bluuebunny/crossref_metadata_2025 huggingface dataset:
Deep learning of antibody epitopes using molecular permutation vectors
Authors: Vardaxis Ioannis , Simovski Boris , Anzar Irantzu , Stratford Richard , Clancy Trevor
Published: March 2024

Background

The accurate computational prediction of B cell epitopes can vastly reduce the cost and time required for identifying potential epitope candidates for the design of vaccines and immunodiagnostics. However, current computational tools for B cell epitope prediction perform poorly and are not fit-for-purpose, and there remains enormous room for improvement and the need for superior prediction strategies.

Results

Here we propose a novel approach that improves B cell epitope prediction by encoding epitopes as binary molecular permutation vectors that represent the position and structural properties of the amino acids within a protein antigen sequence that interact with an antibody, rather than the traditional approach of defining epitopes as scores per amino acid on a protein sequence that pertain to their probability of partaking in a B cell epitope antibody interaction. In addition to defining epitopes as binary molecular permutation vectors, the approach also uses the 3D macrostructure features of the unbound 3D protein structures, and in turn uses these features to train another deep learning model on the corresponding antibody-bound protein 3D structures. We demonstrate that the strategy predicts B cell epitopes with improved accuracy compared to the existing tools. Additionally, we demonstrate that this approach reliably identifies the majority of experimentally verified epitopes on the spike protein of SARS-CoV-2 not seen by the model in training and generalizes in very robust manner on dissimilar data not seen by the model in training.

Conclusions

With the approach described herein, a primary protein sequence with the query molecular permutation vector alone is required to predict B cell epitopes in a reliable manner, potentially advancing the use of computational prediction of B cell epitopes in biomedical research applications.
Imaging genomics reveals genetic architecture of the globular human braincase
Authors: Molz Barbara , Eising Else , Alagöz Gökberk , Schijven Dick , Francks Clyde , Gunz Philipp , Fisher Simon E.
Published: March 2024

Compared with our fossil ancestors and Neandertal kin, modern humans have evolved a distinctive skull shape, with a rounder braincase and more delicate face. Competing explanations for this rounder skull have either linked it to changes in brain organisation, or seen it as a by-product of gracilization (evolution of thinner and lighter skeletal anatomy). Here, we combined palaeoanthropological data from hominin fossils and imaging genomics data from living humans to gain insight into evolutionary and developmental mechanisms shaping this uniquely modern human phenotype. We analysed endocranial globularity from magnetic resonance imaging (MRI) brain scans and genetic data of more than 33,000 adults. We discovered 28 genomic loci significantly associated with endocranial globularity. There was genetic overlap with the brain’s ventricular system, white matter microstructure, and sulcal morphology, and with multivariate genetic analyses of reading/language skills, but not with general cognition. The associated genes exhibited enriched expression in the brain during prenatal development and early childhood. The connection to the ventricular system hints at a role for cerebrospinal fluid pressure in shaping the endocranium during development. Genes linked to endocranial globularity also showed enhanced expression in the cardiovascular and female reproductive systems. This finding suggests co-evolutionary pathways whereby changes impacting factors such as energy needs, pregnancy, or fertility concurrently shape the brain and its structure.
Development of radiofluorinated MLN-4760 derivatives for PET imaging of the SARS-CoV-2 entry receptor ACE2
Authors: Wang Jinling , Beyer Darja , Vaccarin Christian , He Yingfang , Tanriver Matthias , Benoit Roger , Deupi Xavier , Mu Linjing , Bode Jeffrey W. , Schibli Roger , Müller Cristina
Published: March 2024

Purpose

The angiotensin converting enzyme 2 (ACE2) plays a regulatory role in the cardiovascular system and serves SARS-CoV-2 as an entry receptor. The aim of this study was to synthesize and evaluate radiofluorinated derivatives of the ACE2 inhibitor MLN-4760. [18F]F-MLN-4760 and [18F]F-Aza-MLN-4760 were demonstrated to be suitable for non-invasive imaging of ACE2, potentially enabling a better understanding of its expression dynamics.

Methods

Based on computational molecular modeling, the ACE2-binding modes of F-MLN-4760 and F-Aza-MLN-4760 were similar to that of MLN-4760. Co-crystallization of the hACE2/F-MLN-4760 protein complex was performed for confirmation. Displacement experiments using [3H]MLN-4760 enabled the determination of the binding affinities of the synthesized F-MLN-4760 and F-Aza-MLN-4760 to ACE2 expressed in HEK-ACE2 cells. Aryl trimethylstannane-based and pyridine-based radiofluorination precursors were synthesized and used for the preparation of the respective radiotracers. [18F]F-MLN-4760 and [18F]F-Aza-MLN-4760 were evaluated with regard to the uptake in HEK-ACE2 and HEK-ACE cells and in vitro binding to tissue sections of HEK-ACE2 xenografts and normal organs of mice. Biodistribution and PET/CT imaging studies of [18F]F-MLN-4760 and [18F]F-Aza-MLN-4760 were performed using HEK-ACE2 and HEK-ACE xenografted nude mice.

