bluuebunny/crossref_metadata_2025 huggingface dataset:
Sub-percentage measure of distances to redshift of 0.1 by a new cosmic ruler
Authors: Shi Yong , Chen Yanmei , Mao Shude , Gu Qiusheng , Wang Tao , Xia Xiaoyang , Zhang. Zhi-Yu
Published: August 2022

Distance-redshift diagrams probe expansion history of the Universe. We show that the stellar mass-binding energy (massE) relation of galaxies proposed in our previous study offers a new distance ruler at cosmic scales. By using elliptical galaxies in the main galaxy sample of the Sloan Digital Sky Survey Data Release 7, we construct a distance-redshift diagram over the redshift range from 0.05 to 0.2 with the massE ruler. The best-fit dark energy density is 0.675 ± 0.079  for flat Λ-cold dark matter (ΛCDM) model, consistent with those by other probes. At the median redshift of 0.11, the median distance is estimated to have a fractional error of 0.34 per cent, much lower than those by supernova (SN) Ia and baryonic acoustic oscillation (BAO) and even exceeding their future capability at this redshift. The above low-$\mathit{ z}$ measurement is useful for probing dark energy that dominates at the late Universe. For a flat dark energy equation of state model (flat wCDM), the massE alone constrains w to an error that is only a factor of 2.2, 1.7, and 1.3 times larger than those by BAO, SN Ia, and cosmic microwave background (CMB), respectively.
Patterns of failure after radiation therapy in primary spinal high-grade gliomas: A single institutional analysis
Authors: Upadhyay Rituraj , Khose Swapnil , Pokhylevych Halyna , Paulino Arnold C , McAleer Mary Frances , Ghia Amol , Li Jing , Yeboa Debra Nana , Loghin Monica , Harrison Rebecca , O’Brien Barbara , Kamiya-Matsuoka Carlos , De Groot John , Puduvalli Vinay K , Tatsui Claudio , Alvarez-Breckenridge Christopher , Prabhu Sujit , Rhines Larry , Zaky Wafik , Lin Frank , Weinberg Jeffery S , Fuller Gregory , Sandberg David I , Johnson Jason Michael , McGovern Susan L
Published: August 2022

Background

Primary spinal high-grade gliomas (S-HGG) are rare aggressive tumors; radiation therapy (RT) often plays a dominant role in management. We conducted a single-institution retrospective review to study the clinicopathological features and management of S-HGGs.

Methods

Patients with biopsy-proven S-HGG who received RT from 2001 to 2020 were analyzed for patient, tumor, and treatment characteristics. Kaplan–Meier estimates were used for survival analyses.

Results

Twenty-nine patients were identified with a median age of 25.9 years (range 1–74 y). Four patients had GTR while 25 underwent subtotal resection or biopsy. All patients were IDH wildtype and MGMT-promoter unmethylated, where available. H3K27M mutation was present in 5 out of 10 patients tested, while one patient harbored p53 mutation. Median RT dose was 50.4 Gy (range 39.6–54 Gy) and 65% received concurrent chemotherapy, most commonly temozolomide. Twenty-three (79%) of patients had documented recurrence. Overall, 16 patients relapsed locally, 10 relapsed in the brain and 8 developed leptomeningeal disease; only 8 had isolated local relapse. Median OS from diagnosis was 21.3 months and median PFS was 9.7 months. On univariate analysis, age, gender, GTR, grade, RT modality, RT dose and concurrent chemotherapy did not predict for survival. Patients with H3K27M mutation had a poorer PFS compared to those without mutation (10.1 m vs 45.1 m) but the difference did not reach statistical significance (P = .26).

Conclusions

The prognosis of patients with spinal HGGs remains poor with two-thirds of the patients developing distant recurrence despite chemoradiation. Survival outcomes were similar in patients ≤ 29 years compared to adults > 29 years. A better understanding of the molecular drivers of spinal HGGs is needed to develop more effective treatment options.
Impact of Innate Immunity, Endothelial Damage, and Metabolic Biomarkers on COVID-19 Severity and Mortality
Authors: Rocco Joseph M , Laghetti Paola , Di Stefano Mariantonietta , Sereti Irini , Ortega-Villa Ana , Wang Jing , Rupert Adam , Chironna Maria , Ye Peiying , Liu Xiangdong , Anderson Megan V , Burbelo Peter B , Fiore Jose Ramon , Saracino Annalisa , Lisco Andrea
Published: August 2022

In this study, abnormal levels of myeloid activation, endothelial damage, and innate immune markers were associated with severe coronavirus disease 2019 (COVID-19), while higher levels of metabolic biomarkers (irisin, leptin) demonstrated a protective effect. These data support a model for COVID-19 immunopathogenesis linking robust inflammation and endothelial damage in metabolically predisposed individuals.
Myometrial progesterone receptor determines a transcription program for uterine remodeling and contractions during pregnancy
Authors: Wu San-Pin , Wang Tianyuan , Yao Zheng-Chen , Peavey Mary C , Li Xilong , Zhou Lecong , Larina Irina V , DeMayo Francesco J
Published: August 2022

