bluuebunny/crossref_metadata_2025 huggingface dataset:
The efficacy of rituximab plus belimumab or telitacicept in refractory lupus nephritis
Authors: Chen Yiting , Shi Nan , Lei Xin , Ren Pingping , Lan Lan , Chen Liangliang , Wang Yaomin , Xu Ying , Lin Yuxin , Chen Jianghua , Han Fei
Published: December 2023

Objective

Lupus nephritis is a severe and common complication of systemic lupus erythematosus (SLE). The pathogenesis of lupus nephritis is characterized by B-cell activation and autoantibody formation. Rituximab and belimumab, as well as telitacicept, target B cells through different mechanisms, potentially exerting a synergistic effect in the treatment of lupus nephritis. This study aims to investigate the efficacy and safety of treatment with rituximab followed by belimumab or telitacicept in the management of refractory lupus nephritis.

Methods

We conducted a single-center, open-label, retrospective study, including 25 patients with refractory lupus nephritis. All patients received combination therapy with rituximab in individualized dosages to achieve peripheral B-cell depletion, and then followed by belimumab or telitacicept. The follow-up period was at least 12 months, and the primary end point was renal remission rate at the last follow-up.

Results

During a median follow-up of 19 (13, 29) months, 20 of 25 (80%) patients achieved objective remission (OR), including 19 (76%) patients achieved complete renal response (CRR). After rituximab (712 ± 416mg in average), 18 patients received belimumab and seven patients received telitacicept. In the rituximab plus telitacicept group, all patients achieved CRR; while in the rituximab plus belimumab group, 12 (66.7%) patients achieved CRR and 13 (72.2%) patients achieved OR. The mean SLEDAI-2K score decreased from 15 ± 6 to 6 ± 6, representing an average reduction of 60%. At the last follow-up, 18/25 (72%) had prednisone ≤ 5 mg/d or even discontinued prednisone use. Adverse effects were mainly immunoglobulin deficiency, respiratory tract infection, urinary tract infections, and rash. No death occurred.

Conclusions

Rituximab followed by belimumab or telitacicept may be effective in inducing remission in refractory lupus nephritis, with tolerable adverse effects.
Shelterin dysfunction promotes CD4+ T cell senescence in Behçet’s disease
Authors: Shi Jing , Zhang Menghao , Zhang Lili , Yu Xin , Sun Luxi , Liu Jinjing , Zhao Yan , Zheng Wenjie
Published: December 2023

Objectives

To investigate the potential role of shelterin dysfunction in naïve CD4+ T cells in the pathogenesis of Behçet’s disease (BD).

Methods

Naïve CD4+ T cells were isolated from 40 BD patients and 40 sex- and age-matched healthy controls (HC). Senescent profiles, shelterin subunits expression, telomere length, telomerase activity and critical DNA damage response (DDR) were evaluated. Telomere repeat factor-2 (TRF2) silencing was conducted for further validation.

Results

Compared with HC, BD patients had significantly decreased naïve CD4+ T cells, increased cell apoptosis, senescence, and productions of TNF-α and IFN-γ upon activation. Notably, BD naïve CD4+ T cells had shortened telomere, impaired telomerase activity, and expressed lower levels of shelterin subunits TRF2, TRF1- and TRF2-Interacting Nuclear Protein 2 (TIN2) and Repressor/Activator Protein 1 (RAP1). Furthermore, BD naïve CD4+ T cells exhibited significantly increased DDR, evidenced by elevated phosphorylated ataxia telangiectasia (AT) mutated (pATM), phosphorylated p53 (pp53) and p21. Finally, TRF2 silencing markedly upregulated DDR, apoptosis and proinflammatory cytokines production in HC naïve CD4+ T cells.

Conclusion

Our study demonstrated that TRF2 deficiency in BD naïve CD4+ T cells promoted cell apoptosis and senescence, leading to proinflammatory cytokines overproduction. Therefore, restoring TRF2 might be a promising therapeutic strategy for BD.
The Effect of Bacille Calmette-Guérin Vaccination on the Composition of the Intestinal Microbiome in Neonates From the MIS BAIR Trial
Authors: Zimmermann Petra , Pittet Laure F. , Jakob William , Messina Nicole L. , Falquet Laurent , Curtis Nigel
Published: December 2023

Introduction:

The early-life intestinal microbiome plays an important role in the development and regulation of the immune system. It is unknown whether the administration of vaccines influences the composition of the intestinal microbiome.

Objective:

To investigate whether Bacille Calmette-Guérin (BCG) vaccine given in the first few days of life influences the abundance of bacterial taxa and metabolic pathways in the intestinal microbiome at 1 week of age.

Methods:

Healthy, term-born neonates were randomized at birth to receive BCG or no vaccine within the first few days of life. Stool samples were collected at 1 week of age from 335 neonates and analyzed using shotgun metagenomic sequencing and functional analyses.