Results

Crystallography data revealed an equal ACE2-binding mode for F-MLN-4760 as previously found for MLN-4760 and indicated that the same would hold true for F-Aza-MLN-4760. The IC50values were all in the high nM range, but three-fold lower for F-MLN-4760 and seven-fold lower for F-Aza-MLN-4760 than for MLN-4760. [18F]F-MLN-4760 and [18F]F-Aza-MLN-4760 were obtained in 1.4 ± 0.3 GBq and 0.5 ± 0.1 GBq activity with >99% radiochemical purity in a 5.3% and 1.2% radiochemical yield, respectively. Uptake in HEK-ACE2 cells was higher for [18F]F-MLN-4760 (67 ± 9%) than for [18F]F-Aza-MLN-4760 (37 ± 8%) after 3 h incubation while negligible uptake was seen in HEK-ACE cells (<0.3%). [18F]F-MLN-4760 and [18F]F-Aza-MLN-4760 accumulated specifically in HEK-ACE2 xenografts of mice (13 ± 2% IA/g and 15 ± 2% IA/g at 1 h p.i.) with almost no uptake observed in HEK-ACE xenografts (<0.3% IA/g). This was confirmed by PET/CT imaging, which also visualized unspecific accumulation in the gall bladder and intestinal tract.

Conclusion

Both radiotracers showed specific and selective binding to ACE2 in vitro and in vivo. [18F]F-MLN-4760 was, however, obtained in higher yields and the ACE2-binding affinity was superior over that of [18F]F-Aza-MLN-4760. [18F]F-MLN-4760 would, thus, be the candidate of choice for further developlment to enable PET imaging of ACE2 in patients.
Perturbation-aware predictive modeling of RNA splicing using bidirectional transformers
Authors: McNally Colin P , Abdulhay Nour J , Khalaj Mona , Saberi Ali , Zaro Balyn W , Goodarzi Hani , Ramani Vijay
Published: March 2024

Predicting molecular function directly from DNA sequence remains a grand challenge in computational and molecular biology. Here, we engineer and train bidirectional transformer models to predict the chemical grammar of alternative human mRNA splicing leveraging the largest perturbative full-length RNA dataset to date. By combining high-throughput single-molecule long-read “chemical transcriptomics” in human cells with transformer models, we train AllSplice – a nucleotide foundation model that achieves state-of-the-art prediction of canonical and noncanonical splice junctions across the human transcriptome. We demonstrate improved performance achieved through incorporation of diverse noncanonical splice sites in its training set that were identified through long-read RNA data. Leveraging chemical perturbations and multiple cell types in the data, we fine-tune AllSplice to train ChemSplice – the first predictive model of sequence-dependent and cell-type specific alternative splicing following programmed cellular perturbation. We anticipate the broad application of AllSplice, ChemSplice, and other models fine-tuned on this foundation to myriad areas of RNA therapeutics development.
Bivalent COVID-19 vaccines boost the capacity of pre-existing SARS-CoV-2-specific memory B cells to cross-recognize Omicron subvariants
Authors: Fryer Holly A. , Geers Daryl , Gommers Lennert , Zaeck Luca M. , Tan Ngoc H. , Jones-Freeman Bernadette , Goorhuis Abraham , Postma Douwe F. , Visser Leo G. , Hogarth P. Mark , Koopmans Marion P. G. , GeurtsvanKessel Corine H. , O’Hehir Robyn E. , van der Kuy P. Hugo M. , de Vries Rory D. , van Zelm Menno C.
Published: March 2024

Bivalent COVID-19 vaccines comprising ancestral Wuhan-Hu-1 (WH1) and the Omicron BA.1 or BA.5 subvariant elicit enhanced serum antibody responses to emerging Omicron subvariants. We characterized the memory B-cell (Bmem) response following a fourth dose with a BA.1 or BA.5 bivalent vaccine, and compared the immunogenicity with a WH1 monovalent fourth dose. Healthcare workers previously immunized with mRNA or adenoviral vector monovalent vaccines were sampled before and one-month after a monovalent, BA.1 or BA.5 bivalent fourth dose COVID-19 vaccine. RBD-specific Bmem were quantified with an in-depth spectral flow cytometry panel including recombinant RBD proteins of the WH1, BA.1, BA.5, BQ.1.1, and XBB.1.5 variants. All recipients had slightly increased WH1 RBD-specific Bmem numbers. Recognition of Omicron subvariants was not enhanced following monovalent vaccination, while both bivalent vaccines significantly increased WH1 RBD-specific Bmem cross-recognition of all Omicron subvariants tested by flow cytometry. Thus, Omicron-based bivalent vaccines can improve recognition of descendent Omicron subvariants by pre-existing, WH1-specific Bmem, beyond that of a conventional, monovalent vaccine. This provides new insights into the capacity of variant-based mRNA booster vaccines to improve immune memory against emerging SARS-CoV-2 variants.
Extracellular vesicles produced during fungal infection in humans are immunologically active
Authors: de Rezende Caroline P. , Santos Patrick W. S. , Piraine Renan A. , Silvestrini Virgínia C. , Barbosa Julio C. J. , Valera Fabiana C. P. , Tamashiro Edwin , Podolski-Gondim Guilherme G. , Quintana Silvana M. , Calado Rodrigo , Martinez Roberto , P. Fill Taicia , Rodrigues Márcio L. , Almeida Fausto
Published: March 2024

Of the known 1.5 million fungal species,Candidaspp.,Cryptococcusspp., andParacoccidioidesspp. are the main pathogenic species causing serious diseases with almost two million annual deaths. The diagnosis and treatment of fungal infections are challenging since of the limited access to diagnostic tests and the emergence of antifungal resistance. Extracellular vesicles (EVs) promote the interactions of fungal cells with other organisms and play an important role in the pathogen–host relationship. Owing to the complexity of fungal EVs and the lack of clinical studies on their roles in human infections, we studied the EVs from the serum and urine samples of patients with fungal infections caused byCandida albicans,Cryptococcus neoformans, andParacoccidioides brasiliensisand determined their roles. Steroids, sphingolipids, and fatty acids were identified as the main secondary metabolites via mass spectrometry analysis. We asked whether these metabolites in EVs could play roles in modulating the host immune response. Our findings revealed the polarization of the proinflammatory profile in murine and human macrophages, with the increased production of cytokines, such as the tumor necrosis factor-α, interferon-γ, and interleukin-6, and an increased expression of the inducible nitric oxide synthase gene, a M1 response marker. Therefore, circulating EVs from patients with fungal infections are likely involved in the disease pathophysiology. Our findings provide insights into the roles of EVs in fungal infections in clinical samples and in vitro, suggesting possible targets for systemic mycoses therapy.

