bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of protein levels and solubility in distinct brain regions reveals several elements of the protein homeostasis network that are impacted by aging
Authors: Molzahn Cristen , Kuechler Erich , Nierves Lorenz , Cole Gary , Wang Jing , Cashman Neil , Karsan Aly , Lange Philipp F. , Gsponer Jörg , Mayor Thibault
Published: March 2024

The onset of protein conformation diseases is inextricably linked to aging. During aging, cellular protein quality control declines which results in diminished protein homeostasis (proteostasis). In model organisms, such asC. elegansand killifish, proteostatic decline with age has been linked to the onset of aggregation of proteins in wild-type animals, observed through detergent-insoluble fractionation. Analysis of studies applying detergent-insoluble fractionation in mice revealed that the composition of detergent-insoluble proteins changes with age. However, these individual fractionation studies have generally been limited to small numbers of mice. Herein, we expand on our previous analysis by extending the experiments to a larger cohort of mice and to two brain regions implicated in neurodegenerative diseases, the cortex and hippocampus. These experiments unveil insights into alterations in the abundance and solubility of proteins involved in protein quality control and in inflammation. For example, ribosomal proteins and many chaperone proteins are downregulated with age. Consistent enrichment of subunits of the extracellular C1q complex was also observed in both brain regions alongside an increase in immunoglobulin signal indicating that markers of increased inflammation may also become insoluble during aging. More generally, insoluble proteins share features observed in datasets of impaired protein degradation indicating that the loss of activity of cellular protein degradation machinery may contribute to the specific aggregation of these proteins.
Protective effect and molecular mechanisms of human non-neutralizing cross-reactive spike antibodies elicited by SARS-CoV-2 mRNA vaccination
Authors: Clark Jordan , Hoxie Irene , Adelsberg Daniel C. , Sapse Iden A. , Andreata-Santos Robert , Yong Jeremy S. , Amanat Fatima , Tcheou Johnstone , Raskin Ariel , Singh Gagandeep , González-Domínguez Irene , Edgar Julia E. , Bournazos Stylianos , Sun Weina , Carreño Juan Manuel , Simon Viviana , Ellebedy Ali H. , Bajic Goran , Krammer Florian
Published: March 2024

Neutralizing antibodies correlate with protection against SARS-CoV-2. Recent studies, however, show that binding antibody titers, in the absence of robust neutralizing activity, also correlate with protection from disease progression. Non-neutralizing antibodies cannot directly protect from infection but may recruit effector cells thus contribute to the clearance of infected cells. Also, they often bind conserved epitopes across multiple variants. We characterized 42 human mAbs from COVID-19 vaccinated individuals. Most of these antibodies exhibited no neutralizing activityin vitrobut several non-neutralizing antibodies protected against lethal challenge with SARS-CoV-2 in different animal models. A subset of those mAbs showed a clear dependence on Fc-mediated effector functions. We determined the structures of three non-neutralizing antibodies with two targeting the RBD, and one that targeting the SD1 region. Our data confirms the real-world observation in humans that non-neutralizing antibodies to SARS-CoV-2 can be protective.
Sec23IP recruits the Cohen syndrome factor VPS13B/COH1 to ER exit site-Golgi interface for tubular ERGIC formation
Authors: Du Yuanjiao , Fan Xinyu , Song Chunyu , Xiong Juan , Ji Wei-Ke
Published: March 2024

VPS13B/COH1 is the only known causative factor for Cohen syndrome, an early-onset autosomal recessive developmental disorder with intellectual inability, developmental delay, joint hypermobility, myopia and facial dysmorphism as common features, but the molecular basis of VPS13B/COH1 in pathogenesis is unknown. Here, we identify Sec23 interacting protein (Sec23IP) at ER exit site (ERES) as a VPS13B adaptor that recruits VPS13B to ERES-Golgi interfaces. VPS13B interacts directly with Sec23IP via the VPS13 adaptor binding domain (VAB), and the interaction promotes the association between ERES and the Golgi. Disease-associated missense mutations of VPS13B-VAB impair the interaction with Sec23IP. Knockout of VPS13B or Sec23IP blocks the formation of tubular ERGIC, an unconventional cargo carrier that expedites ER-to-Golgi transport. In addition, depletion of VPS13B or Sec23IP delays ER export of procollagen, suggesting a link between procollagen secretion and joint laxity in patients with Cohen disease. Together, our study reveals a crucial role of VPS13B-Sec23IP interaction at ERES-Golgi interface in the pathogenesis of Cohen syndrome.
Peptide Mold: A Novel Strategy for Mapping Potential Binding Sites in Protein Targets
Authors: Bagwe Pritam V. , Jagtap Yogesh , Ghegade Vaibhav , Machhar Janvhi , Martis Elvis , Joshi Shreerang V. , Kharkar Prashant S.
Published: March 2024