Results:

The composition of the intestinal microbiome was different between neonates born by cesarean section (CS) and those born vaginally. Differences in the composition between BCG-vaccinated and BCG-naïve neonates were only minimal. CS-born BCG-vaccinated neonates had a higher abundance of Staphylococcus lugdunensis compared with CS-born BCG-naïve neonates. The latter had a higher abundance of Streptococcus infantis and Trabulsiella guamensis. Vaginally-born BCG-vaccinated neonates had a higher abundance of Clostridiaceae and Streptococcus parasanguinis compared with vaginally-born BCG-naïve neonates, and a lower abundance of Veillonella atypica and Butyricimonas faecalis. Metabolic pathways that were differently abundant between BCG-vaccinated and BCG-naïve neonates were mainly those involved in sugar degradation and nucleotide/nucleoside biosynthesis.

Conclusion:

BCG given in the first few days of life has little effect on the composition of the intestinal microbiome at 1 week of age but does influence the abundance of certain metabolic pathways.
Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data
Authors: Sutcliffe Steven G. , Kraemer Susanne A. , Ellmen Isaac , Knapp Jennifer J. , Overton Alyssa K. , Nash Delaney , Nissimov Jozef I. , Charles Trevor C. , Dreifuss David , Topolsky Ivan , Baykal Pelin I. , Fuhrmann Lara , Jablonski Kim P. , Beerenwinkel Niko , Levy Joshua I. , Olabode Abayomi S. , Becker Devan G. , Gugan Gopi , Britnell Erin , Poon Art F.Y. , Valieris Renan , Drummond Rodrigo D. , Defelicibus Alexandre , Dias-Neto Emmanuel , Rosales Rafael A. , da Silva Israel Tojal , Orfanou Aspasia , Psomopoulos Fotis , Pechlivanis Nikolaos , Pipes Lenore , Chen Zihao , Baaijens Jasmijn A. , Baym Michael , Shapiro B. Jesse
Published: December 2023

Wastewater-based surveillance (WBS) is an important epidemiological and public health tool for tracking pathogens across the scale of a building, neighbourhood, city, or region. WBS gained widespread adoption globally during the SARS-CoV-2 pandemic for estimating community infection levels by qPCR. Sequencing pathogen genes or genomes from wastewater adds information about pathogen genetic diversity which can be used to identify viral lineages (including variants of concern) that are circulating in a local population. Capturing the genetic diversity by WBS sequencing is not trivial, as wastewater samples often contain a diverse mixture of viral lineages with real mutations and sequencing errors, which must be deconvoluted computationally from short sequencing reads. In this study we assess nine different computational tools that have recently been developed to address this challenge. We simulated 100 wastewater sequence samples consisting of SARS-CoV-2 BA.1, BA.2, and Delta lineages, in various mixtures, as well as a Delta-Omicron recombinant and a synthetic “novel” lineage. Most tools performed well in identifying the true lineages present and estimating their relative abundances, and were generally robust to variation in sequencing depth and read length. While many tools identified lineages present down to 1% frequency, results were more reliable above a 5% threshold. The presence of an unknown synthetic lineage, which represents an unclassified SARS-CoV-2 lineage, increases the error in relative abundance estimates of other lineages, but the magnitude of this effect was small for most tools. The tools also varied in how they labelled novel synthetic lineages and recombinants. While our simulated dataset represents just one of many possible use cases for these methods, we hope it helps users understand potential sources of noise or bias in wastewater sequencing data and to appreciate the commonalities and differences across methods.
Translationally active soil microorganisms during substrate-induced respiration
Authors: Camillone Nina Rose , Bruns Mary Ann Victoria , Román Raúl , Wasner Daniel , Couradeau Estelle
Published: December 2023

Soil microorganisms carry out many processes that are fundamental to soil functions. Among the millions of microbial cells present in a gram of soil, however, less than 2% are commonly estimated to be active at any point in time. Because the respiratory response of a bulk soil to carbon substrate addition would be expected to reflect the number of active cells, we hypothesized a positive correlation between active cells and soil respiration rates during substrate-induced respiration (SIR) assays. To test this, we monitored respiration and active cell counts during 24-h incubations of agricultural soil subsamples after treating with two carbon substrates or a water-only control. We enumerated active cells with the Bioorthogonal Non-canonical Amino Acid Tagging (BONCAT) method. BONCAT provides a labeled amino acid for active cells to incorporate into newly synthesized proteins, which can then be tagged with a fluorescent dye to enable enumeration by flow cytometry. Both respiration rates and active cell counts increased over time and were positively correlated with each other after 6 h of incubation. After 24 h, increases in active cells were proportionally greater than increases in respiration. Additionally, carbon-amended soils had higher respiration rates than water-only soils with similar active cell counts, suggesting differences in carbon use efficiency. Our study documents for the first time the respiratory response fromin-situmicrobial activation induced by substrate amendment of soil within 6 h, a short enough timescale to exclude most cell replication. This study also demonstrates that the correlation between active cell numbers and respiration is substrate-dependent.