Significance Statement

Fungal infections cause approximately 1.6 million deaths annually. Due to therapeutic and diagnostic limitations, it is mandatory to understand and develop new immunological interventions. Despite several in vitro studies on the production of extracellular vesicles (EVs) from fungal pathogens, this study is a pioneer in the identification and characterization of EVs in the course of fungal infection in humans. Our group demonstrated the presence of EVs in clinical samples from patients diagnosed with candidiasis, cryptococcosis, and paracoccidioidomycosis, as well as the EVs interaction produced by host and fungal pathogen with the immune system, resulting in relationships that may be beneficial for the progression or elimination of fungal disease.
Combination of AID2 and BromoTag expands the utility of degron-based protein knockdowns
Authors: Hatoyama Yuki , Islam Moutushi , Bond Adam G. , Hayashi Ken-ichiro , Ciulli Alessio , Kanemaki Masato T.
Published: March 2024

Acute protein knockdown is a powerful approach to dissecting protein function in dynamic cellular processes. We previously reported an improved auxin-inducible degron system, AID2, but recently noted that its ability to induce degradation of some essential replication factors, such as ORC1 and CDC6, was not enough to induce lethality. Here, we present combinational degron technologies to control two proteins and enhance target depletion. For this purpose, we initially compared PROTAC-based degrons, dTAG and BromoTag, with AID2 to reveal their key features and then demonstrated control of cohesin and condensin with AID2 and BromoTag, respectively. We developed a double-degron system with AID2 and BromoTag to enhance target depletion and accelerate depletion kinetics and demonstrated that both ORC1 and CDC6 are pivotal for MCM loading. Finally, we found that co-depletion of ORC1 and CDC6 by the double-degron system completely suppressed DNA replication, and the cells entered mitosis with single-chromatid chromosomes, indicating DNA replication was uncoupled from the cell cycle control. Our combinational degron technologies will expand the application scope for functional analyses.
MixtureFinder: Estimating DNA mixture models for phylogenetic analyses
Authors: Ren Huaiyan , Wong Thomas KF , Minh Bui Quang , Lanfear Robert
Published: March 2024

In phylogenetic studies, both partitioned models and mixture models are used to account for heterogeneity in molecular evolution among the sites of DNA sequence alignments. Partitioned models require the user to specify the grouping of sites into subsets, and then assume that each subset of sites can be modelled by a single common process. Mixture models do not require users to pre-specify subsets of sites, and instead calculate the likelihood of every site under every model, while co-estimating the model weights and parameters. While much research has gone into the optimisation of partitioned models by merging user-specified subsets, there has been less attention paid to the optimisation of mixture models for DNA sequence alignments. In this study, we first ask whether a key assumption of partitioned models – that each user-specified subset can be modelled by a single common process – is supported by the data. Having shown that this is not the case, we then design, implement, test, and apply an algorithm, MixtureFinder, to select the optimum number of classes for a mixture model of Q matrices for the standard models of DNA sequence evolution. We show this algorithm performs well on simulated and empirical datasets and suggest that it may be useful for future empirical studies. MixtureFinder is available in IQ-TREE2, and a tutorial for using MixtureFinder can be found here:http://www.iqtree.org/doc/Complex-Models#mixture-models.
Preeclampsia in mice carrying fetuses with APOL1 risk variants
Authors: Yoshida Teruhiko , Latt Khun Zaw , Shrivastav Shashi , Lu Huiyan , Reidy Kimberly J. , Charlton Jennifer R. , Zhao Yongmei , Winkler Cheryl A. , Reznik Sandra E. , Rosenberg Avi Z. , Kopp Jeffrey B.
Published: March 2024

African-American women have a maternal mortality rate approximately three times higher than European-American women. This is partially due to hypertensive disorders of pregnancy, including preeclampsia. FetalAPOL1high-risk genotype increases preeclampsia risk, although mechanisms remain elusive. We characterized two mouse models to investigate whether fetal-origin APOL1 induces preeclampsia and which cell types contribute. Wein vitrofertilized mice with sperm from two transgenic mouse lines:APOL1transgenic mice carrying human genomic locus constructs from bacterial artificial chromosomes (BAC) containing theAPOL1gene, mimicking expression and function of human APOL1 (BAC/APOL1 mice) and albumin promoterAPOL1transgenic mice expressingAPOL1in liver and plasma (Alb/APOL1 mice). Dams carrying either BAC/APOL1-G1 or Alb/APOL1-G1 fetuses had elevated systolic blood pressure, while dams carrying BAC/APOL1-G0 or Alb/APOL1-G0 fetuses did not. BAC/APOL1-G1 and Alb/APOL1-G1 fetuses weighed less than littermates, indicating intrauterine growth restriction. Single-nucleus RNA-seq of APOL1-G1 placentas showed increased expression of osteopontin/Spp1, most prominently in vascular endothelial cells with robust APOL1 expression. Cell-cell interaction analysis indicated pro-inflammatory signaling between placental cells and maternal monocytes. These models show that fetal origin APOL1-G1 causes preeclampsia, inducing pro-inflammatory response in placenta and maternal monocytes. The APOL1-G1 variant poses a multi-generational problem, causing effects in mothers and offspring.
Comprehensive analysis of the genetic variation in theLPAgene from short-read sequencing
Authors: Betschart Raphael O. , Koliopanos Georgios , Garg Paras , Guo Linlin , Rossi Massimiliano , Schönherr Sebastian , Blankenberg Stefan , Twerenbold Raphael , Zeller Tanja , Ziegler Andreas
Published: March 2024