A novel concept titled ‘Peptide Mold’ for mapping potential binding sites in protein targets is presented. A large multiconformer tetrapeptide library comprising of 32 million conformations of all possible combinations of naturally-occurring amino acids was constructed and used for molecular docking analysis in the substrate-binding site of SARS-CoV-2 PLpro enzyme. The top-ranking, structurally-diverse tetrapeptide docked conformations (symbolizing peptide mold, analogous to a clay mold) were used then for elucidating a five-point pharmacophore. Ligand-based virtual screening of a large, multiconformer library of phytoconstituents using the derived five-point pharmacophore led to identification of potential binders for SARS-CoV-2 PLpro at its substrate-binding site. The approach is based on generating the imprint of a macromolecular binding site (cavity) using tetrapeptides (clay), thereby generating a reverse mold (with definitive shape and size), which can further be used for identifying small-molecule ligands matching the captured features of the target binding site. The approach is based on the fact that the individual amino acids in the tetrapeptide represent all possible drug-receptor interaction features (electrostatic, H-bonding, van der Waals, dispersion and hydrophobic among others). The ‘peptide mold’ approach can be extended to any protein target for mapping the binding site(s), and further use of the generated pharmacophore model for virtual screening of potential binders. The peptide mold approach is a robust, hybrid computational screening strategy, overcoming the present limitations of structure-based methods, e.g., molecular docking and the ligand-based methods such as pharmacophore search. Exploration of the peptide mold strategy is expected to yield high-quality, reliable and interesting virtual hits in the computational screening campaigns during the hit and lead identification stages.
Validation of the performance of a point of care molecular test for leprosy: from a simplified DNA extraction protocol to a portable qPCR
Authors: Bertão-Santos Amanda , Dias Larisse da Silva , Ribeiro-Alves Marcelo , Pinheiro Roberta Olmo , Moraes Milton Ozório , Manta Fernanda Saloum de Neves , Costa Alexandre Dias Tavares
Published: March 2024

The study aimed to optimize qPCR reactions using oligonucleotides from the first Brazilian molecular diagnostic kit for leprosy on a portable platform (Q3-Plus). In addition, we sought to develop a simplified protocol for DNA extraction that met point-of-care criteria. During optimization on the Q3-Plus, optical parameters, thresholds, and cutoffs for the16S rRNAand RLEP targets ofM. lepraewere established using synthetic DNA, purified DNA fromM. leprae, and pre-characterized clinical samples. In the simplified extraction step, different lysis solutions were evaluated using chaotropic agents, and purification was carried out by depositing the lysed material on FTA cards. The complete protocol (simplified extraction + qPCR on the portable platform) was evaluated with pre-characterized clinical skin biopsy samples and compared with standard equipment (QuantStudio-5). LOD95%for the optimized reactions was 113.31 genome-equivalents/μL for16S rRNAand 17.70 genome-equivalents/μL for RLEP. Among the lysis solutions, the best-performing was composed of urea (2 M), which provided good dissolution of the skin fragment and a lower Ct value, indicating higher concentrations of DNA. The complete technological solution showed a sensitivity of 52% in reactions. Our results highlight the need for additional optimization to deal with paucibacillary samples, but also demonstrate the applicability of the portable platform in the detection ofM.leprae in low infrastructure settings.
Oro-faecal transmission of SARS-CoV-2: A systematic review of studies employing viral culture from gastrointestinal and other potential sources
Authors: Gandini Sara , Conly John , Spencer Elizabeth A. , Evans David , Rosca Elena C , Brassey Jon , Maltoni Susanna , Onakpoya Igho , Plüddemann Annette , Jefferson Tom , Heneghan Carl
Published: March 2024

Background

The extent to which the oro-faecal route contributes to the transmission of SARS-CoV-2 is not established.

Methods

We systematically reviewed the evidence on the presence of infectious SARS-CoV-2 in faeces and other gastrointestinal sources by examining studies that used viral culture to investigate the presence of replication-competent virus in these samples. We conducted searches in the WHO Covid-19 Database, LitCovid, medRxiv, and Google Scholar for SARS-CoV-2 using keywords and associated synonyms, with a search date up to 28th of November 2023.

Results

We included 13 studies involving 328 COVID-19 subjects - providing 314 faecal or rectal swab SARS-CoV2 positive samples tested also with viral culture. The methods used for viral culture across the studies were heterogeneous. Three studies (2 cohorts and 1 case-series) reported observing replication-competent SARS-CoV-2 confirmed by quantitative RT-PCR (qPCR) and whole genome sequencing, and qPCR including appropriate cycle threshold changes. Overall, six (1.9%) of 314 faecal samples subjected to cell culture showed replication-competent virus. One study found replication competent samples from one immunocompromised patient. No studies were identified demonstrating direct evidence of oro-faecal transmission to humans.

Conclusions

Our review found a relatively low frequency of replication-competent SARS-CoV-2 in faecal and other gastrointestinal sources. Although it is biologically plausible, more research is needed, using standardized cell culture methods, control groups, adequate follow-up and robust epidemiologic methods, including whether secondary infections occurred, to determine the role of the oro-faecal route in the transmission of SARS-CoV-2.
How many labels do I need? Self-supervised learning strategies for multiple blood parasites classification in microscopy images
Authors: Mancebo-Martín Roberto , Lin Lin , Dacal Elena , Luengo-Oroz Miguel , Bermejo-Peláez David
Published: March 2024