IMPORTANCE

While many critical ecosystem services provided by soil are known to rely on microbial activity, the soil microbial community largely remains a black box. While respiration is a common indicator of bulk soil microbial activity, this study demonstrates that the relationship between respiration and the number of active cells differs based on available carbon substrates. Advancing knowledge in this area will both enable better interpretation of biological soil tests by land managers and inform researchers modeling contributions of soil microbial respiration to global carbon dynamics.
PARP inhibitors enhance reovirus-mediated cell killing through the death-inducing signaling complex (DISC) with an associated NF-κB-regulated immune response
Authors: Kyula-Currie Joan , Roulstone Victoria , Wright James , Butera Francesca , Legrand Arnaud , Elliott Richard , McLaughlin Martin , Bozhanova Galabina , Krastev Dragomir , Pettitt Stephen , Tenev Tencho , Dillon Magnus , Foo Shane , Patin Emmanuel , Jennings Victoria , Chan Charleen , Appleton Elizabeth , Pedersen Malin , Rullan Antonio , Choudhary Jyoti , Bakal Chris , Meier Pascal , Lord Christopher J , Melcher Alan , Harrington Kevin
Published: December 2023

Oncolytic Reovirus type 3 Dearing (RT3D), is a naturally occurring double-stranded (ds) RNA virus that is under development as an oncolytic immunotherapy We used an unbiased high-throughput cytotoxicity screen of different targeted therapeutic agents with the aim of identifying potential drug-viral sensitizers to enhance RT3D tumour killing. Talazoparib, a clinical poly(ADP)-ribose polymerase 1 (PARP-1) inhibitor, was identified as a top hit and found to cause profound sensitisation to RT3D. This effect was not seen with other classes of oncolytic virus and was not mediated by enhanced viral replication or PARP inhibitor-related effects on the DNA damage response.

RT3D interacts with retinoic acid-induced gene-1 (RIG-I) and activates PARP-1, with consequent PARylation of components of the extrinsic apoptosis pathway. Pharmacological and genetic inhibition of PARP-1 abrogates this PARylation and increases levels of extrinsic apoptosis, NF-kB signalling and pro-inflammatory cell death. Direct interaction between PARP-1 and RIG-I following RT3D/talazoparib treatment is a key factor in activating downstream signaling pathways that lead to IFN-β and TNF-α/TRAIL production which, in turn, amplify the therapeutic effect through positive feedback. Critically, it was possible to phenocopy the effect of RT3D through the use of non-viral ds-RNA therapy and RIG-I agonism. Inin vivostudies, we demonstrated profound combinatorial efficacy of RT3D and talazoparib in human A375 melanoma in immunodeficient mice. More impressively, in immunocompetent mouse models of 4434 murine melanoma, we achieved 100% tumour control and protection from subsequent tumour rechallenge with the combination regimen. Correlative immunophenotyping confirmed significant innate and adaptive immune activation with the combination of RT3D and PARP inhibition. Taken together, these data provide a clear line of sight to clinical translation of combined regimens of PARP inhibition or ds-RNA agonism, with either viral or non-viral agents, in tumour types beyond the relatively narrow confines of current licensed indications for PARP inhibition.
Lateralization of feeding behaviour in white-fronted lemur (Eulemur albifrons) and ring-tailed lemur (Lemur catta) in captivity
Authors: Calvo Heredia Laura , de Miguel Águeda Francisco Javier
Published: December 2023

Functional cerebral asymmetry is reflected in the lateralization of some behavioural patterns in many vertebrate species. In primates, behavioural lateralization has been related to both life style and age and sex, and it affects behaviours such as feeding and other tasks that require precision movements.

We have studied feeding lateralization concerning the use of right and left hand to take the food in two species of lemurs, the mainly arboreal white-fronted lemur and the more terrestrial ring-tailed lemur, taking also account the age and the sex of the individuals. Half of the white-fronted lemurs (7 of 14) showed lateralization in feeding, while only a few ring-tailed lemurs (3 of 19) showed it. In the first species, a light bias seems to emerge (5 individuals used mostly the right hand for taking the food, while only 2 used mainly the left hand), while in the second species no bias could really be appreciated. No clear effect of age and sex on the presence and direction of lateralization could be evidenced.

The results somehow contrast with what the postural theory of lateralization postulates about the preferential use of the right hand in terrestrial species.
IRAK4 autophosphorylation controls inflammatory signaling by activating IRAK oligomerization
Authors: Srikanth Niranjan , Deliz-Aguirre Rafael , Gola Deepika Kumari , Bilay Margaux , Ziska Elke , Taylor Marcus J.
Published: December 2023

The controlled oligomerization of signaling proteins is an essential feature of many inflammatory signaling pathways. An example is IL-1 receptor signaling, which relies on the oligomerization of the Death Domain (DD)-containing proteins MyD88 and IRAK family kinases. This process leads to the assembly of the Myddosome signaling complex, and disrupting assembly holds potential for anti-inflammatory treatments. However, IRAKs’ signaling activity is also regulated by auto-/trans-phosphorylation, and it is unclear if these processes operate at or downstream of Myddosome assembly. Here, we find that the initial stage of Myddosome assembly is solely controlled by MyD88:IRAK4 DD interactions. In later stages, IRAK4 auto-phosphorylation serves as a switch, regulating IRAK1/2/3 incorporation and DD oligomerization. Small molecule inhibitors of IRAK4 kinase activity block this later stage of assembly, explaining how they dampen inflammatory signaling. Our data reveals IRAK4 auto-phosphorylation as an energy-dependent switch activating the heterotypic assembly of IRAKs’ DDs and downstream inflammatory IL-1 signaling. This highlights how a signaling cascade integrates phosphorylation and protein oligomerization steps.
Characterization and hierarchy of the spermatogonial stem cell compartment in human spermatogenesis by spectral cytometry using a 16-colors panel
Authors: Lapoujade C. , Blanco M. , Givelet M. , Gille A.S , Allemand I. , Lenez L. , Thiounn N. , Roux S. , Wolf J.P. , Patrat C. , Riou L. , Barraud-Lange V. , Fouchet P.
Published: December 2023