The uterine myometrium expands and maintains contractile quiescence before parturition. While the steroid hormone progesterone blocks labor, the role of progesterone signaling in myometrial expansion remains elusive. This study investigated the myometrial functions of the progesterone receptor, PGR. Pgr ablation in mouse smooth muscle leads to subfertility, oviductal embryo retention, and impaired myometrial adaptation to pregnancy. While gross morphology between mutant and control uteri are comparable, mutant uteri manifest a decrease of 76.6% oxytocin-stimulated contractility in a pseudopregnant context with a reduced expression of intracellular calcium homeostasis genes including Pde5a and Plcb4. At mid-pregnancy, the mutant myometrium exhibits discontinuous myofibers and disarrayed extracellular matrix at the conceptus site. Transcriptome of the mutant mid-pregnant uterine wall manifests altered muscle and extracellular matrix profiles and resembles that of late-pregnancy control tissues. A survey of PGR occupancy, H3K27ac histone marks, and chromatin looping annotates cis-acting elements that may direct gene expression of mid-pregnancy uteri for uterine remodeling. Further analyses suggest that major muscle and matrix regulators Myocd and Ccn2 and smooth muscle building block genes are PGR direct downstream targets. Cataloging enhancers that are topologically associated with progesterone downstream genes reveals distinctive patterns of transcription factor binding motifs in groups of enhancers and identifies potential regulatory partners of PGR outside its occupying sites. Finally, conserved correlations are found between estimated PGR activities and RNA abundance of downstream muscle and matrix genes in human myometrial tissues. In summary, PGR is pivotal to direct the molecular program for the uterus to remodel and support pregnancy.
Containing novel SARS-CoV-2 variants at source is possible with high-intensity sequencing
Authors: Brett Tobias S , Rohani Pejman
Published: August 2022

Throughout the COVID-19 pandemic, control of transmission has been repeatedly thwarted by the emergence of variants of concern (VOC) and their geographic spread. Key questions remain regarding effective means of minimizing the impact of VOC, in particular the feasibility of containing them at source, in light of global interconnectedness. By analysing a stochastic transmission model of COVID-19, we identify the appropriate monitoring requirements that make containment at source feasible. Specifically, precise risk assessment informed primarily by epidemiological indicators (e.g. accumulated hospitalization or mortality reports), is unlikely prior to VOC escape. Consequently, decision makers will need to make containment decisions without confident severity estimates. In contrast, successfully identifying and containing variants via genomic surveillance is realistic, provided sequence processing and dissemination is prompt.
SECANT: a biology-guided semi-supervised method for clustering, classification, and annotation of single-cell multi-omics
Authors: Wang Xinjun , Xu Zhongli , Hu Haoran , Zhou Xueping , Zhang Yanfu , Lafyatis Robert , Chen Kong , Huang Heng , Ding Ying , Duerr Richard H , Chen Wei
Published: August 2022

The recent advance of single cell sequencing (scRNA-seq) technology such as Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) allows researchers to quantify cell surface protein abundance and RNA expression simultaneously at single cell resolution. Although CITE-seq and other similar technologies have gained enormous popularity, novel methods for analyzing this type of single cell multi-omics data are in urgent need. A limited number of available tools utilize data-driven approach, which may undermine the biological importance of surface protein data. In this study, we developed SECANT, a biology-guided SEmi-supervised method for Clustering, classification, and ANnoTation of single-cell multi-omics. SECANT is used to analyze CITE-seq data, or jointly analyze CITE-seq and scRNA-seq data. The novelties of SECANT include (1) using confident cell type label identified from surface protein data as guidance for cell clustering, (2) providing general annotation of confident cell types for each cell cluster, (3) utilizing cells with uncertain or missing cell type label to increase performance, and (4) accurate prediction of confident cell types for scRNA-seq data. Besides, as a model-based approach, SECANT can quantify the uncertainty of the results through easily interpretable posterior probability, and our framework can be potentially extended to handle other types of multi-omics data. We successfully demonstrated the validity and advantages of SECANT via simulation studies and analysis of public and in-house datasets from multiple tissues. We believe this new method will be complementary to existing tools for characterizing novel cell types and make new biological discoveries using single-cell multi-omics data.
A computational approach to study the gap and barriers between science and policy
Authors: Li Nancy , Luczak-Roesch Markus , Donadelli Flavia
Published: August 2022

Research on the gap between science and policymaking and the barriers to utilizing science in policy remains controversial, since previous research methods have dominated data collection with perceived participant responses. This approach makes research findings applicable to particular contexts, particular participants, and particular times but cannot be generalized. We used a computational model to analyse linguistic text data from two communities and compared the results with self-reported research findings. The outcomes support that scientists and policymakers have their own linguistic characteristics, with scientists in the medical field preferring jargon and policymakers’ language containing public satisfaction pressures. Language representation also validates the existence of barriers in the use of science.
A Population-Based Study of Associations Among Child Screen Media Use, Social-Contextual Factors, and School Readiness
Authors: Griffith Shayl F. , Qiu Yuxi
Published: August 2022

Objective:

Results of studies examining relations between child media use and school readiness have been inconsistent. Importantly, studies often focus on a single outcome domain (e.g., academic, social, or behavioral), making the comparison of relative importance difficult; fail to account for confounding variables; and fail to investigate social-contextual moderators. This study investigated relations among child media use exposure, social-contextual factors, and multiple domains of school readiness in preschool-aged children.

Methods:

Multivariate regression analyses were used to examine relations between child media use and 3 domains of school readiness (early learning, social-emotional skills, and self-regulation), controlling for demographic and social-contextual factors, and to investigate differential susceptibility by examining family income and 4 social-contextual factors (sleep, exposure to adverse childhood events, frequency of shared reading, and parent stress) as moderators in a large US population–based sample (N = 9323) of 3 to 5 year olds.