Lipoprotein (a) [LP(a)] is a risk factor for cardiovascular diseases and mainly regulated by the complex LPA gene. We investigated the types of variation in the LPA gene and their predictive performance on LP(a) concentration. We determined the Kringle IV-type 2 (KIV-2) copy number (CN) using the DRAGEN LPA Caller (DLC) and a read-depth based CN estimator in 8351 whole genome sequencing samples from the GENESIS-HD study. The pentanucleotide repeat in the promoter region was genotyped with GangSTR and ExpansionHunter. LP(a) concentration was available in 4861 population-based subjects. Predictive performance on LP(a) concentration was investigated using random forests. The agreement of the KIV-2 CN between the two specialized callers was high (r=0.9966; 95% confidence interval [CI] 0.9965–0.9968). Allele-specific KIV-2 CN could be determined in 47.0% of the subjects using the DLC. Lp(a) concentration can be better predicted from allele-specific KIV-2 CN than total KIV-2 CN. Two single nucleotide variants 4925G>A and rs41272114 further improved prediction. The genetically complex LPA gene can be analyzed with excellent agreement between different callers. The allele-specific KIV-2 CN is more important for predicting LP(a) concentration than the total KIV-2 CN. It would be important that the allele-specific KIV-2 CN is determinable in all subjects.
Elevated expression ofB4GALT6,GABRA1,GAD2,GLRA3,HTR2A,PCSK1, andSLC17A6are postmortem markers for the ALS-Ox subtype
Authors: Eshima Jarrett , Pennington Taylor R. , Choudhury Raiyan , Garcia Jordan M. , Fricks John , Smith Barbara S.
Published: March 2024

In this work, we stratify 428 bulk RNA-seq spinal cord transcriptomes from 206 ALS patients to assess concordance with cortical phenotype. We find the postmortem spinal cord generally recaptures the molecular phenotypes observed in the postmortem cortex and observe weaker differences in patient survival after correction for repeat measures. We compare intra-patient subtype assigned in the cortex and spinal cord, finding modest agreement between the cortex and lumbar region specifically, ranging from 46.2 – 66.7%. We leverage differential expression analysis to identify seven marker genes for the oxidative stress (ALS-Ox) subtype that show consistent upregulation in both the cortex and spinal cord and utilize three to construct classifiers that achieve notable predictive power for the ALS-Ox subtype in three different holdout cohorts, with AUCs ranging from 0.81 – 0.89. Our study shows the ALS-Ox subtype is conserved in the spinal cord of the same patients, offering a postmortem foundation for clinical stratification.
Low-Cost, Label-Free Blue Light Cystoscopy through Digital Staining of White Light Cystoscopy Videos
Authors: Chang Shuang , Wintergerst Greyson A , Carlson Camella , Yin Haoli , Scarpato Kristen R. , Luckenbaugh Amy N. , Chang Sam S. , Kolouri Soheil , Bowden Audrey K.
Published: March 2024

Bladder cancer is 10thmost common malignancy and carries the highest treatment cost among all cancers. The high cost of bladder cancer treatment stems from its high recurrence rate, which necessitates frequent surveillance. White light cystoscopy (WLC), the standard of care surveillance tool to examine the bladder for lesions, has limited sensitivity for early-stage bladder cancer. Blue light cystoscopy (BLC) utilizes a fluorescent dye to induce contrast in cancerous regions, improving the sensitivity of detection by 43%. Nevertheless, the added cost and lengthy administration time of the dye limits the availability of BLC for surveillance. Here, we report the first demonstration of digital staining on clinical endoscopy videos collected with standard-of-care clinical equipment to convert WLC images to accurate BLC-like images. We introduce key pre-processing steps to circumvent color and brightness variations in clinical datasets needed for successful model performance; the results show excellent qualitative and quantitative agreement of the digitally stained WLC (dsWLC) images with ground truth BLC images as measured through staining accuracy analysis and color consistency assessment. In short, dsWLC can provide the fluorescent contrast needed to improve the detection sensitivity of bladder cancer, thereby increasing the accessibility of BLC contrast for bladder cancer surveillance use without the cost and time burden associated with the dye and specialized equipment.
Understanding the impact of antenatal care policies in Georgia (USA) and Scotland (UK): A textual synthesis
Authors: Shim J. , Burnett V. , Vernon M. , Work F. , Uwaifo I. , Ray C. , Reddi P.
Published: March 2024

Objectives

This study aims to (1) understand the role of policy in maternal health outcomes, and (2) establish any differences or similarities between health systems, providing benchmarks for future maternal and infant care policies in Georgia and Scotland.

Methods

Guided by JBI methodology, a textual review of policies and public health interventions that have influenced the antenatal care process in both health systems was conducted. Inclusion criteria for this review were classified using the “PCC” mnemonic: Population-Pregnant women and mothers; Concept-Policies and strategies that supports prenatal and maternal health; and Context-Relevant to Scotland and Georgia. Published primary and secondary research, and grey literature (guidelines, reports, and legislation from authoritative sources) were included.