Abstract

Bloodborne parasitic diseases such as malaria, filariasis or chagas pose significant challenges in clinical diagnosis, with microscopy as the primary tool for diagnosis. However, limitations such as time-consuming processes and the dependence on trained microscopists is critical, particularly in resource-constrained settings. Deep learning techniques have shown value to interpret microscopy images using large annotated databases for training. In this work, we propose a methodology leveraging self-supervised learning as a foundational model for blood parasite classification. Using a large unannotated database of blood microscopy images, the model is able to learn important image representations that are subsequently transferred to perform parasite classification of 11 different species of parasites requiring a smaller amount of labeled data. Our results show enhanced performance over fully supervised approaches, with ∼100 labels per class sufficient to attain an F1 score of ∼0.8. This approach is promising for advancing in-vitro diagnostic systems in primary healthcare settings.
Systematic mutagenesis assay promotes comprehension of the strand-bias laws for mutations induced by oxidative DNA damage
Authors: Kawai Hidehiko , Ebi Shungo , Sugihara Ryusei , Fujiwara Chiho , Fujikawa Yoshihiro , Kimura Shingo , Kamiya Hiroyuki
Published: March 2024

We have recently developed an efficient and sensitive method for analyzing mutations caused by various environmental and endogenous factors which utilizes nucleotide-barcodedsupFshuttle vector libraries with a multiplexed NGS assay, referred to hereafter assupFNGS assay. Ionizing-radiation-induced cancer is known to be difficult to distinguish from spontaneous cancer, especially in the case of low-dose and low-dose-rate exposure, and discerning the underlying mechanisms of ionizing-radiation-induced cancer, especially the relationship between mutagenesis and carcinogenesis, is likely to be an arduous task. In the present study, we have attempted to address the mutations characteristic for exposure to low levels of ionizing radiation by using thesupFNGS assay. As a result, a significant increase in mutations was detected at cytosines and guanines within 5’-TC-3’:5’-GA-3’ sites following chronic gamma-irradiation at a dose-rate of 1 Gy per day for the duration of 2 days. Since the number of detected mutations exceeded the expectations based on the quantity of DNA-damage induced by irradiation, we proceeded to explore the possibilities that a single DNA-lesion induced by irradiation may cause amplification of mutations. For this purpose, we utilized shuttle vector libraries with a single 8-oxo-7,8-dihydroguanine (8-oxo-G)-damaged residue introduced at different sites via anin vitroenzymatic method. Through a set of experiments, we revealed that a single 8-oxo-G-damaged residue can become a trigger for peripheral mutagenesis; intense generation of strand-biased mutations occured at 5’-TC-3’:5’-GA-3’ sites with specific localization in the secondary structures of single-stranded DNA, more frequently than not at sites different from the 8-oxo-G-damaged sites. Thus, this study provides a novel prospect for the role of DNA-lesions induced by environmentally or endogenously generated ROS in additional mutations. The high-performance mutagenesis assay presented in this study will advance research aimed at uncovering the mechanisms of mutagenesis and the intricacies relevant to carcinogenesis.
Study of Impacts of Two Types of Cellular Aging on the Yeast Bud Morphogenesis
Authors: Tsai Kevin , Zhou Zhen , Yang Jiadong , Xu Zhiliang , Xu Shixin , Zandi Roya , Hao Nan , Chen Weitao , Alber Mark
Published: March 2024

Understanding the mechanisms of cellular aging processes is crucial for attempting to extend organismal lifespan and for studying age-related degenerative diseases. Yeast cells divide through budding, providing a classical biological model for studying cellular aging. With their powerful genetics, relatively short lifespan and well-established signaling pathways also found in animals, yeast cells offer valuable insights into the aging process. Recent experiments suggested the existence of two aging modes in yeast characterized by nucleolar and mitochondrial declines, respectively. In this study, by analyzing experimental data it was shown that cells evolving into those two aging modes behave differently when they are young. While buds grow linearly in both modes, cells that consistently generate spherical buds throughout their lifespan demonstrate greater efficacy in controlling bud size and growth rate at young ages. A three-dimensional chemical-mechanical model was developed and used to suggest and test hypothesized mechanisms of bud morphogenesis during aging. Experimentally calibrated simulations showed that tubular bud shape in one aging mode could be generated by locally inserting new materials at the bud tip guided by the polarized Cdc42 signal during the early stage of budding. Furthermore, the aspect ratio of the tubular bud could be stabilized during the late stage, as observed in experiments, through a reduction on the new cell surface material insertion or an expansion of the polarization site. Thus model simulations suggest the maintenance of new cell surface material insertion or chemical signal polarization could be weakened due to cellular aging in yeast and other cell types.