Results:

After controlling for confounding variables, higher screentime was negatively related to children's social-emotional skills and self-regulation, but less so for early learning. Effect sizes were small. The relation between screentime and self-regulation was significantly moderated by family income, such that the relation was stronger for children from low-income backgrounds. No other evidence of significant moderation was found.

Conclusion:

Results add to evidence that the relation between screen media use and outcomes in young children is likely complex. Future work should prioritize examining impacts of screen media use on social and behavioral functioning to further inform the evaluation of relative benefits and costs of child screen media use.
Molecular mechanism of dynein-dynactin activation by JIP3 and LIS1
Authors: Singh Kashish , Lau Clinton K. , Manigrasso Giulia , Gama José B. , Gassmann Reto , Carter Andrew P.
Published: August 2022

Microtubule motors, like cytoplasmic dynein-1, are tightly regulated to prevent inappropriate activity in cells. Dynein functions as a ∼4 MDa complex containing its cofactor dynactin and a cargo-specific coiled-coil adaptor. However, how dynein and dynactin recognise diverse adaptors, how they interact with each other during complex formation, and the role of critical regulators such as LIS1 remain unclear. To address this, we determine the cryo-EM structure of dynein-dynactin on microtubules with LIS1 and the lysosomal adaptor JIP3. We show how JIP3 specifies complex formation despite a shorter coiled coil and lack of identifiable motifs compared to typical adaptors. We find LIS1 directly binds dynactin’s p150 subunit, closely tethering it to dynein. This interaction is necessary for dynein’s cellular andin vitroactivity. We also show how dynein’s intermediate chain relieves p150’s autoinhibition to enable LIS1 binding. Together, our data suggest LIS1 and p150 constrain dynein-dynactin to ensure efficient complex formation.
Recently evolved combination of unique sulfatase and amidase genes enables bacterial degradation of the wastewater micropollutant acesulfame worldwide
Authors: Bonatelli Maria L. , Rohwerder Thore , Popp Denny , Liu Yu , Akay Caglar , Schultz Carolyn , Liao Kuan-Po , Ding Chang , Reemtsma Thorsten , Adrian Lorenz , Kleinsteuber Sabine
Published: August 2022

Xenobiotics often challenge the principle of microbial infallibility. One example is acesulfame introduced in the 1980s as zero-calorie sweetener, which was recalcitrant in wastewater treatment plants until the early 2010s. Then, efficient removal has been reported with increasing frequency. By studying acesulfame metabolism in alphaproteobacterial degraders of the genera Bosea and Chelatococcus, we experimentally confirmed the previously postulated route of two subsequent hydrolysis steps via acetoacetamide-N-sulfonate (ANSA) to acetoacetate and sulfamate. Genome comparison of wildtype Bosea sp. 100-5 and a spontaneous acesulfame degradation-defective mutant revealed the involvement of two plasmid-borne gene clusters. The acesulfame-hydrolyzing sulfatase is strictly manganese-dependent and belongs to the metallo beta-lactamase family. In all degraders analyzed, it is encoded on a highly conserved gene cluster embedded in a composite transposon. The ANSA hydrolase, on the other hand, is an amidase signature domain enzyme encoded in another gene cluster showing variable length among degrading strains. Transposition of the sulfatase gene cluster between chromosome and plasmid explains how the two catabolic gene clusters recently combined for the degradation of acesulfame. Searching available genomes and metagenomes for the two hydrolases and associated genes indicates that the acesulfame plasmid evolved and spread worldwide in short time. While the sulfatase is unprecedented and unique for acesulfame degraders, the amidase occurs in different genetic environments and might have evolved for the degradation of other substrates. Evolution of the acesulfame degradation pathway might have been supported by the presence of structurally related natural and anthropogenic compounds, such as aminoacyl sulfamate ribonucleotide or sulfonamide antibiotics.
Outer surface lipoproteins from the Lyme disease spirochete exploit the molecular switch mechanism of the complement protease C1s
Authors: Garrigues Ryan J. , Thomas Sheila , Leong John M. , Garcia Brandon L.
Published: August 2022

Proteolytic cascades comprise several important physiological systems, including a primary arm of innate immunity called the complement cascade. To safeguard against complement-mediated attack, the etiologic agent of Lyme disease, Borreliella burgdorferi, produces numerous outer surface-localized lipoproteins that contribute to successful complement evasion. Recently, we discovered a pair of B. burgdorferi surface lipoproteins of the OspEF-related protein family – termed ElpB and ElpQ – that inhibit antibody-mediated complement activation. In this study, we investigate the molecular mechanism of ElpB and ElpQ complement inhibition using an array of biochemical and biophysical approaches. In vitro assays of complement activation show that an independently folded homologous C-terminal domain of each Elp protein maintains full complement inhibitory activity and selectively inhibits the classical pathway. Using surface plasmon resonance, Alpha bead-based technology, and C1s enzyme assays, we show that binding of Elp proteins to activated C1s blocks C4 cleavage by competing with C1s/C4 binding without occluding the active site. C1s-mediated C4 cleavage is dependent on activation-induced binding sites, termed exosites. To test whether these exosites are involved in Elp/C1s binding, we performed site-directed mutagenesis which showed that ElpB– and ElpQ-binding require C1s residues in the anion-binding exosite located on the serine protease domain of C1s. Based on these results, we propose a model whereby ElpB and ElpQ exploit activation-induced conformational changes that are normally important for C1s-mediated C4 cleavage. Our study expands the known complement evasion mechanisms of microbial pathogens and reveals a novel molecular mechanism for selective C1s inhibition by Lyme disease spirochetes.
Evolutionary analysis in Enterobacterales of the Rcs-repressor protein IgaA unveils two cytoplasmic small β-barrel domains central for function
Authors: Rodríguez Leticia , Peñalver Marcos , Casino Patricia , García-del Portillo Francisco
Published: August 2022