Results

Overall, 60 sources contributed to the report on maternal health system topics. Findings of the textual synthesis presented a regionalized system of maternity care led by physician-provided care models in Georgia compared to the nationalized health system in Scotland with an extended scope for midwife-led care models. On a secondary, organizational level, Scotland also widely operates on protocolized, standardized care informed by clinical guidelines such as NICE. The Georgia health systems also follow national guidelines for care, but extent of standardization may vary based on a mixed system of private and public insurance coverage.

Discussion/Conclusion

This is the first study to comprehensively examine maternal health policies in the distinct contexts of Georgia and Scotland, shedding light on the diverse approaches within their respective healthcare systems. These observed variations stem from historical, cultural, and policy contexts unique to each region. As the United States continue to prioritize maternal and child health through public health initiatives, our findings feature crucial considerations for maternal antenatal care policies. Specifically, there is a discernible need to increase access to antenatal care and invest in the maternity care provider workforce, revealing opportunities for targeted improvements in support of maternal health.
Equalizing prognostic disparities in stage III KRAS-mutant NSCLC: addition of durvalumab to combined chemoradiotherapy improves survival
Authors: Eklund Ella A. , Orgard Mathilda , Wallin Delice , Sayin Sama I. , Fagman Henrik , Raghavan Sukanya , Akyürek Levent M , Nyman Jan , Wiel Clotilde , Hallqvist Andreas , Sayin Volkan I.
Published: March 2024

Introduction

Stage III non-small cell lung cancer (NSCLC) is heterogeneous and identification of subgroups with differential responses is crucial to optimize treatment. Addition of durvalumab to concurrent chemoradiotherapy (cCRT) has previously been shown to improve survival outcomes. Meanwhile, subgroups harboring KRAS mutations have been shown to have worse prognosis. We investigated whether KRAS mutational status may affect survival outcomes after adjuvant durvalumab following cCRT in stage III NSCLC.

Methods

In this retrospective study, we present a real-world dataset of all stage III NSCLC patients treated with cCRT with a curative intent and molecularly assessed between 2016-2021 in West Sweden. Primary study outcomes were overall survival (OS) and progression free survival (PFS).

Results

We identified 145 patients receiving cCRT with a curative intent, 32% harbored an activating mutation in the KRAS gene (KRASMUT). Compared to KRAS wild-type (KRASWT), KRASMUThad a worse OS (p=0.047) and PFS (p=0.038). The finding persisted on multivariate analysis with OS (HR 1.703, 95%CI 1.074-2.702,p= 0.024) and PFS (HR 1.628, 95% CI 1.081-2.453,p= 0.020). After the addition of durvalumab to cCRT, there were no longer any significant differences between KRASWTand KRASMUTin OS or PFS.

Conclusions

KRASmutations are a negative prognostic factor after cCRT in stage III NSCLC, and the addition of durvalumab equalizes the negative impact of harboring this mutation.
Long non-coding RNAs direct the SWI/SNF complex to cell-specific enhancers
Authors: Oo James A. , Warwick Timothy , Pálfi Katalin , McNicoll Francois , Cao Can , Prieto-Garcia Cristian , Zhou Yinuo , Gavrilov Alexey A. , Razin Sergey V. , Lam Frederike , Günther Stefan , Cabrera-Orefice Alfredo , Wittig Ilka , Pullamsetti Soni Savai , Kurian Leo , Gilsbach Ralf , Schulz Marcel H. , Dikic Ivan , Müller-McNicoll Michaela , Brandes Ralf P. , Leisegang Matthias S.
Published: March 2024

The coordination of chromatin remodeling is essential for DNA accessibility and gene expression control1. The highly conserved and ubiquitously expressed SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex plays a central role in cell type- and context-dependent gene expression2. Despite the absence of a defined DNA recognition motif, SWI/SNF binds lineage specific enhancers genome-wide where it actively maintains open chromatin state2–5. It does so while retaining the ability to respond dynamically to cellular signals4. However, the mechanisms that guide SWI/SNF to specific genomic targets have remained elusive. Here we demonstrate thattrans-acting long non-coding RNAs (lncRNAs) direct the SWI/SNF complex to cell type-specific enhancers. SWI/SNF preferentially binds lncRNAs and these predominantly bind DNA targets intrans. Together they localize to enhancers, many of which are cell type-specific. Knockdown of SWI/SNF- and enhancer-bound lncRNAs causes the genome-wide redistribution of SWI/SNF away from enhancers and a concomitant differential expression of spatially connected target genes. These lncRNA-SWI/SNF-enhancer networks support an enhancer hub model of SWI/SNF genomic targeting. Our findings reveal a competitive recruitment of SWI/SNF by lncRNAs which provide a specific and dynamic layer of control in chromatin accessibility and gene expression.
Base composition at the start of the coding sequence controls the balance between translation initiation and mRNA degradation inE. coli
Authors: Lipońska Anna , Monlezun Laura , Wilkins Isaac , Ngo Saravuth , Oïffer Thomas , Bouchachi Cylia , Hunt John F. , Aalberts Daniel P. , Boël Grégory
Published: March 2024

