” platform and promote data sharing. UKC has its computational engine fully optimized, and the computational efficiency of UKC is about 70 times faster than that of UKB. We package UKC as a Docker image of 20 GB (https://github.com/Ttttt47/UKBioCoin), which can be easily deployed on an average computer (e.g. laptop).

One sentence summary

We develop UK BioCoin (UKC), which allows fine-tuning of covariates for each UK Biobank trait but does not relay on UK Biobank individual-level data. It will change the current landscape of GWAS and reshape its downstream analyses.
Metabolically intact nuclei are fluidized by the activity of the chromatin remodeling motor BRG1
Authors: Byfield Fitzroy J. , Eftekhari Behnaz , Kaymak-Loveless Kaeli , Mandal Kalpana , Li David , Wells Rebecca G. , Chen Wenjun , Brujic Jasna , Bergamaschi Guilia , Wuite Gijs J.L. , Patteson Alison E. , Janmey Paul A.
Published: April 2024

The structure and dynamics of the cell nucleus regulate nearly every facet of the cell. Changes in nuclear shape limit cell motility and gene expression. Although the nucleus is generally seen as the stiffest organelle in the cell, cells can nevertheless deform the nucleus to large strains by small mechanical stresses. Here, we show that the mechanical response of the cell nucleus exhibits active fluidization that is driven by the BRG 1 motor of the SWI/SNF/BAF chromatin-remodeling complex. Atomic force microscopy measurements show that the nucleus alters stiffness in response to the cell substrate stiffness, which is retained after the nucleus is isolated and that the work of nuclear compression is mostly dissipated rather than elastically stored. Inhibiting BRG 1 stiffens the nucleus and eliminates dissipation and nuclear remodeling both in isolated nuclei and in intact cells. These findings demonstrate a novel link between nuclear motor activity and global nuclear mechanics.
Copper trafficking inTrypanosoma cruzi: the transcriptional response of candidates to balance toxicity and recruitment
Authors: Merli Marcelo L. , Mediavilla María G. , Zhu Xinyu , Cobine Paul A. , Cricco Julia A.
Published: April 2024

Trypanosoma cruzi(Chagas disease) depends on acquiring nutrients and cofactors, like copper (Cu), from its hosts. Cu is essential for aerobic organisms, but it can also be toxic, so its transport and storage must be regulated. In the present study, we characterized the effects of changes in Cu availability on growth, intracellular ion content, and oxygen consumption. Our results show that Cu is essential for epimastigote proliferation and for metacyclogenesis, while intracellular amastigotes suffered from Cu stress during infection. We identify several genes potentially involved in Cu metabolism among which orthologs of the conserved P-type Cu ATPases involved in Cu export and loading of secreted enzymes were found and namedTcCuATPase.TcCuATPase transcription is regulated during infective stages and by Cu availability in epimastigotes. No homologs were identified for the high affinity importer CTR1 instead we propose that the iron transportTcIT a ZIP family transporter is involved in Cu uptake based on its transcriptional response to Cu. Further canonical Cu targets (based on homology to yeast and mammals) such as the iron reductaseTcFR and the cupro-oxidaseTcFet3 are up regulated during infective stages and under intracellular Cu stress. We also demonstrated that Cu, iron, and heme metabolisms are related. In sum, Cu metabolism is essential inT. cruzilife cycle. Even though cytosolic Cu-chaperons are still missing, we propose a model for Cu transport and intracellular distribution inT. cruziincluding conserved factors such asTcCuATPase and others such asTcFR andTcIT playing novel functions.
Free fatty acid receptor 4 in cardiac myocytes ameliorates ischemic cardiomyopathy
Authors: Zhang Michael J. , Karachenets Sergey , Gyberg Dylan J. , Puccini Sara , Healy Chastity L. , Wu Steven C. , Shearer Gregory C. , O’Connell Timothy D.
Published: April 2024

Aims

Free fatty acid receptor 4 (Ffar4) is a receptor for long-chain fatty acids that attenuates heart failure driven by increased afterload. Recent findings suggest that Ffar4 prevents ischemic injury in brain, liver, and kidney, and therefore, we hypothesized that Ffar4 would also attenuate cardiac ischemic injury.

Methods and Results

Using a mouse model of ischemia-reperfusion (I/R), we found that mice with systemic deletion of Ffar4 (Ffar4KO) demonstrated impaired recovery of left ventricular systolic function post-I/R with no effect on initial infarct size. To identify potential mechanistic explanations for the cardioprotective effects of Ffar4, we performed bulk RNAseq to compare the transcriptomes from wild-type (WT) and Ffar4KO infarcted myocardium 3-days post-I/R. In the Ffar4KO infarcted myocardium, gene ontology (GO) analyses revealed augmentation of glycosaminoglycan synthesis, neutrophil activation, cadherin binding, extracellular matrix, rho signaling, and oxylipin synthesis, but impaired glycolytic and fatty acid metabolism, cardiac repolarization, and phosphodiesterase activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated impaired AMPK signaling and augmented cellular senescence in the Ffar4KO infarcted myocardium. Interestingly, phosphodiesterase 6c (PDE6c), which degrades cGMP, was the most upregulated gene in the Ffar4KO heart. Further, the soluble guanylyl cyclase stimulator, vericiguat, failed to increase cGMP in Ffar4KO cardiac myocytes, suggesting increased phosphodiesterase activity. Finally, cardiac myocyte-specific overexpression of Ffar4 prevented systolic dysfunction post-I/R, defining a cardioprotective role of Ffa4 in cardiac myocytes.

Conclusions

Our results demonstrate that Ffar4 in cardiac myocytes attenuates systolic dysfunction post-I/R, potentially by attenuating oxidative stress, preserving mitochondrial function, and modulation of cGMP signaling.