The Rcs sensor system, comprised by the proteins RcsB/RcsC/RcsD and RcsF, is used by bacteria of the order Enterobacterales to withstand envelope damage. Under non-stress conditions, the system is repressed by the membrane protein IgaA. How IgaA has evolved within Enterobacterales in concert with the Rcs system has not been explored. Here, we report phylogenetic data supporting co-evolution of IgaA with the inner membrane proteins RcsC and RcsD. Functional assays showed that IgaA from representative genera as Shigella and Dickeya, but not those from Yersinia or the endosymbionts Photorhabdus and Sodalis, repress the Rcs system when expressed in a heterogenous host like Salmonella enterica serovar Typhimurium. IgaA structural features have therefore diverged among Enterobacterales. Modelling of IgaA structure unveiled one periplasmic and two cytoplasmic β-rich architectures forming partially-closed small β-barrel (SBB) domains related to OB (oligonucleotide/oligosaccharide binding motif) fold domains. Interactions among conserved residues were mapped in a connector linking SBB-1 domain of cytoplasmic region cyt1 to SBB-2 domain of region cyt2 (residues E180-R265); the C-terminus of cyt1 facing cyt2 (R188-E194-D309 and T191-H326); and, between cyt2-cyt3 regions (H293-E328-R686). These interactions identify a previously unnoticed "hybrid" SBB-2 domain. We also identified interactions absent in the IgaA variants not functional in S. Typhimurium, including H192-P249, which links cyt1 to cyt2, R255-D313 and D287-R314. A short α-helix (α6) located in the SSB-1 domain is also missing in the non-complementing IgaA tested. Taken together, our data support a central role of the two cytoplasmic SBB domains in IgaA function and evolution.

SIGNIFICANCE

The "intracellular growth attenuator A" protein (IgaA) was first reported as repressor of the Rcs system in S. enterica serovar Typhimurium. IgaA orthologs were later studied in other genera and families of the Enterobacterales order, mainly in Escherichia coli. Despite intense investigation about the mechanism by which IgaA controls the Rcs system, the extent at which IgaA evolved within families of the Enterobacterales order has not been investigated. Using a combination of functional assays and in silico structural analyses, our work provides a detail map of conserved and divergent residues in IgaA representing interactions occurring in all Enterobacterales and others that may have diverged concomitantly to interacting proteins, probably for responding to specific environments. Future studies involving mutagenesis of these residues in IgaA of Enterobacterales families and genera of interest will certainly provide valuable insights into the regulation acting in the IgaA-Rcs axis.
Hypoxia truncates and constitutively activates the key cholesterol synthesis enzyme squalene monooxygenase
Authors: Coates Hudson W. , Olzomer Ellen M. , Du Ximing , Farrell Rhonda , Yang Hongyuan , Byrne Frances L. , Brown Andrew J.
Published: August 2022

Cholesterol synthesis is both energy- and oxygen-intensive, yet relatively little is known of the regulatory effects of hypoxia on pathway enzymes. We previously showed that the rate-limiting and first oxygen-requiring enzyme of the committed cholesterol synthesis pathway, squalene monooxygenase (SM), can undergo partial proteasomal degradation that renders it constitutively active. Here, we show that hypoxia is the physiological trigger for this truncation, which occurs through a two-part mechanism: (1) increased targeting of SM to the proteasomeviastabilization of the E3 ubiquitin ligase MARCHF6, and (2) accumulation of the SM substrate, squalene, which impedes the complete degradation of SM and liberates its truncated form. Truncation of SM is also increased in endometrial cancer tissues, where it correlates with levels of hypoxia-inducible factor−1α. These results uncover a feedforward mechanism that enables SM to accommodate fluctuations in substrate levels yet is also a likely contributor to its widely reported oncogenic properties.
Evolution of giant pandoravirus from small icosahedral viruses revealed by CRISPR/Cas9
Authors: Bisio Hugo , Legendre Matthieu , Giry Claire , Philippe Nadege , Alempic Jean-Marie , Jeudy Sandra , Abergel Chantal
Published: August 2022

Giant viruses (GVs) are a hotspot of unresolved controversies since their discovery, including the definition of “Virus” and the existence of a fourth domain of life1-3. While increasing knowledge of genome diversity has accumulated4, functional genomics was largely neglected. Here, we describe an experimental framework to genetically modify nuclear GVs and its host Acanthamoeba castellanii using CRISPR/Cas9, allowing us to uncover the evolution from small icosahedral viruses to amphora-shaped GVs. Ablation of the icosahedral major capsid protein in the evolutionary intermediate mollivirus highlights a stepwise transition in virion shape and size. We additionally demonstrate the existence of a reduced core essential genome in pandoravirus, reminiscent of their proposed smaller ancestors. Genetic expansion led to increased genome robustness, indicating selective pressures for adaptation to uncertain environments. Overall, we introduce new tools for manipulation of the unexplored genome of nuclear GVs and demonstrate that viral gigantism can arise as an emerging trait.
Using developmental rules to align microevolution with macroevolution
Authors: Machado Fabio Andrade , Mongle Carrie S. , Slater Graham , Penna Anna , Wisniewski Anna , Soffin Anna , Dutra Vitor , Uyeda Josef C.
Published: August 2022