About one in six couples experience fertility problems, and male infertility accounts for about half of these cases. Spermatogenesis originates from a small pool of spermatogonial stem cells (SSCs), which are of interest for the treatment of infertility but remain poorly characterized in humans. Using multiparametric spectral flow cytometric analysis with a 16-colours (16-C) panel of cell markers, we identify novel markers of SSCs and provide insights into unravelling and resolving the heterogeneity of the human spermatogonial cells. This 16-C panel of markers allowed the identification of a primitive SSCs state with the β-2M−CD51/61−ITGA6+SSEA4+TSPAN33+THY1+CD9+EPCAMmedCD155+CD148+CD47highCD7highphenotype, with a profile close to the most primitive SSCs states 0 and SSC1-B previously defined by sc-RNAseq approach. The hierarchy of events in the spermatogonial stem cell and progenitor compartment of human spermatogenesis has been delineated. This highlights the importance of a multi-parametric and spectral cytometry approach. The in-depth characterization of testicular cells should help to overcome the lack of stem cell knowledge, that hinders the understanding of the regenerative potential of SSCs, and is a critical parameter for the successful development of new SSCs-based cell therapies.
A new guest to the blood feast: a novel symbiotic lineage associated with a haematophagous leech from the genusHaementeria
Authors: Sosa-Jiménez Víctor Manuel , Kvist Sebastian , Manzano-Marín Alejandro , Oceguera-Figueroa Alejandro
Published: December 2023

Similarly to other strict blood-feeders, leeches from theHaementeriagenus (Hirudinida: Glossiphoniidae) have established a symbiotic association with bacteria harboured intracellularly in oesophageal bacteriomes. Previous genome sequence analyses of these endosymbionts revealed co-divergence with their hosts, a strong genome reduction, and a simplified metabolism largely dedicated to the production of B vitamins, which are nutrients lacking from a blood diet.CandidatusProvidencia siddallii has been identified as the obligate nutritional endosymbiont of a monophyletic clade of Mexican and South AmericanHaementeriaspp. Nonetheless, given a lack of molecular investigations, the identity of the symbiont housed in the bacteriomes of its sister clade of Central and South American congeners remained unknown. In this work, we report on a novel bacterial endosymbiont found in a representative from thisHaementeriaclade. We found that this symbiont lineage has evolved from within thePluralibactergenus, known mainly from clinical, but also environmental strains. Similarly toCa. Providencia siddallii, theHaementeria-associatedPluralibactersymbiont displays clear signs of genome reduction, accompanied by an A+T-biased sequence composition. Genomic analysis of its metabolic potential revealed a retention of pathways related to B vitamin biosynthesis, supporting its role as a nutritional endosymbiont. Finally, comparative genomics of bothHaementeriasymbiont lineages suggests that the ancientProvidenciasymbiont was likely replaced by the novelPluralibacterone, thus constituting the first reported case of nutritional symbiont replacement in a leech without morphological changes in the bacteriome.
Sopa: a technology-invariant pipeline for analyses of image-based spatial-omics
Authors: Blampey Quentin , Mulder Kevin , Dutertre Charles-Antoine , Gardet Margaux , André Fabrice , Ginhoux Florent , Cournède Paul-Henry
Published: December 2023

Spatial-omics data allow in-depth analysis of tissue architectures, opening new opportunities for biological discovery. In particular, imaging techniques offer single-cell resolutions, providing essential insights into cellular organizations and dynamics. Yet, the complexity of such data presents analytical challenges and demands substantial computing resources. Moreover, the proliferation of diverse spatial-omics technologies, such as Xenium, MERSCOPE, CosMX in spatial-transcriptomics, and MACSima and PhenoCycler in multiplex imaging, hinders the generality of existing tools. We introduce Sopa (https://github.com/gustaveroussy/sopa), a technology-invariant, memory-efficient pipeline with a unified visualizer for all image-based spatial omics. Built upon the universal SpatialData framework, Sopa optimizes tasks like segmentation, transcript/channel aggregation, annotation, and geometric/spatial analysis. Its output includes user-friendly web reports and visualizer files, as well as comprehensive data files for in-depth analysis. Overall, Sopa represents a significant step toward unifying spatial data analysis, enabling a more comprehensive understanding of cellular interactions and tissue organization in biological systems.
Multi-omics investigations uncover unique pathogenic markers in clinicalKlebsiella pneumoniaethat could be leveraged as novel antimicrobial targets
Authors: Swiatek Lena-Sophie , Surmann Kristin , Eger Elias , Müller Justus Ursus , Salazar Manuela Gesell , Guenther Sebastian , Werner Guido , Hübner Nils-Olaf , Bohnert Jürgen A. , Becker Karsten , Heiden Stefan E. , Völker Uwe , Schwabe Michael , Schaufler Katharina
Published: December 2023

Background

Klebsiella pneumoniae(KP), often multidrug-resistant (MDR), is a significant public health concern and frequently associated with various diseases including urinary-tract infection. In addition, in recent years, an increasing number of studies reports on the emergence of convergent KP that combine MDR with hypervirulence leading to severely limited treatment options and thus calling for alternative approaches.