Significance Statement

Aging yeast exhibits two modes with different bud shapes. Experimental data analysis reveals that control of growth rate and bud size is more robust in cells aging in a spherical budding mode than in cells aging in a tubular budding mode. A computational model was developed and used in combination with experiments to test the hypothesized mechanisms underlying different types of budding in aging cells. Model simulations suggest that localized growth is sufficient to generate tubular budding and its aspect ratio can be stabilized through the regulation of chemical signals with an expanding polarization site or a decline on the new cell surface material insertion. Proposed mechanisms of morphological changes in aging yeast can be present in other cell types.
DELE1 promotes translation-associated homeostasis, growth, and survival in mitochondrial myopathy
Authors: Lin Hsin-Pin , Petersen Jennifer D. , Gilsrud Alexandra J. , Madruga Angelo , D’Silva Theresa M. , Huang Xiaoping , Shammas Mario K. , Randolph Nicholas P. , Li Yan , Jones Drew R. , Pacold Michael E. , Narendra Derek P.
Published: March 2024

Mitochondrial dysfunction causes devastating disorders, including mitochondrial myopathy. Here, we identified that diverse mitochondrial myopathy models elicit a protective mitochondrial integrated stress response (mt-ISR), mediated by OMA1-DELE1 signaling. The response was similar following disruptions in mtDNA maintenance, from knockout ofTfam, and mitochondrial protein unfolding, from disease-causing mutations in CHCHD10 (G58R and S59L). The preponderance of the response was directed at upregulating pathways for aminoacyl-tRNA biosynthesis, the intermediates for protein synthesis, and was similar in heart and skeletal muscle but more limited in brown adipose challenged with cold stress. Strikingly, models with early DELE1 mt-ISR activation failed to grow and survive to adulthood in the absence ofDele1, accounting for some but not all of OMA1’s protection. Notably, the DELE1 mt-ISR did not slow net protein synthesis in stressed striated muscle, but instead prevented loss of translation-associated proteostasis in muscle fibers. Together our findings identify that the DELE1 mt-ISR mediates a stereotyped response to diverse forms of mitochondrial stress and is particularly critical for maintaining growth and survival in early-onset mitochondrial myopathy.
Pulses of Class I PI3kinase activity identify the release and recapture of prey from neutrophil phagosomes
Authors: Muir Clare F , Reyes-Aldasoro Constantino Carlos , Ellett Felix E , Prajsnar Tomasz K , Ho Yin X , Bernut Audrey , Loynes Catherine A , Elworthy Stone , Bowden Kieran A , Cadbury Ashley J , Prince Lynne R , King Jason S , Condliffe Alison M , Renshaw Steven A
Published: March 2024

Class I PI3kinases coordinate the delivery of microbicidal effectors to the phagosome by forming the phosphoinositide lipid second messenger, phosphatidylinositol (3, 4, 5)-trisphosphate (PIP3). However, the dynamics of PIP3 in neutrophils during a bacterial infection are unknown. We have therefore developed anin vivo,live zebrafish infection model that enables visualisation of dynamic changes in Class 1 PI3kinases (PI3K) signalling on neutrophil phagosomes in real-time. We have identified that on approximately 12% of neutrophil phagosomes PHAkt-eGFP, a reporter for Class 1 PI3K signalling, re-recruits in pulsatile bursts. This phenomenon occurred on phagosomes containing structurally and morphologically distinct prey, includingStaphylococcus aureusandMycobacterium abscessus, and was dependent on the activity of the Class 1 PI3K isoform, PI3kinase γ. Detailed imaging suggested that ‘pulsing phagosomes’ represent neutrophils transiently reopening and reclosing phagosomes. This finding challenges the concept that phagosomes remain closed after prey engulfment and we propose that neutrophils occasionally use this alternative pathway of phagosome maturation to release phagosome contents and/or to restart phagosome maturation if digestion has stalled.
Diverse cell death signature based subtypes predict the prognosis and immune characteristics within glioma
Authors: Wang Lin , Song Jia , Xu Jing , Qin Yidan , Li Jia , Sun Yajuan , Jin Hui , Chen Jiajun , Wang Ziqian
Published: March 2024

Background

Cell death plays an essential role in the pathogenesis, progression, drug resistance and recurrence of glioma. Although multiple cell death pathways are involved in glioma development, there is lack of a stratification and prognostic modelling for glioma based on the integration of diverse genes for cell deaths.

Methods

In this study, 1254 diverse cell death (DCD)-related genes were assessed using the ConsensusClusterPlus assessment to identify DCD patterns in glioma. CIBERSORT, ssGSEA, and ESTIMATE algorithms were applied to evaluate immune microenvironment differences between subtypes. LASSO Cox regression was used to screen prognosis-related DCD genes, and a risk score model was constructed. TMB, TIDE, immune infiltration, and immunotherapy response was analyzed to evaluate the immune characteristics.

Results

Two DCD-related subgroups named Clusters 1 and 2, with distinct DCD levels, immune characteristics, and prognoses, were determined from glioma samples. A DCD-based risk score model was developed to assess DCD levels in glioma patients and divide patients into high- and low-risk groups. We found this risk model can be used as an independent prognostic factor for glioma patients. Notably, glioma patients with low risk scores exhibited subdued DCD activity, prolonged survival, and a favorable disposition towards benefiting from immune checkpoint blockade therapies.