Protein synthesis efficiency is highly dependent on mRNA coding sequence. Furthermore, there is extensive evidence of a correlation between mRNA stability and protein expression level, though the mechanistic determinants remain unclear. Using yellow fluorescent protein (YFP) as a reporter gene, we herein demonstrate that adenosine (A) abundance in the first six codons is a critical determinant for achieving high protein synthesis inE. coli. Increasing A and/or decreasing guanosine (G) content in this region results in substantial increases in protein expression level bothin vivoandin vitrothat are correlated with steady-state mRNA concentrationin vivo, and this effect is attributable to changes in the stability of the mRNA that are directly coupled to its translation efficiency. Increasing A content promotes mRNA incorporation into the functional 70S ribosomal initiation complex without altering its affinity for the 30S ribosomal subunit. These results support a model in which base composition in the first six codons modulates local mRNA folding energy to control the balance between productive translation initiationversusdegradation of mRNAs bound to the 30S ribosomal subunit. Based on these findings, we developed a short N-terminal coding sequence that optimizes translation initiation efficiency for protein production inE. coli.
Loss of KIF13B causes time-dependent changes in ciliary polycystin-2 levels and extracellular vesicle release
Authors: Rezi Csenge K. , Frei Alina , Campestre Fabiola , Berggreen Christina R. , Laplace Julie , Sicot Aurelien , Li Geyi , Johansen Søren L. , Sørensen Julie K. T. , Berchtold Martin W. , Chamlali Mohamed , Christensen Søren T. , Boldt Karsten , Anvarian Zeinab , May-Simera Helen L. , Pedersen Lotte B.
Published: March 2024

The polycystic kidney disease gene product polycystin-2 (PC2) localizes to and is released from primary cilia in extracellular vesicles (EVs). We report that KIF13B regulates ciliary EV release and PC2 levels in kidney epithelial cells in a time-dependent manner and show that KIF13B itself is released from the ciliary tip. In early stages of ciliation,Kif13b-/-cells displayed excessive ciliary accumulation of PC2 and initially released fewer small EVs than control cells. Over time, ciliatedKif13b-/-cells increased their small EV release rate to control levels, however proteomic analysis identified >50 proteins depleted from mutant EV samples. These included the ubiquitin E3 ligase ITCH and palmitoyl transferase ZDHHC5, which localized to primary cilia. MatureKif13b-/-cilia exhibited aberrant membrane bulges and decreased PC2 and ALIX, an ITCH substrate that negatively regulated ciliary PC2 levels. Our work provides new insight into the mechanisms of ciliary EV release, which is important for regulating ciliary membrane homeostasis and signalling function.
Inhibition of eukaryotic translation initiation factor 1A (eIF1A) and 3B (eIF3B) diminishes the psoriatic phenotype in two mouse models and human 3D model samples
Authors: Golob-Schwarzl Nicole , Pilic Johannes , Vrebo Azelma , Bordag Natalie , Shirsath Nitesh , Müller Christin-Therese , El-Heliebi Amin , Wolf Peter
Published: March 2024

Background

Psoriasis is a systemic inflammatory disease for which new topical treatments are required. Psoriatic inflammation is associated with overexpression of eukaryotic translation initiation factors (eIFs), which critically regulate gene expression in many important cellular processes, including proliferation, apoptosis, and differentiation. However, the exact link between overexpression of eIF and psoriasis is unknown. Here, we investigated the role of eIFs, particularly eIF1A and eIF3B, and the impact of their inhibition on the pathophysiology of psoriasis.

Methods

We used two mouse models reflecting the pathophysiology of psoriasis: (i) BALB/c mice topically treated with the immune activator imiquimod (IMQ) and (ii) K5.TGFβ transgenic mice. eIF1A and eIF3B were inhibited by either topical or systemic application of specific small interfering RNA (siRNA). In addition, we employed commercial human 3D psoriatic skin model samples. Importantly,in situmRNA detection-based padlock probes against transcript variants of eIF1A und eIF3B was performed.

Results

Topical and systemic inhibition of eIF1A and eIF3B inhibited inflammation in both imiquimod and TGFß mouse models as well as in a human 3D psoriasis model. Downregulation of eIF1A and eIF3B was associated with normalization of cell proliferation, restoration of the inflammatory milieu and epidermal hyperplasia of psoriasis, and normalization of levels of proinflammatory cytokines (e.g., TNFα, IL-1b, IL-17, and IL-22) and keratinocyte differentiation markers (e.g., KRT16 and FLG).

Conclusion

These results reveal an imbalance in translation and emphasize the crucial role of eIF1A and eIF3B in the pathophysiology of psoriasis. Targeting eIFs opens new avenues for the development of novel therapeutic treatment strategies against psoriasis.
Cell class-specific long-range axonal projections of neurons in mouse whisker-related somatosensory cortices
Authors: Liu Yanqi , Bech Pol , Tamura Keita , Délez Lucas T. , Crochet Sylvain , Petersen Carl C.H.
Published: March 2024

The extensive long-range axonal projections of diverse classes of neocortical excitatory neurons are thought to contribute importantly to the highly integrative brain-wide interactions underlying the processing of sensory, cognitive and motor signals. Here, we investigated the long-range axonal output of various classes of genetically-defined projection neurons with cell bodies located in the whisker-related somatosensory cortices of the mouse through brain-wide light-sheet imaging of fluorescently-labeled axons segmented by specifically-trained convolutional networks quantified within the Allen Mouse Brain Atlas Common Coordinate Framework. We injected Cre-dependent virus to express GFP or tdTomato in the posterior primary somatosensory barrel cortex and the posterior supplemental somatosensory cortex, which contain the representations of the large posterior mystacial whiskers. We investigated the six following transgenic mouse lines which preferentially express Cre in different glutamatergic neocortical cell classes: Rasgrf2-dCre for layer 2/3 intratelencephalic projection neurons, Scnn1a-Cre for layer 4 intratelencephalic projection neurons, Tlx3-Cre for layer 5 intratelencephalic projection neurons, Sim1-Cre for layer 5 pyramidal tract projection neurons, Rbp4-Cre for layer 5 projection neurons and Ntsr1-Cre for layer 6 corticothalamic neurons. We found long-range axonal projections in many diverse downstream brain areas with largely similar output from primary and secondary cortices, but with genetically-defined cell classes showing distinct innervation patterns, with Rbp4-Cre mice showing the broadest innervation targets, subsets of which were innervated in the other mouse lines. To test whether the revealed axonal projections might underpin functional circuits, we compared the spatial organization of the axonal innervation with functional connectivity maps obtained from optogenetic stimulation of sensory cortex and wide-field imaging of the activity propagation to frontal cortices. Both methods indicated that neurons located more laterally in somatosensory cortex topographically signaled to more anteriorly located regions in motor cortex. The current methodology therefore appears to quantify brain-wide axonal innervation patterns supporting brain-wide signaling, and, together with further technological advances, this will help provide increasingly detailed connectivity information of the mouse brain, essential for understanding the complex neuronal circuitry underlying even simple goal-directed behaviors.
Translational impacts of enzymes that modify ribosomal RNA around the peptidyl transferase centre
Authors: Bao Letian , Liljeruhm Josefine , Crespo Blanco Rubén , Brandis Gerrit , Remme Jaanus , Forster Anthony C.
Published: March 2024