Macroevolutionary biologists have classically rejected the notion that higher level patterns of divergence arise through microevolutionary processes acting within populations. For morphology, this consensus partly derives from the inability of quantitative genetics models to correctly predict the behavior of evolutionary processes at the scale of millions of years. Developmental studies (evo-devo) have been proposed to reconcile micro and macroevolution. However, there has been little progress in establishing a formal framework to apply evo-devo models of phenotypic diversification. Here, we reframe this issue by asking if using evo-devo models to quantify biological variation can improve the explanatory power of comparative models, thus helping us bridge the gap between micro- and macroevolution. We test this prediction by evaluating the evolution of primate lower molars in a comprehensive dataset densely sampled across living and extinct taxa. Our results suggest that biologically-informed morphospaces alongside quantitative genetics models allow a seamless transition between the micro and macro scales, while biologically uninformed spaces do not. We show that the adaptive landscape for primate teeth is corridor-like, with changes in morphology within the corridor being nearly neutral. Overall, our framework provides a basis for integrating evo-devo into the modern synthesis, allowing an operational way to evaluate the ultimate causes of macroevolution.
The CD103-XCR1 axis mediates the recruitment of immunoregulatory dendritic cells after traumatic injury
Authors: Lokwani Ravi , Ngo Tran B , DeStefano Sabrina , Adusei Kenneth M , Bhuiyan Minhaj , Josyula Aditya , Faust Mondreakest , Lin Aaron , Karkanitsa Maria , Fathi Parinaz , Sadtler Kaitlyn
Published: August 2022

During wounding and material implantation there is a disturbance in tissue homeostasis and release of self-antigen, and regulation between tolerance and auto-inflammation in injury is not well understood. Here, we analyzed antigen-presenting cells in biomaterial-treated muscle injury and found that pro-regenerative materials enrich Batf3-dependent CD103+XCR1+CD301b+ dendritic cells associated with cross-presentation and self-tolerance. Muscle trauma was accompanied by CD8+ iTregs and expansion of CD103+XCR1+CD62L- adaptive immune cells. Up-regulation of E-Cadherin (the ligand for CD103) and XCL-1 in injured tissue suggests a mechanism for cell recruitment to trauma. Without cross-presenting cells T cell activation increases, pro-regenerative macrophage polarization decreases, and muscle healing is impaired. These data describe a regulatory communication network through CD103+XCR1+ immune cells resulting in downstream effects on tissue regeneration.
Evaluation of tumor antigen-specific antibody responses in patients with metastatic triple negative breast cancer treated with cyclophosphamide and pembrolizumab
Authors: Routh Eric D. , Woodcock Mark G. , Serody Jonathan S. , Vincent Benjamin G.
Published: August 2022

Background

The role of B cells in antitumor immunity is becoming increasingly appreciated, as B cell populations have been associated with response to immune checkpoint blockade (ICB) in breast cancer patients and murine models of breast cancer. Deeper understanding of antibody responses to tumor antigens is needed to clarify the function of B cells in determining response to immunotherapy.

Methods

We evaluated tumor antigen-specific antibody responses in patients with metastatic triple negative breast cancer treated with pembrolizumab following low dose cyclophosphamide therapy using computational linear epitope prediction and custom peptide microarrays.

Results

We found that a minority of predicted linear epitopes were associated with antibody signal, and signal was associated with both neoepitopes and self-peptides. No association was observed between signal presence and subcellular localization or RNA expression of parent proteins. Patient-specific patterns of antibody signal boostability were observed that were independent of clinical response. Intriguingly, measures of cumulative antibody signal intensity relative to immunotherapy treatment showed that the one complete responder in the trial had the greatest increase in total antibody signal, which supports a potential association between ICB-dependent antibody boosting and clinical response. The antibody boost in the complete responder was largely driven by increased levels of IgG specific to a sequence of N-terminal residues in native Epidermal Growth Factor Receptor Pathway Substrate 8 (EPS8) protein, a known oncogene in several cancer types including breast cancer. Structural protein prediction showed that the targeted epitope of EPS8 was in a region of the protein with mixed linear/helical structure, and that this region was solvent-exposed and not predicted to bind to interacting macromolecules.