Methods

In this study, we compared high-risk clonal KP lineages with less pathogenicKlebsiella variicola(KV) andKlebsiella quasipneumoniae(KQ) strains on multiple-omics levels and performed integrative data analysis to identify unique markers that could be subsequently leveraged as novel targets in alternative treatment strategies.

Results

Our initial genomic analysis revealed 107 genes as part of the patho-core genome in eight clinical KP that were associated with different metabolic pathways. Subsequent transcriptome and proteome analyses in infection-mimicking media demonstrated similar regulatory patterns among KP vs. otherKlebsiellastrains, again with metabolic responses playing a pivotal role. In total, we identified 193 KP-specific, differentially expressed genes on transcriptomic and/or proteomic levels. When then comparing these regulated genes to over 6,000 publicly availableKlebsiellagenomes, we identified unique markers either in KP genomes or adaptively regulated on transcriptomics and/or proteomics levels. An example for the latter was a gene cluster for the cellobiose phosphotransferase system that has been previously described in the context of bacterial virulence and biofilm formation.

Conclusion

In conclusion, our study not only highlights that KP strains demonstrate metabolic flexibility in response to particular environmental conditions, which is potentially important for their success as opportunistic pathogens, but identified unique KP-markers. Subsequent studies are needed to explore whether these markers might be prospectively used as novel anti-virulence targets, providing alternatives to traditional antibiotics.
Histone H2A variant H2A.B is enriched in transcriptionally active HSV-1 lytic chromatin
Authors: Flores Esteban , Saddoris Sarah M. , Owens Arryn K , Gibeault Rebecca , Depledge Daniel P. , Schang Luis M.
Published: December 2023

Herpes simplex virus 1 (HSV-1) transcription is restricted in latently infected neurons and the genomes are in mostly silenced chromatin, whereas all viral genes are transcribed in lytically infected cells, in which the genomes are dynamically chromatinized. Epigenetic regulation modulates HSV-1 transcription during lytic, latent, and reactivating infections, but the precise mechanisms are not fully defined. Nucleosomes are dynamic; they slide, breathe, assemble and disassemble. We and others have proposed that the most dynamic HSV-1 chromatin is transcriptionally competent whereas the least dynamic is silenced. However, the mechanisms yielding the unusually dynamic viral chromatin remain unknown. Histone variants affect nucleosome dynamics. The dynamics of H2A, H2A.X and macroH2A were enhanced in infected cells, whereas those of H2A.B uniquely decreased. We constructed stably transduced cells expressing tagged histone H2A, H2A.B, macroH2A, or H2B, which assembles the H2A/H2B nucleosome dimers with all H2A variants. All H2A variants, ectopic, and endogenous H2B, were assembled into HSV-1 chromatin evenly throughout the genome, but canonical H2A was relatively depleted from the viral chromatin whereas H2A.B was enriched in the most dynamic viral chromatin. When viral transcription was restricted, H2A.B became as depleted from the viral chromatin through the entire genome as H2A. We propose that lytic HSV-1 nucleosomes are enriched in the dynamic variant H2A.B/H2B dimers to promote HSV-1 chromatin dynamics and transcriptional competency, and conclude that the dynamics of HSV-1 chromatin are determined in part by the H2A variants.

Importance

HSV-1 transcription is epigenetically regulated during latent and lytic infections, and epigenetic inhibitors have been proposed as potential antiviral drugs to modulate latency and reactivation. However, the detailed mechanisms of regulation of HSV-1 transcription by epigenetics have not been fully characterized and may differ from those regulating cellular transcription. In particular, the lytic HSV-1 chromatin is unusually dynamic, whereas the latent silenced one is not, but the mechanisms resulting in the unique dynamics of the lytic chromatin remain unknown. Here we identify the enrichment on the highly dynamic histone 2A variant H2A in the most dynamic viral chromatin, which provides a mechanistic understanding for its unique dynamics. Future work to identify the mechanisms of enrichment in H2A.B on the viral chromatin may identify novel druggable epigenetic regulators that modulate HSV-1 latency and reactivation.
The ICF2 gene Zbtb24 specifically regulates the differentiation of B1 cellsviapromoting heme synthesis
Authors: Wang Jun , Gao He , Zhao Sai , Dai Xiao-Qiu , Qin Xiao-Yuan , Zheng Wei-Long , Zhu Can , Wang Hong-Min , Zhu Xue-Mei , Gong Fang-Yuan , Gao Xiao-Ming , Zhao Ying
Published: December 2023