Large ribosomal RNAs (rRNAs) are modified heavily post-transcriptionally in functionally-important regions but, paradoxically, individual knockouts (KOs) of the modification enzymes have minimal impact onEscherichia coligrowth. Furthermore, we recently constructed a strain with combined KOs of five modification enzymes (RluC, RlmKL, RlmN, RlmM and RluE) of the “critical region” of the peptidyl transferase center (PTC) in 23S rRNA that exhibited only a minor growth defect at 37°C (although major at 20°C). However, our combined KO of modification enzymes RluC and RlmE resulted in conditional lethality (at 20°C). Although the growth rates for both multiple-KO strains were characterized, the molecular explanations for such deficits remain unclear. Here, we pinpoint biochemical defects in these strains.In vitrofast kinetics at 20 and 37°C with ribosomes purified from both strains revealed, counterintuitively, the slowing of translocation, not peptide bond formation or peptidyl release. Rates of protein synthesisin vivo, as judged by the kinetics of β-galactosidase induction, were also slowed. For the five-KO strain, the biggest deficit at 37°C was in 70S ribosome assembly, as judged by a dominant 50S peak in ribosome sucrose gradient profiles at 5 mM Mg2+. Reconstitution of this 50S subunit from purified five-KO rRNA and ribosomal proteins supported a direct role in ribosome biogenesis of the PTC region modificationsper se, rather than of the modification enzymes. These results clarify the importance and roles of the enigmatic rRNA modifications.
The gases H2and O2in open-culture reactors influence the performance and microbiota of chain elongation inton-caproate andn-caprylate
Authors: Spirito Catherine M. , Lucas Timo N. , Patz Sascha , Jeon Byoung Seung , Werner Jeffrey J. , Trondsen Lauren H. , Guzman Juan J. , Huson Daniel H. , Angenent Largus T.
Published: March 2024

Medium-chain carboxylates are used in various industrial applications. These chemicals are typically extracted from palm oil, which is deemed not sustainable. Recent research has focused on microbial chain elongation using reactors to produce medium-chain carboxylates, such asn-caproate (C6) andn-caprylate (C8), from organic substrates such as wastes. Even though the production ofn-caproate is relatively well-characterized, bacteria and metabolic pathways that are responsible forn-caprylate production are not. Here, three 5-L reactors with continuous membrane-based liquid-liquid extraction (i.e., pertraction) were fed ethanol and acetate and operated for an operating period of 234 days with different operating conditions. Metagenomic and metaproteomic analyses were employed.n-Caprylate production rates and reactor microbiomes differed between reactors even when operated similarly due to differences in H2and O2between the reactors. The complete reverse β-oxidation pathway was present and expressed by several bacterial species in theClostridiaclass. SeveralOscillibacterspp., includingOscillibacter valericigenes, were positively correlated withn-caprylate production rates, whileClostridium kluyveriwas positively correlated withn-caproate production.Pseudoclavibacter caeni, which is a strictly aerobic bacterium, was abundant across all the operating periods, regardless ofn-caprylate production rates. This study provides insight into microbiota that are associated withn-caprylate production in open-culture reactors and provides ideas for further work.

Importance

Microbial chain elongation pathways in open-culture biotechnology systems can be utilized to convert organic waste and industrial side streams into valuable industrial chemicals. Here, we investigated the microbiota and metabolic pathways that produce medium-chain carboxylates, includingn-caproate (C6) andn-caprylate (C8), in reactors with in-line product extraction. Although the reactors in this study were operated similarly, different microbial communities dominated and were responsible for chain elongation. We found that different microbiota were responsible forn-caproate orn-caprylate production, and this can inform engineers on how to operate the systems better. We also observed which changes in operating conditions steered the production toward and away fromn-caprylate, but more work is necessary to ascertain a mechanistic understanding that could be predictive. This study provides pertinent research questions for future work.
Adherens junctions limit the extent of the septate junctions inDrosophilamidgut enterocytes but are not required for apical-basal polarity
Authors: Carvalho Cátia A. , Tame Mihoko , St Johnston Daniel
Published: March 2024