Conclusions

This study highlights the potential importance of the humoral immune response targeting neoepitopes as well as self epitopes in shaping clinical response to immunotherapy.
NBR1-mediated selective autophagy of ARF7 modulates root branching
Authors: Ebstrup E , Ansbøl J , Paez-Garcia A , Culp H , Chevalier J , Clemmens P , Coll NS , Moreno-Risueno M A , Rodriguez E
Published: August 2022

Auxin dictates root architecture via the Auxin Response Factor (ARF) family of transcription factors, which control lateral root (LR) formation. InArabidopsis, ARF7 regulates the specification of prebranch sites (PBS) generating LRs through gene expression oscillations and plays a pivotal role during LR initiation. Despite the importance of ARF7 in this process, there is a surprising lack of knowledge about how ARF7 turnover is regulated and how this impacts root architecture. Here, we show that ARF7 accumulates in autophagy mutants and is degraded through NBR1-dependent selective autophagy. We demonstrate that the previously reported rhythmic changes to ARF7 abundance in roots are modulated via autophagy and might occur in other tissues. Additionally, we prove that the level of co- localization between ARF7 and autophagy markers oscillates and can be modulated by auxin to trigger ARF7 turnover. Furthermore, we observed that autophagy impairment prevents ARF7 oscillation and reduces both PBS establishment and LR formation. In conclusion we report a novel role for autophagy during development, namely by enacting auxin-induced selective degradation of ARF7 to optimize periodic root branching.
The ELF3 transcription factor is associated with an epithelial phenotype and represses epithelial-mesenchymal transition
Authors: Subbalakshmi Ayalur Raghu , Sahoo Sarthak , Manjunatha Prakruthi , Goyal Shaurya , Kasiviswanathan Vignesh A , Yeshwanth M , Soundharya R , McMullen Isabelle , Somarelli Jason A. , Jolly Mohit Kumar
Published: August 2022

Epithelial-mesenchymal plasticity (EMP) involves bidirectional transitions between epithelial, mesenchymal and multiple intermediary hybrid epithelial/mesenchymal phenotypes. While the process of epithelial-mesenchymal transition (EMT) and its associated transcription factors are well-characterised, the transcription factors that promote mesenchymal-epithelial transition (MET) and stabilise hybrid E/M phenotypes are less well understood. Here, we analyse multiple publicly-available transcriptomic datasets at bulk and single-cell level and pinpoint ELF3 as a factor that is strongly associated with an epithelial phenotype and is inhibited during EMT. Using mechanism-based mathematical modelling, we also show that ELF3 inhibits the progression of EMT, suggesting ELF3 may be able to counteract EMT induction, including in the presence of EMT-inducing factors, such as WT1. Our model predicts that the MET induction capacity of ELF3 is stronger than that of KLF4, but weaker than that of GRHL2. Finally, we show that ELF3 levels correlates with worse patient survival in a subset of solid tumor types, suggesting cell-of-origin or lineage specificity in the prognostic capacity of ELF3.
Inflation induced motility for long-distance vertical migration
Authors: Larson Adam G. , Chajwa Rahul , Li Hongquan , Prakash Manu
Published: August 2022

The daily vertical migrations of plankton play a crucial role in shaping marine ecosystems and influencing global biogeochemical cycles. They also form the foundation of the largest daily biomass movement on Earth. Surprisingly, amongst this diverse group of organisms, some single cell protists transit these depths exceeding 50 meters without employing flagella or cilia, and the underlying mechanisms remain poorly understood. It has been previously proposed that this capability relies on the cell’s ability to regulate its internal density relative to seawater. Here, usingPyrocystis noctilucaas a model system, we demonstrate the primary mechanism for this density control is a rapid cellular inflation event, during which a single plankton cell expands its volume six-fold in less than 10 minutes. This self-regulated cellular inflation selectively imports fluid less dense than surrounding seawater, and can effectively sling-shot a cell and reverse sedimentation within minutes. This ability is made possible by a reticulated cytoplasmic architecture inPyrocystis noctilucathat enables this rapid increase in overall cell volume without dilution of its cytoplasmic content. We further present a generalized mathematical framework that unifies cell cycle driven density regulation, stratified ecology, and associated cell behavior in the open ocean. Our study unveils an ingenious strategy employed by non-motile plankton to evade the gravitational sedimentation trap, highlighting how precise control of cell size was essential for survival in the ocean.
Structural analyses of the plant PRT6-UBR box in the Cys-Arg/N-degron pathway and insights into the plant submergence response
Authors: Kim Leehyeon , Lin Chih-Cheng , Lin Ting-Jhen , Cao Yan-Cih , Chen Min-Chun , Chou Mei-Yi , Lin Wen-Hsuan , Kim Minki , Wu Jian-Li , Shih Ming-Che , Song Hyun Kyu , Ho Meng-Chiao
Published: August 2022

The submergence response in higher plants is highly dependent on the protein stability of group VII ethylene response factors, which are primarily degraded through the oxygen-dependent Cys-Arg branch of the N-degron pathway of targeted proteolysis. Knockout of PRT6, an E3 ligase and a vital component of the N-degron pathway, improves submergence tolerance in Arabidopsis and barley but is associated with side effects such as germination deficiency. In this study, we determined structures of rice and Arabidopsis PRT6-UBR box in complex with various Arg/N-degron related peptides. We identified two highly conserved motifs in the plant PRT6-UBR box, which is responsible for Cys-Arg/N-degron recognition. Structural and mutagenesis studies revealed the importance of two conserved motifs for Cys-Arg/N-degron recognition. The phenotype of Arabidopsis seedlings with PRT6-UBR mutants in these newly identified conserved motifs showed superior submergence survival suggesting that rational manipulation of the PRT6-UBR box can improve flood tolerance. Our results provide an engineering platform for generating crops with improved submergence tolerance.
Dynamics and length distributions of microtubules with a multistep catastrophe mechanism
Authors: Schwietert Felix , Heydenreich Lina , Kierfeld Jan
Published: August 2022