Conclusions

This study established a novel signature classification and a risk model by comprehensively analyzing patterns of various DCDs to stratify glioma patients and to predict the prognosis and immune characteristics of glioma. We provided a theoretical basis for the clinical application of DCD-related genes in glioma prognosis and immunotherapy.
Limited Cell-Autonomous Anticancer Mechanisms in Long-Lived Bats
Authors: Athar Fathima , Zheng Zhizhong , Riquier Sebastien , Zacher Max , Alcock Dominic , Galazyuk Alex , Cooper Lisa Noelle , Schountz Tony , Wang Lin-Fa , Teeling Emma C. , Seluanov Andrei , Gorbunova Vera
Published: March 2024

Bats are remarkably long-lived for their size with many species living more than 20-40 years, suggesting that they possess efficient anti-aging and anti-cancer defenses. Here we investigated requirements for malignant transformation in primary bat fibroblasts in four bat species - little brown bat (Myotis lucifugus), big brown bat (Eptesicus fuscus), cave nectar bat (Eonycteris spelaea) and Jamaican fruit bat (Artibeus jamaicensis) – spanning the bat evolutionary tree and including the longest-lived genera. We show that bat fibroblasts do not undergo replicative senescence and express active telomerase. Bat cells displayed attenuated stress induced premature senescence with a dampened secretory phenotype. Unexpectedly, we discovered that bat cells could be readily transformed by only two oncogenic perturbations or “hits”: inactivation of either p53 or pRb and activation of oncogenic RASV12. This was surprising because other long-lived mammalian species require up to five hits for malignant transformation. Additionally, bat fibroblasts exhibited increased p53 and MDM2 transcript levels, and elevated p53-dependent apoptosis. The little brown bat showed a genomic duplication of the p53 gene. We hypothesize that bats evolved enhanced p53 activity through gene duplications and transcriptional upregulation as an additional anti-cancer strategy, similar to elephants. In summary, active telomerase and the small number of oncogenic hits sufficient to malignantly transform bat cells suggest thatin vivobats rely heavily on non-cell autonomous mechanisms of tumor suppression.
SIEGA the integrated genomic surveillance system of Andalusia, a One Health regional resource connected with the clinic
Authors: Casimiro-Soriguer Carlos S , Perez-Florido Javier , Robles Enrique A , Lara Maria , Aguado Andrea , Iglesias Manuel A Rodriguez , Lepe Jose A , Garcia Federico , Perez-Alegre Monica , Andujar Eloisa , Jimenez Victoria E , Camino Lola P , Lorusso Nicola , Ameyugo Ulises , Vazquez Isabel M , Lozano Carlota M , Chaves J. Alberto , Dopazo Joaquin
Published: March 2024

The One Health approach, recognizing the interconnectedness of human, animal, and environmental health, has gained significance amid emerging zoonotic diseases and antibiotic resistance concerns. This paper aims to demonstrate the utility of a collaborative tool, the SIEGA, for monitoring infectious diseases across domains, fostering a comprehensive understanding of disease dynamics and risk factors, highlighting the pivotal role of One Health surveillance systems. Raw whole-genome sequencing is processed through different species-specific open software that additionally reports the presence of genes associated to anti-microbial resistances and virulence. The SIEGA application is a Laboratory Information Management System, that allows customizing reports, detect transmission chains, and promptly alert on alarming genetic similarities. The SIEGA initiative has successfully accumulated a comprehensive collection of more than 1900 bacterial genomes, including Salmonella enterica, Listeria monocytogenes, Campylobacter jejuni, Escherichia coli, Yersinia enterocolitica and Legionella pneumophila, showcasing its potential in monitoring pathogen transmission, resistance patterns, and virulence factors. SIEGA enables customizable reports and prompt detection of transmission chains, highlighting its contribution to enhancing vigilance and response capabilities. Here we show the potential of genomics in One Health surveillance when supported by an appropriate bioinformatic tool. By facilitating precise disease control strategies and antimicrobial resistance management, SIEGA enhances global health security and reduces the burden of infectious diseases. The integration of health data from humans, animals, and the environment, coupled with advanced genomics, underscores the importance of a holistic One Health approach in mitigating health threats.
Enzymatic Assembly for CRISPR Split-Cas9 System: The Emergence of a Sortase-based Split-Cas9 Technology
Authors: Helalat Seyed Hossein , Kristinsdóttir Helga Thora , Petersen Astrid Dolinger , Téllez Rodrigo Coronel , Boye Mads Nordlund , Sun Yi
Published: March 2024

CRISPR-Cas9 has been widely used in scientific research and medical investigations as a pioneering technology. However, challenges such as the large size of the Cas9 sequence and potential off-target effects have impeded its widespread adoption. In response, various alternatives, such as split-Cas9 technology, have emerged. Split-Cas9 systems allow the large Cas9 sequence to be divided into two segments to aid in the delivery of the enzyme. Nevertheless, challenges persist in achieving precise control over the timing and location of Cas9 reassembly and activity to minimize off-target effects. This study presents an enzymatic-based split-Cas9 system, introducing a new approach utilizing the Sortase enzyme for the reconstitution of the full Cas9 protein. The developed method eliminates the need for chemical or physical induction and allows for precise genome editing in specific cells through the utilization of various specific promoters or targeted drug delivery. Experimental validation of the enzymatic system was conducted inE. coli, HEK cells, and Jurkat cells, demonstrating successful assembly and activity of the assembled Cas9 enzyme. In addition, this study explored the incorporation of nuclear localization signals, the evaluation of inducible promoters, and the delivery of the system’s components in mRNA or protein form. Furthermore, we investigated the potential of S/MAR minicircle technology instead of viral vectors within the system. Overall, we highlighted the feasibility and utility of the Sortase-based split-Cas9 system to enhance control and efficiency compared to traditional CRISPR-Cas9 approaches. Additionally, this study revealed the potential of using the Sortase enzyme for posttranslational modifications and protein assembly in human cells.
DistinctEscherichia colitranscriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection
Authors: Young Mark G. , Straub Timothy J. , Worby Colin J. , Metsky Hayden C. , Gnirke Andreas , Bronson Ryan A. , van Dijk Lucas R. , Desjardins Christopher A. , Matranga Christian , Qu James , Villicana Jesús Bazan , Azimzadeh Philippe , Kau Andrew , Dodson Karen W. , Schreiber Henry L. , Manson Abigail L. , Hultgren Scott J. , Earl Ashlee M.
Published: March 2024