Loss-of-function mutations ofZBTB24cause the Immunodeficiency, Centromeric Instability and Facial Anomalies syndrome 2 (ICF2). ICF2 is a rare autosomal recessive disorder with immunological defects in serum antibodies and circulating memory B cells, indicating an essential role of ZBTB24 in the terminal differentiation of B cells. Here we generated B-cell specific Zbtb24-deficient mice and systemically investigated its role in B cell development and function bothin vivoandin vitro. Zbtb24 is dispensable for B cell development & maintenance in naive mice. Surprisingly, B-cell specific deletion of Zbtb24 does not evidently compromise germinal center reactions and the resulting primary & secondary antibody responses induced by T-cell dependent antigens, but significantly inhibits T-cell independent antigen-elicited antibody productionsin vivo. At the cellular level, Zbtb24-deficiency specifically impedes the plasma cell differentiation of B1 cells without impairing their survival, activation and proliferationin vitro. Mechanistically, Zbtb24-ablation attenuates heme biosynthesis partially through mTORC1 in B1 cells, and addition of exogenous hemin abrogates the differentiation defects of Zbtb24-null B1 cells. Our study suggests that the defected B1 functions may contribute to recurrent infections in ICF2 patients, and discloses a B1-specific role of Zbtb24 in regulating plasma cell differentiation and antibody production, which is relevant for barrier defenses against invading pathogens.
Classification of iPSC-Derived Cultures Using Convolutional Neural Networks to Identify Single Differentiated Neurons for Isolation or Measurement
Authors: Patel Purva , Mohammed Ali Lina K , Kaushik Uma , Wright Mallory G , Green Kaylee P , Waligorski Jason E , Kremitzki Colin L , Bachman Graham W , Elia Serena N , Buchser William J
Published: December 2023

Understanding neurodegenerative disease pathology depends on a close examination of neurons and their processes. However, image-based single-cell analyses of neurons often require laborious and time-consuming manual classification tasks. Here, we present a machine learning approach leveraging convolutional neural network (CNN) classifiers that have the capability to accurately identify various classes of neuronal images, including single neurons. We developed the Single Neuron Identification Model 20-Class (SNIM20) which was trained on a dataset of induced pluripotent stem cell (iPSC)-derived motor neurons, containing over 12,000 images from 20 distinct classes. SNIM20 is built in TensorFlow and trained on images of differentiated iPSC cultures stained for nuclei and microtubules. This classifier demonstrated high predictive accuracy (AUC = 0.99) for distinguishing single neurons. Additionally, the 2-stage training framework can be used more broadly for cellular classification tasks. A variation was successfully trained on images of a human osteosarcoma cell line (U2OS) for single-cell classification (AUC = 0.99). While this framework was primarily designed for single-cell microraft-based identification and capture, it also works with cells in standard plate formats. We additionally explore the impact of specific fluorescent channels and brightfield images, class groupings, and transfer learning on the quality of the classification. This framework can both assist in high throughput neuronal or cellular identification and be used to train a custom classifier for the user’s needs.
Virus-like DNA tracers for characterizing wastewater-based pathogen monitoring systems
Authors: Gopal Anjali , Machtinger Ari N. , Wang Brian , Rice Daniel P. , Bradshaw William J. , McLaren Michael R. , Esvelt Kevin M.
Published: December 2023

Wastewater-based pathogen monitoring has recently become a ubiquitous method for tracking the abundance and evolution of pathogens in a community or port of entry. But accurate inference of disease incidence from wastewater remains challenging, in large part due to noise and bias arising from wastewater transport and measurement. We developed a new system of tracer particles designed to enhance wastewater monitoring of viral pathogens. These tracers, which consist of synthetic DNA barcodes packaged into non-infectious viral capsids, can be deposited at known amounts and times into the sewer system and measured in wastewater samples to assess features such as assay sensitivity, and the decay and delay in viral signal arising from a shedding event. Here we describe the design, construction, and initial characterization of a 25-plex tracer library. Our tracer library supports simultaneous measurement of up to 5 distinct tracers by qPCR and up to 25 distinct tracers by amplicon or metagenomic sequencing. We demonstrate experimentally that the tracers are biologically inert and exhibit good stability and qPCR-assay performance in wastewater. These features collectively suggest that barcoded, virus-like tracers have the required properties for high-accuracy, high-resolution characterization of wastewater monitoring systems.
Genetic Mapping of Monocyte Fate Decisions Following Myocardial Infarction
Authors: Koenig Andrew L , Kadyrov Farid F , Amrute Junedh M , Yang Steven , Weinheimer Carla J , Nigro Jessica M , Kovacs Attila , Smith Gabriella , Lavine Kory J
Published: December 2023

Inflammation contributes to the pathogenesis of myocardial infarction and heart failure and represents a viable therapeutic target. Monocytes and their progeny are highly abundant and display incredible functional diversity, serving as key determinants of myocardial inflammation and tissue repair. Much remains to be learned regarding mechanisms and signaling events that instruct monocyte fate decisions. We devised a genetic lineage tracing strategy usingCcr2crERT2Rosa26LSL-tdTomatomice in combination with single cell RNA-sequencing to map the differentiation trajectories of monocytes that infiltrate the heart after reperfused myocardial infarction. Monocytes are recruited to the heart early after injury and give rise to transcriptionally distinct and spatially restricted macrophage and dendritic cell-like subsets that are specified prior to extravasation and chronically persist within the myocardium. Pseudotime analysis predicted two differentiation trajectories of monocyte-derived macrophages that are partitioned into the border and infarct zones, respectively. Among these trajectories, we show that macrophages expressing a type I IFN responsive signature are an intermediate population that gives rise to MHC-IIhimacrophages, are localized within the border zone, and promote myocardial protection. Collectively, these data uncover new complexities of monocyte differentiation in the infarcted heart and suggest that modulating monocyte fate decisions may have clinical implications.
Metabolic cost for isometric force scales nonlinearly and predicts how humans distribute forces across limbs
Authors: Muralidhar Sriram Sekaripuram , Marin Nadja , Melick Colin , Alwan Aya , Wang Zhengcan , Baldwin Ross , Walcott Sam , Srinivasan Manoj
Published: December 2023