Regarding the experimental observation that microtubule catastrophe can be described as a multistep process, we extend the Dogterom–Leibler model for dynamic instability in order to discuss the effect that such a multistep catastrophe mechanism has on the distribution of microtubule lengths in the two regimes of bounded and unbounded growth. We show that in the former case, the steady state length distribution is non-exponential and has a lighter tail if multiple steps are required to undergo a catastrophe. If rescue events are possible, we detect a maximum in the distribution, i.e., the microtubule has a most probable length greater than zero. In the regime of unbounded growth, the length distribution converges to a Gaussian distribution whose variance decreases with the number of catastrophe steps. We extend our work by applying the multistep catastrophe model to microtubules that grow against an opposing force and to microtubules that are confined between two rigid walls. We determine critical forces below which the microtubule is in the bounded regime, and show that the multistep characteristics of the length distribution are largely lost if the growth of a microtubule in the unbounded regime is restricted by a rigid wall. All results are verified by stochastic simulations.
Recombinant reporter phage rTUN1::nLuc enables rapid detection and real-time antibiotic susceptibility testing of Klebsiella pneumoniae K64 strains
Authors: Braun Peter , Raab Rene , Bugert Joachim J , Eckstein Simone
Published: August 2022

The emergence of multi drug resistant (MDR) Klebsiella pneumoniae (Kp) strains constitutes an enormous threat to global health as MDR associated treatment failure causes high mortality rates in nosocomial infections. Rapid pathogen detection and antibiotic resistance screening is therefore crucial for successful therapy and thus, patient survival. Reporter phage-based diagnostics offer a way to speed up pathogen identification and resistance testing, as integration of reporter genes into highly specific phages allow real-time detection of phage replication and thus, living host cells. Kp specific phages use the host’s capsule, a major virulence factor of Kp, as receptor for adsorption. To date, 80 different Kp capsule types (K-serotypes) have been described with predominant capsule types varying between different countries and continents. Therefore, reporter phages need to be customized according to the locally prevailing variants. Recently, we described the autographivirus vB_KpP_TUN1 (TUN1), which specifically infects Kp K64 strains, the most predominant capsule type at the military hospital in Tunis (MHT) that is also associated with high mortality rates. In this work, we developed the highly specific recombinant reporter phage rTUN1::nLuc, which produces Nanoluciferase (nLuc) upon host infection and thus, enables rapid detection of Kp K64 cells in clinical matrices such as blood and urine. At the same time, rTUN1::nLuc allows for rapid antibiotic susceptibility testing and therefore identification of suitable antibiotic treatment in less than 3 hours.
SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks
Authors: González-Blas Carmen Bravo , De Winter Seppe , Hulselmans Gert , Hecker Nikolai , Matetovici Irina , Christiaens Valerie , Poovathingal Suresh , Wouters Jasper , Aibar Sara , Aerts Stein
Published: August 2022

Joint profiling of chromatin accessibility and gene expression of individual cells provides an opportunity to decipher enhancer-driven gene regulatory networks (eGRN). Here we present a new method for the inference of eGRNs, called SCENIC+. SCENIC+ predicts genomic enhancers along with candidate upstream transcription factors (TF) and links these enhancers to candidate target genes. Specific TFs for each cell type or cell state are predicted based on the concordance of TF binding site accessibility, TF expression, and target gene expression. To improve both recall and precision of TF identification, we curated and clustered more than 40,000 position weight matrices that we could associate with 1,553 human TFs. We validated and benchmarked each of the SCENIC+ components on diverse data sets from different species, including human peripheral blood mononuclear cell types, ENCODE cell lines, human melanoma cell states, and Drosophila retinal development. Next, we exploit SCENIC+ predictions to study conserved TFs, enhancers, and GRNs between human and mouse cell types in the cerebral cortex. Finally, we provide new capabilities that exploit the inferred eGRNs to study the dynamics of gene regulation along differentiation trajectories; to map regulatory activities onto tissues using spatial omics data; and to predict the effect of TF perturbations on cell state. SCENIC+ provides critical insight into gene regulation, starting from multiome atlases of scATAC-seq and scRNA-seq. The SCENIC+ suite is available as a set of Python modules at https://scenicplus.readthedocs.io.
MesoTIRF: a Total Internal Reflection Fluorescence illuminator for axial super-resolution membrane imaging at the mesoscale
Authors: Foylan S. , Amos W. B. , Dempster J. , Kölln L. , Hansen C. G. , Shaw M. , McConnell G.
Published: August 2022

Total Internal Reflection Fluorescence (TIRF) illumination bypasses the axial diffraction limit of light by using an evanescent field to excite fluorophores close to a sample substrate. TIRF illumination significantly improves image contrast, allowing researchers to study membrane structure and dynamics with localized reductions in photobleaching. However, a significant limitation of most TIRF microscopes is the relatively small field of view (FOV). TIRF objectives require a high numerical aperture (NA) to generate the evanescent wave. Such lenses invariably have a high magnification and result in a ∼ 50 µm diameter imaging field, requiring many subsequent images for accurate statistical analysis. Waveguide and prism-based TIRF systems are, in principle, compatible with lower magnification lenses to widen the FOV but these have a correspondingly low NA and lateral resolution. To overcome these limitations, we present a prism-based TIRF illuminator for the Mesolens - a specialist objective lens with the unusual combination of low magnification and high NA. This new imaging mode - MesoTIRF - enables TIRF imaging across a 4.4 mm x 3.0 mm FOV. We demonstrate evanescent wave illumination of cell specimens, and show the multi-wavelength capability of the modality across more than 700 cells in a single image. MesoTIRF images have up to a 6-fold improvement in signal-to-background ratio compared to widefield epi-fluorescence illumination, and we illustrate the benefit of this improved contrast for the detection and quantification of focal adhesions in fixed cells. Fluorescence intensities and resolvable structural detail do not vary considerably in homogeneity across the MesoTIRF FOV.
The pro-inflammatory response to influenza A virus infection is fueled by endothelial cells
Authors: Bauer Lisa , Rijsbergen Laurine C. , Leijten Lonneke , Benavides Feline F. W. , Noack Danny , Lamers Mart M. , Haagmans Bart. L. , de Vries Rory D. , de Swart Rik L. , van Riel Debby
Published: August 2022