Low-abundance members of microbial communities are difficult to study in their native habitats. This includesEscherichia coli, a minor, but common inhabitant of the gastrointestinal tract and opportunistic pathogen, including of the urinary tract, where it is the primary pathogen. While multi-omic analyses have detailed critical interactions between uropathogenicEscherichia coli(UPEC) and the bladder that mediate UTI outcome, comparatively little is known about UPEC in its pre-infection reservoir, partly due to its low abundance there (<1% relative abundance). To accurately and sensitively explore the genomes and transcriptomes of diverseE. coliin gastrointestinal communities, we developedE. coliPanSelect which uses a set of probes designed to specifically recognize and captureE. coli’s broad pangenome from sequencing libraries. We demonstrated the ability ofE. coliPanSelect to enrich, by orders of magnitude, sequencing data from diverseE. coliusing a mock community and a set of human stool samples collected as part of a cohort study investigating drivers of recurrent urinary tract infections (rUTI). Comparisons of genomes and transcriptomes betweenE. coliresiding in the gastrointestinal tracts of women with and without a history of rUTI suggest that rUTI gutE. coliare responding to increased levels of oxygen and nitrate, suggestive of mucosal inflammation, which may have implications for recurrent disease.E. coliPanSelect is well suited for investigations of nativein vivobiology ofE. coliin other environments where it is at low relative abundance, and the framework described here has broad applicability to other highly diverse, low abundance organisms.
Conserved helical motifs in the Ikaros IDR mediate NuRD interaction and transcriptional repression
Authors: Zhang Tianyi , Wang Yi-Fang , Montoya Alex , Nebioglu Nehir , Pallikonda Husayn A. , Georgieva Radina , Patrascan Ilinca , King James WD , Kramer Holger B. , Shliaha Pavel V. , Rueda David S. , Merkenschlager Matthias
Published: March 2024

The transcription factor IKZF1/Ikaros is essential for B cell development, and recurrently mutated in human B-ALL. Ikaros has been ascribed both activating and repressive functions via interactions with coactivator and corepressor complexes, but the relative abundance of Ikaros-associated coregulatory complexes and their contribution to Ikaros-mediated gene regulation are not well understood. To address this issue, we performed an unbiased identification of Ikaros-interacting proteins in pre-B cells, and found that Ikaros interacts overwhelmingly with corepressors and heterochromatin-associated proteins. Time-resolved analysis of transcription and chromatin state identified transcriptional repression as the immediate response to Ikaros induction. Transcriptional repression preceded transcriptional activation by several hours, and was accompanied by a rapid loss of chromatin accessibility and reduced levels of H3K27ac particularly at enhancers. Functional characterisation of intrinsically disordered regions in the Ikaros protein identified highly conserved helical motifs that mediate Ikaros association with the NuRD corepressor complex and contribute to the silencing of target genes in pre-B cells and antiproliferative functions of Ikaros in human B-ALL.
Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer
Authors: Liu Yang , Botelho João , Iranzo Jaime
Published: March 2024

Prokaryotes have evolved a wide repertoire of defense systems to prevent invasion by mobile genetic elements (MGE). However, because MGE are vehicles for the exchange of beneficial accessory genes, defense systems could consequently impede rapid adaptation in microbial populations. Here, we study how defense systems impact horizontal gene transfer (HGT) in the short and long terms. By combining comparative genomics and phylogeny-aware statistical methods, we quantified the association between the presence of 7 widespread defense systems and the abundance of MGE in the genomes of 196 bacterial and 1 archaeal species. We also calculated the differences in the rates of gene gain and loss between lineages that possess and lack each defense system. Our results show that the impact of defense systems on HGT is highly taxon- and system-dependent. CRISPR-Cas stands out as the defense system that most often associates with a decrease in the number of MGE and reduced gene acquisition. Timescale analysis reveals that defense systems must persist in a lineage for a relatively long time to exert an appreciable negative impact on HGT. In contrast, at short evolutionary times, defense systems, MGE, and gene gain rates tend to be positively correlated. Based on these results and given the high turnover rates experienced by defense systems, we propose that the inhibitory effect of most defense systems on HGT is masked by recent co-transfer events involving MGE.
FHOD-1/profilin-mediated actin assembly protects sarcomeres against contraction-induced deformation inC. elegans
Authors: Kimmich Michael J. , Sundaramurthy Sumana , Geary Meaghan A. , Lesanpezeshki Leila , Yingling Curtis V. , Vanapalli Siva A. , Littlefield Ryan S. , Pruyne David
Published: March 2024