Muscles consume metabolic energy for force production and movement. A mathematical model of metabolic energy cost will be useful in predicting instantaneous costs during human exercise and in computing effort-minimizing movements via simulations. Previous in vivo data-derived models usually assumed either zero or linearly increasing cost with force, but a nonlinear relation could have significant metabolic or behavioural implications. Here, we show that metabolic cost scales nonlinearly with joint torque with an exponent of about 1.64, using calorimetric measurements of isometric squats. We then demonstrate that this metabolic nonlinearity is reflected in human behaviour: minimizing this nonlinear cost predicts how humans share forces between limbs in additional experiments involving arms and legs. This shows the utility of the nonlinear energy cost in predictive models and its generalizability across limbs. Finally, we show mathematical evidence that the same nonlinear metabolic objective may underlie force sharing at the muscle level.
Tissue of origin detection for cancer tumor using low-depth cfDNA samples through combination of tumor-specific methylation atlas and genome-wide methylation density in graph convolutional neural networks
Authors: Nguyen Trong Hieu , Doan Nhu Nhat Tan , Tran Trung Hieu , Huynh Le Anh Khoa , Doan Phuoc Loc , Nguyen Thi Hue Hanh , Nguyen Van Thien Chi , Nguyen Giang Thi Huong , Nguyen Hoai-Nghia , Giang Hoa , Tran Le Son , Phan Minh Duy
Published: December 2023

Background

Cell free DNA (cfDNA)-based assays hold great potential in detecting early cancer signals yet determining the tissue-of-origin (TOO) for cancer signals remains a challenging task. Here, we investigated the contribution of a methylation atlas to TOO detection in low depth cfDNA samples.

Methods

We constructed a tumor-specific methylation atlas (TSMA) using whole-genome bisulfite sequencing (WGBS) data from five types of tumor tissues (breast, colorectal, gastric, liver and lung cancer) and paired white blood cells (WBC). TSMA was used with a non-negative least square matrix factorization (NNLS) deconvolution algorithm to identify the abundance of tumor tissue types in a WGBS sample. We showed that TSMA worked well with tumor tissue but struggled with cfDNA samples due to the overwhelming amount of WBC-derived DNA. To construct a model for TOO, we adopted the multi-modal strategy and used as inputs the combination of deconvolution scores from TSMA with other features of cfDNA.

Results

Our final model comprised of a graph convolutional neural network using deconvolution scores and genome-wide methylation density features, which achieved an accuracy of 69% in a held-out validation dataset of 239 low-depth cfDNA samples.

Conclusions

In conclusion, we have demonstrated that our TSMA in combination with other cfDNA features can improve TOO detection in low-depth cfDNA samples.
Systematic screens for fertility genes essential for malaria parasite transmission reveal conserved aspects of sex in a divergent eukaryote
Authors: Sayers Claire , Pandey Vikash , Balakrishnan Arjun , Michie Katharine , Svedberg Dennis , Hunziker Mirjam , Calvo Mercedes Pardo , Choudhary Jyoti , Berntsson Ronnie , Billker Oliver
Published: December 2023

Sexual reproduction in malaria parasites is essential for their transmission to mosquitoes. It also offers a divergent eukaryote model to understand the evolution of sex. Through a panel of genetic screens, where each sex ofPlasmodium bergheiwas mutagenised separately with barcoded vectors, we identify 401 sex and transmission-related gene functions and define roles for hundreds of unstudied fertility genes as putative targets for transmission blocking interventions. The functional data provide a deeper understanding of female metabolic reprogramming, meiosis and the axoneme. We identify a protein complex of a SUN domain protein, SUN1, and a moonlighting putative allantoicase, ALLC1, that is essential for male fertility by linking the microtubule organising centre to the nuclear envelope and enabling mitotic spindle formation during male gametogenesis. Both proteins have orthologs in mouse testis, and the data point to an ancient role for atypical SUN domain proteins in fertility. Altogether, our data provide an unbiased picture of the molecular processes that underpin malaria parasite transmission but also highlight ancestral aspects of sex that have evolved close to the last eukaryotic common ancestor.
Dining in the daylight: Nocturnal rhinoceros beetles extend feeding periods on host trees with reduced sap exudation
Authors: Kanda Asahi , Shibata Ryo , Ueno Takahiro , Yamashita Namifu , Kojima Wataru
Published: December 2023