Morbidity and mortality from influenza are associated with high levels of systemic inflammation. Endothelial cells have been shown to play a key role in this systemic inflammatory response during severe influenza A virus (IAV) infections, despite the fact that these are rarely infected in humans. However, how endothelial cells contribute to these systemic inflammatory responses is unclear. To investigate this, we developed a transwell-system in which airway organoid-derived differentiated human lung epithelial cells at the apical side were co-cultured with primary human lung microvascular endothelial cells (LMEC) at the basolateral side. We compared the susceptibility of endothelial cells to pandemic H1N1 virus isolated in 2009 and seasonal H1N1 and H3N2 virus isolated in 2019, and assessed the associated immune responses. Despite the detection of IAV nucleoprotein in LMEC monocultures, there was no evidence for productive infection. In epithelial-endothelial co-cultures, abundant IAV infection of epithelial cells resulted in the breakdown of the epithelial barrier, but infection of LMECs was rarely detected. Furthermore, we observed a significantly higher secretion of pro-inflammatory cytokines in LMECs when co-cultured with IAV-infected epithelial cells, compared to LMEC monocultures exposed to IAV. Taken together, our data show that endothelial cells are abortively infected by IAV, but can fuel the inflammatory response. As endothelial cells are a prominent cell type in the lung, it is possible that they play an important role in the systemic inflammatory response during IAV infections.
Immunopeptidomics-based design of highly effective mRNA vaccine formulations againstListeria monocytogenes
Authors: Mayer Rupert L. , Verbeke Rein , Asselman Caroline , Aernout Ilke , Gul Adillah , Eggermont Denzel , Boucher Katie , Thery Fabien , Maia Teresa M. , Demol Hans , Gabriels Ralf , Martens Lennart , Bécavin Christophe , De Smedt Stefaan , Vandekerckhove Bart , Lentacker Ine , Impens Francis
Published: August 2022

Listeria monocytogenesis a foodborne intracellular bacterial pathogen leading to human listeriosis. Despite a high mortality rate and increasing antibiotic resistance no clinically approved vaccine againstListeriais available. AttenuatedListeriastrains offer protection and are tested as antitumor vaccine vectors, but would benefit from a better knowledge on immunodominant vector antigens. To identify novel antigens, we screened forListeriaepitopes presented on the surface of infected human cell lines by mass spectrometry-based immunopeptidomics. In between more than 15,000 human self-peptides, we detected 68Listeriaepitopes from 42 different bacterial proteins, including several known antigens. Peptide epitopes presented on different cell lines were often derived from the same bacterial surface proteins, classifying these antigens as potential vaccine candidates. Encoding these highly presented antigens in lipid nanoparticle mRNA vaccine formulations resulted in specific CD8+ T-cell responses and high levels of protection in vaccination challenge experiments in mice. Our results pave the way for the development of a clinical mRNA vaccine againstListeriaand aid to improve attenuatedListeriavaccines and vectors, demonstrating the power of immunopeptidomics for next-generation bacterial vaccine development.
Asymmetric expression of homoeologous genes in wheat roots modulates the early phase of iron-deficiency signalling
Authors: Kaur Gazaldeep , Meena Varsha , Kumar Anil , Suman Gaurav , Tyagi Deepshikha , Joon Riya , Balk Janneke , Pandey Ajay K
Published: August 2022

Iron (Fe) limitation leads to dramatic changes in gene expression in plants, to induce iron uptake and mobilization, while at the same time restrict Fe-dependent metabolism and growth. Although transcriptional changes in response to Fe deficiency have recently been charted in wheat, this was performed at a stage when photosynthesis and growth were severely impacted, confounding primary and secondary responses. Here, we specifically uncover the transcriptional landscape of wheat roots during the early stages of the Fe deficiency response (4 and 8 days) and after Fe resupply. Root growth was significantly inhibited at day 4, but chlorosis only became apparent on day 8. The number of differentially expressed genes increased from 1386 on day 4 to 3538 on day 8, with an overlap of 2006 genes. Genes with dynamic changes in expression patterns include membrane transporters and transcription factors shown to be involved in Fe homeostasis in other plant species. Comparative analysis of the Fe deficiency response at 4, 8 and 20 days identified a core set of Fe-regulated genes.

Analysis of the expression of homoeologs suggests an increase in induction bias at 8 days compared to 4 days particularly, A genome contributing high at 4 days and the A+D genomes at 8 days. Overall, our work will contribute towards fundamental knowledge of the Fe signalling networks in wheat and point to the interplay of the three sub-genomes in this hexaploid species to fine tune the transcriptional response.