Formin HOmology Domain 2-containing (FHOD) proteins are a subfamily of actin-organizing formins important for striated muscle development in many animals. We showed previously that absence of the sole FHOD protein, FHOD-1, fromC. elegansresults in thin body-wall muscles with misshapen dense bodies that serve as sarcomere Z-lines. We demonstrate here that actin polymerization by FHOD-1 is required for its function in muscle development, and that FHOD-1 cooperates with profilin PFN-3 for dense body morphogenesis, and profilins PFN-2 and PFN-3 to promote body-wall muscle growth. We further demonstrate dense bodies infhod-1andpfn-3mutants are less stable than in wild type animals, having a higher proportion of dynamic protein, and becoming distorted by prolonged muscle contraction. We also observe accumulation of actin depolymerization factor/cofilin homolog UNC-60B in body-wall muscle of these mutants. Such accumulations may indicate targeted disassembly of thin filaments dislodged from unstable dense bodies, and may account for the abnormally slow growth and reduced strength of body-wall muscle infhod-1mutants. Overall, these results show the importance of FHOD protein-mediated actin assembly to forming stable sarcomere Z-lines, and identify profilin as a new contributor to FHOD activity in striated muscle development.
High resolution live cell imaging to define ultrastructural and dynamic features of the halotolerant yeastDebaryomyces hansenii
Authors: Xelhuantzi Martha S.C. , Ghete Daniel , Milburn Amy , Ioannou Savvas , Mudd Phoebe , Calder Grant , Ramos José , O’Toole Peter J. , Genever Paul G. , MacDonald Chris
Published: March 2024

Although some budding yeasts have proved tractable and intensely studied models, others are more recalcitrant.Debaryomyces hansenii, an important yeast species in food and biotechnological industries with curious physiological characteristics, has proved difficult to manipulate genetically and remains poorly defined. To remedy this, we have combined live cell fluorescent dyes with high resolution imaging techniques to define the sub-cellular features ofD. hansenii, such as the mitochondria, nuclei, vacuoles and the cell wall. Using these tools, we define biological processes like the cell cycle, organelle inheritance and different membrane trafficking pathways ofD. hanseniifor the first time. Beyond this, reagents designed to studySaccharomyces cerevisiaeproteins were used to access proteomic information aboutD. hansenii. Finally, we optimised the use of label free holotomography to image yeast, defining the physical parameters and visualising sub-cellular features like membranes and vacuoles. Not only does this work shed light onD. hanseniibut this combinatorial approach serves as a template for how other cell biological systems, which are not amenable to standard genetic procedures, can be studied.
Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes
Authors: Yu Wenjuan , Luo Haohui , Yang Jinbao , Zhang Shengchen , Jiang Heling , Zhao Xianjia , Hui Xingqi , Sun Da , Li Liang , Wei Xiu-qing , Lonardi Stefano , Pan Weihua
Published: March 2024

Pacific Biosciences (PacBio) HiFi sequencing technology generates long reads (>10 kbp) with very high accuracy (<0.01% sequencing error). Although several de novo assembly tools are available for HiFi reads, there are no comprehensive studies on the evaluation of these assemblers. We evaluated the performance of 11 de novo HiFi assemblers on (1) real data for three eukaryotic genomes; (2) 34 synthetic data sets with different ploidy, sequencing coverage levels, heterozygosity rates, and sequencing error rates; (3) one real metagenomic data set; and (4) five synthetic metagenomic data sets with different composition abundance and heterozygosity rates. The 11 assemblers were evaluated using quality assessment tool (QUAST) and benchmarking universal single-copy ortholog (BUSCO). We also used several additional criteria, namely, completion rate, single-copy completion rate, duplicated completion rate, average proportion of largest category, average distance difference, quality value, run-time, and memory utilization. Results show that hifiasm and hifiasm-meta should be the first choice for assembling eukaryotic genomes and metagenomes with HiFi data. We performed a comprehensive benchmarking study of commonly used assemblers on complex eukaryotic genomes and metagenomes. Our study will help the research community to choose the most appropriate assembler for their data and identify possible improvements in assembly algorithms.
The African Turquoise Killifish: A Scalable Vertebrate Model for Aging and Other Complex Phenotypes
Authors: Boos Felix , Chen Jingxun , Brunet Anne
Published: March 2024

The African turquoise killifishNothobranchius furzeriis currently the shortest-lived vertebrate that can be bred in captivity. Because of its short life span of only 4–6 months, rapid generation time, high fecundity, and low cost of maintenance, the African turquoise killifish has emerged as an attractive model organism that combines the scalability of invertebrate models with the unique features of vertebrate organisms. A growing community of researchers is using the African turquoise killifish for studies in diverse fields, including aging, organ regeneration, development, “suspended animation,” evolution, neuroscience, and disease. A wide range of techniques is now available for killifish research, from genetic manipulations and genomic tools to specialized assays for studying life span, organ biology, response to injury, etc. This protocol collection provides detailed descriptions of the methods that are generally applicable to all killifish laboratories and those that are limited to specific disciplines. Here, we give an overview of the features that render the African turquoise killifish a unique fast-track vertebrate model organism.
Prospects for testing
CPT
and Lorentz symmetry with deuterium ground-state Zeeman-hyperfine transitions
Authors: Vargas Arnaldo J.
Published: March 2024