While the Japanese rhinoceros beetleTrypoxylus dichotomustypically feeds on the sap of the oakQuercus acutissimaand the crape myrtleLagerstroemia subcostataduring the night, it exhibits feeding activity both during the day and night when it utilizes the ash treeFraxinus griffithii. However, the mechanisms underlying the variations in temporal activity patterns remain unknown. We compared feeding rates (measured as body mass increments) and sap exudation rates amongF. griffithii, Q. acutissima, andL. subcostata. We found that beetles feeding onL. subcostataandQ. acutissimaexhibited significantly higher feeding rates than those feeding onF. griffithii. No significant differences in feeding rates were observed betweenL. subcostataandQ. acutissima. The sap exudation rate was significantly higher forQ. acutissimathan forF. griffithii. However, there were no significant differences in the sap exudation rates betweenF. griffithiiandL. subcostataor betweenQ. acutissimaandL. subcostata. These findings suggest that lower feeding rates onF. griffithiiprolong the feeding duration, resulting in daytime activity. While the low sap exudation inL. subcostataseems inconsistent with high feeding rates on this host, this apparent contradiction could be related to the extended duration of sap exudation.
Taking flight with food: investigating the determinants of user acceptance toward drone-based food delivery services in India
Authors: Kumar Sachin , Singh Bhagwan , Kumar Vinod , Chaudhuri Ranjan , Chatterjee Sheshadri , Vrontis Demetris
Published: December 2023

Purpose

The present study intends to discover and analyze the determinants of users' intention to use (ITU) drone-based online food delivery (OFD) services. The study mainly focuses on the drone-based food delivery system in India and its implications.

Design/methodology/approach

This study has used the purposive sampling method. With the support of the technology acceptance model (TAM) and the theory of planned behavior (TPB), a theoretical model was developed conceptually. Later, the model was validated using the partial least square-structure equation modeling (PLS-SEM) technique with consideration of 324 responses mainly from university students in Delhi- National Capital Region (NCR).

Findings

The findings reveal that all the determinants are positively and significantly related to ITU, except for perceived behavioral control that does not influence the consumer’s ITU drone-based OFD services. The study also shows that how food delivery system through drone can revolutionize the entire food delivery system in India.

Research limitations/implications

The present study has developed a unique model that can be used by practitioners, future researchers in this field and policymakers in government departments. The present study is limited to Delhi-NCR in India, and thus, there is an issue of generalizability in the present study.

Practical implications

This study has examined the future of food delivery system through drone-based system. Thus, the leaders in the food industry will be better positioned to understand consumers' intentions to use OFD services using drones and be able to make more informed decisions about investment in drone technology in their respective organizations.

Originality/value

The present study has combined both the technology adoption model and the TPB and developed a theoretical model. The study enriches the literature on drone-based OFD services. Since users' acceptance of OFD services using drones is an under-researched area, the present study will make a meaningful contribution to bring the body of literature in this domain.
Gender inequalities in unpaid public work: Retention, stratification and segmentation in the volunteer leadership of charities in England and Wales
Authors: Clifford David
Published: December 2023

While gender inequalities in employment (paid public work) and domestic and reproductive labour (unpaid private work) are a prominent focus within the sociological literature, gender inequalities in volunteering (unpaid public work) have received much less scholarly attention. We analyse a unique longitudinal dataset of volunteer leaders, that follows through time every individual to have served as a board member (trustee) for a charity in England and Wales between 2010 and 2023, to make three foundational contributions to our understanding of gender inequalities in unpaid public work. First, the salience of vertical gender stratification and horizontal gender segmentation in trusteeship shows that gendered inequalities in work extend to public work in general—encompassing unpaid public work, and not only paid public work. In terms of gender segmentation, we find that women are over‐represented as trustees in a small number of fields of charitable activity but under‐represented across the majority of fields. In terms of gender stratification, we find that women are under‐represented on the boards of the largest charities; under‐represented as chairs of trustee boards; and particularly under‐represented as chairs of the largest charities. Second, the dynamics underlying gendered differences in unpaid public work, which show higher rates of resignation for women trustees, resonate with research on paid employment which emphasises the importance of attrition to an understanding of how gendered inequalities in work are reproduced. This means that increasing the retention of women, not only the recruitment of women, becomes central to the policy agenda. Third, we show that there has been a decline in gender stratification and gender segmentation in trusteeship since 2010. This decline over time in gendered inequalities in unpaid public work provides an interesting counterpoint to influential research documenting a ‘stall’ in the reduction of gendered inequalities in paid employment.
Searching for desirable bodies: How recruiters value physically exertive extracurricular activities for graduate hiring at elite professional firms in China
Authors: Ren Ran
Published: December 2023

The field of research in evaluating and applying Bourdieu's theories has seen growing interests in studying how the formation and effect of cultural capital vary in different contexts and fields. While existing studies have increasingly focussed on evaluating the role of cultural capital in creating educational inequalities in the Chinese context, little is known about how activities and taste are valued in the Chinese labour market. Drawing on semi‐structured interviews with 73 recruiters in elite professional firms in China, this article presents a study on how recruiters interpret physically exertive extracurricular activities (ECAs) for graduate hiring. It shows that these ECAs were valorised for assessing individual qualities and competences in job interviews, while other cultural activities, leisure or tastes carried little value. The notion of the body appeared central to this valorisation, conferring symbolic value onto physical exertive ECAs. The value of these activities was twofold, serving to convey candidates' possession of physical and embodied capital, which resonated to the normative dimension of elite professional firms. Recruiters thus used these activities to seek new professional bodies consumable for demanding professional work and resonating with the normative discourses of professionalism. This study provides more nuanced understandings of cultural capital in a non‐Western context and the role of ECAs in elite hiring. It also contributes to the development of physical and embodied capital by integrating perspective that links the body with labour process and professional control.