Adherens junctions formed by E-cadherin adhesion complexes play central roles in the organisation and apical-basal polarisation of both mammalian and insect epithelia. Here we investigate the function of the components of the E-cadherin adhesion complex in theDrosophilamidgut epithelium, which establishes polarity by a different mechanism from other fly epithelia and has an inverted junctional arrangement, in which the adherens junctions lie below the septate junctions. Unlike other epithelial tissues, loss of E-cadherin, Armadillo (β-catenin) or α-catenin has no effect on the polarity or organisation of the adult midgut epithelium. This is not due to redundancy with N-cadherin, providing further evidence that the midgut polarises in distinct way from other epithelia. However,E-cadherin(shg) andarmadillomutants have an expanded septate junction domain and a smaller lateral domain below the septate junctions. Thus, E-cadherin adhesion complexes limit the basal extent of the septate junctions. This function does not appear to depend on the linkage of E-cadherin to the actin cytoskeleton because α-catenin mutants do not significantly perturb the relative sizes of the septate and sub-septate junction domains.
Evaluating IBM’s Watson natural language processing artificial intelligence as a short-answer categorization tool for physics education research
Authors: Campbell Jennifer , Ansell Katie , Stelzer Tim
Published: March 2024

Recent advances in publicly available natural language processors (NLP) may enhance the efficiency of analyzing student short-answer responses in physics education research (PER). We train a state-of-the-art NLP, IBM’s Watson, and test its agreement with human coders using two different studies that gathered text responses in which students explain their reasoning on physics-related questions. The first study analyzes 479 student responses to a lab data analysis question and categorizes them by main idea. The second study analyzes 732 student answers to identify the presence or absence of each of the two conceptual themes. When training Watson with approximately one-third to half of the samples, we find that samples labeled with high confidence scores have similar accuracy to human agreement; yet for lower confidence scores, humans outperform the NLP’s labeling accuracy. In addition to studying Watson’s overall accuracy, we use this analysis to better understand factors that impact how Watson categorizes. Using the data from the categorization study, we find that Watson’s algorithm does not appear to be impacted by the disproportionate representation of categories in the training set, and we examine mislabeled statements to identify vocabulary and phrasing that may increase the rate of false positives. Based on this work, we find that, with careful consideration of the research study design and an awareness of the NLP’s limitations, Watson may present a useful tool for large-scale PER studies or classroom analysis tools.

Published by the American Physical Society
2024
Phase transition kinetics revealed by
in situ
x-ray diffraction in laser-heated dynamic diamond anvil cells
Authors: Ricks Matthew , Gleason Arianna E. , Miozzi Francesca , Yang Hong , Chariton Stella , Prakapenka Vitali B. , Sinogeikin Stanislav V. , Sandberg Richard L. , Mao Wendy L. , Pandolfi Silvia
Published: March 2024

We report successful coupling of dynamic loading in a diamond anvil cell and stable laser heating, which enables compression rates up to 500 GPa/s along high-temperature isotherms. Dynamic loading in a diamond-anvil cell allows exploration of a wider range of pathways in the pressure-temperature space compared to conventional dynamic compression techniques. By x-ray diffraction, we are able to characterize and monitor the structural transitions with the appropriate time resolution i.e., millisecond timescales. Using this method, we investigate the γ−ε phase transition of iron under dynamic compression, reaching compression rates of hundreds of GPa/s and temperatures of 2000 K. Our results demonstrate a distinct response of the γ−ε and α−ε transitions to the high compression rates achieved, possibly due to the different transition mechanisms. These findings open up new avenues to study tailored dynamic compression pathways in the pressure-temperature space and highlight the potential of this platform to capture kinetic effects (over ms time scales) in a diamond anvil cell.

Published by the American Physical Society
2024
Higher-order quantum transformations of Hamiltonian dynamics
Authors: Odake Tatsuki , Kristjánsson Hlér , Soeda Akihito , Murao Mio
Published: March 2024

We present a quantum algorithm to achieve higher-order transformations of Hamiltonian dynamics. Namely, the algorithm takes as input a finite number of queries to a black-box seed Hamiltonian dynamics to simulate a desired Hamiltonian. Our algorithm efficiently simulates linear transformations of any seed Hamiltonian with a bounded energy range consisting of a polynomial number of terms in system size, making use of only controlled-Pauli gates and time-correlated randomness. This algorithm is an instance of quantum functional programming, where the desired function is specified as a concatenation of higher-order quantum transformations. By way of example, we demonstrate the simulation of negative time-evolution and time-reversal, and perform a Hamiltonian learning task.

Published by the American Physical Society
2024
Synthesis, crystal structure and Hirshfeld surface analysis of bromidotetrakis[5-(prop-2-en-1-ylsulfanyl)-1,3,4-thiadiazol-2-amine-κN
3]copper(II) bromide
Authors: Atashov Aziz , Azamova Mukhlisakhon , Ziyatov Daminbek , Uzakbergenova Zamira , Torambetov Batirbay , Holczbauer Tamas , Ashurov Jamshid , Kadirova Shakhnoza
Published: March 2024

A novel cationic complex, bromidotetrakis[5-(prop-2-en-1-ylsulfanyl)-1,3,4-thiadiazol-2-amine-κN
3]copper(II) bromide, [CuBr](C5H7N3S2)4Br, was synthesized. The complex crystallizes with fourfold molecular symmetry in the tetragonal space group P4/n. The CuII atom exhibits a square-pyramidal coordination geometry. The Cu atom is located centrally within the complex, being coordinated by four nitrogen atoms from four AAT molecules, while a bromine anion is located at the apex of the pyramid. The amino H atoms of AAT interact with bromine from the inner and outer spheres, forming a two-dimensional network in the [100] and [010] directions. Hirshfeld surface analysis reveals that 33.7% of the intermolecular interactions are from H...H contacts, 21.2% are from S...H/H...S contacts, 13.4% are from S...S contacts and 11.0% are from C...H/H...C, while other contributions are from Br...H/H...Br and N...H/H...N contacts.