This work presents a model for testing Lorentz and CPT symmetry through sidereal-variation studies of the hyperfine-Zeeman deuterium ground-state transition frequencies. It represents an advancement over previous models by using a well-established deuteron wave function parametrization to calculate contributions from nucleon Lorentz-violating operators toward the Lorentz-violating frequency shift. Furthermore, this work extends the analysis beyond the zeroth-boost order previously considered. This study centers on deuterium’s potential for testing Lorentz-violating nonminimal terms. Specifically, it compares the prospects of an ongoing deuterium experiment with the current best limits on nonminimal coefficients. The conclusion drawn is that the deuterium experiment holds the potential to enhance and establish first-time limits on nonminimal proton, neutron, and electron SME coefficients, marking it as a valuable experiment in the current worldwide systematic search for Lorentz and CPT violation.

Published by the American Physical Society
2024
Long-lived heavy neutral leptons at lepton colliders as a probe of left-right-symmetric models
Authors: Urquía-Calderón Kevin A.
Published: March 2024

Left-right symmetric models (LRSM) were proposed to reconcile the apparent parity violation in weak interactions with our intrinsic notion of fundamental parity symmetry. It was quickly realized that LRSM offers a viable framework for explaining neutrino masses by incorporating right-handed neutrinos, N, into its spectrum. In this study, we investigate for the first time the potential of future lepton colliders (including the FCC-ee, CEPC, ILC, CLIC, and a muon collider) to detect signals stemming from N’s, focusing primarily on displaced vertex signals, and on prompt signals to a lesser degree. Our results demonstrate that these signals can effectively probe the characteristic scales of LRSM, providing evidence that would be unobtainable through any other experimental means.

Published by the American Physical Society
2024
Drop encapsulation and bubble bursting in surfactant-laden flows in capillary channels
Authors: Pico P. , Kahouadji L. , Shin S. , Chergui J. , Juric D. , Matar O. K.
Published: March 2024

We present a parametric study of the unsteady phenomena associated with the flow of elongated gas bubbles traveling through liquid-filled square capillaries under high Weber number conditions. These conditions induce the formation of an indentation at the back of the bubble that commonly gives way to a deep reentrant liquid jet penetrating the bubble. Subsequent steps include pinch-off events in the penetrating liquid to generate one or multiple encapsulated drops which may coalesce, in conjunction with the bursting of the bubble-liquid interface by either the liquid jet or the drops. Some of these interfacial instabilities have previously been reported experimentally and numerically for liquid-liquid flow in microchannels. We carry out three-dimensional direct numerical simulations based on a hybrid interface-tracking/level-set method capable of accounting for the presence and dynamic exchange of surfactants between the liquid bulk phase and the liquid-gas interface. Our results indicate that the delicate interplay among inertia, capillarity, viscosity, surfactant adsorption/desorption kinetics, and Marangoni stresses has a dramatic influence over the nonaxisymmetric morphological structures of the encapsulated drops-elongated bubble. This strong coupling also influences the pinch-off time, penetration depth of the liquid, and number, size, and velocity of the encapsulated drops across the bubble. The observed phenomena are summarized in three main morphological regimes based on surfactant-related parameters and dimensionless groups. A discussion of the flow regime maps is also provided.

Published by the American Physical Society
2024
Multiparticle Factorization and the Rigidity of String Theory
Authors: Arkani-Hamed Nima , Cheung Clifford , Figueiredo Carolina , Remmen Grant N.
Published: March 2024

Is string theory uniquely determined by self-consistency? Causality and unitarity seemingly permit a multitude of putative deformations, at least at the level of two-to-two scattering. Motivated by this question, we initiate a systematic exploration of the constraints on scattering from higher-point factorization, which imposes extraordinarily restrictive sum rules on the residues and spectra defined by a given amplitude. These bounds handily exclude several proposed deformations of the string: the simplest “bespoke” amplitudes with tunable masses and a family of modified string integrands from “binary geometry.” While the string itself passes all tests, our formalism directly extracts the three-point amplitudes for the low-lying string modes without the aid of worldsheet vertex operators.

Published by the American Physical Society
2024
Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation
Authors: Sack Stefan H. , Egger Daniel J.
Published: March 2024

Quantum computers are increasing in size and quality but are still very noisy. Error mitigation extends the size of the quantum circuits that noisy devices can meaningfully execute. However, state-of-the-art error mitigation methods are hard to implement and the limited qubit connectivity in superconducting qubit devices restricts most applications to the hardware's native topology. Here we show a quantum approximate optimization algorithm (QAOA) on nonplanar random regular graphs with up to 40 nodes enabled by a machine learning-based error mitigation. We use a swap network with careful decision-variable-to-qubit mapping and a feed-forward neural network to optimize a depth-two QAOA on up to 40 qubits. We observe a meaningful parameter optimization for the largest graph which requires running quantum circuits with 958 two-qubit gates. Our paper emphasizes the need to mitigate samples, and not only expectation values, in quantum approximate optimization. These results are a step towards executing quantum approximate optimization at a scale that is not classically simulable. Reaching such system sizes is key to properly understanding the true potential of heuristic algorithms like QAOA.

Published by the American Physical Society
2024